Starting phenix.real_space_refine on Tue Aug 4 12:26:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/27wm_81514/08_2026/27wm_81514.cif Found real_map, /net/cci-nas-00/data/ceres_data/27wm_81514/08_2026/27wm_81514.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/27wm_81514/08_2026/27wm_81514.cif" } default_model = "/net/cci-nas-00/data/ceres_data/27wm_81514/08_2026/27wm_81514.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/27wm_81514/08_2026/27wm_81514.map" default_real_map = "/net/cci-nas-00/data/ceres_data/27wm_81514/08_2026/27wm_81514.map" } resolution = 2.7 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: 3 Type Number sf(0) Gaussians C 1705 2.51 5 N 460 2.21 5 O 455 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2620 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 229 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "B" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 229 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "C" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Restraints were copied for chains: D, G, J, M, E, H, K, N, F, I, L, O Time building chain proxies: 0.46, per 1000 atoms: 0.18 Number of scatterers: 2620 At special positions: 0 Unit cell: (80.152, 79.22, 39.144, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 455 8.00 N 460 7.00 C 1705 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: 0.18 Conformation dependent library (CDL) restraints added in 79.1 milliseconds 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 570 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 60.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 14 removed outlier: 7.125A pdb=" N VAL A 10 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N VAL D 13 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ASN A 12 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N VAL D 10 " --> pdb=" O LEU G 11 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N VAL G 13 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ASN D 12 " --> pdb=" O VAL G 13 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N VAL G 10 " --> pdb=" O LEU J 11 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N VAL J 13 " --> pdb=" O VAL G 10 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ASN G 12 " --> pdb=" O VAL J 13 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N VAL J 10 " --> pdb=" O LEU M 11 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N VAL M 13 " --> pdb=" O VAL J 10 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ASN J 12 " --> pdb=" O VAL M 13 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 31 removed outlier: 9.155A pdb=" N GLU A 18 " --> pdb=" O ALA D 19 " (cutoff:3.500A) removed outlier: 9.733A pdb=" N ILE D 21 " --> pdb=" O GLU A 18 " (cutoff:3.500A) removed outlier: 8.982A pdb=" N ASP A 20 " --> pdb=" O ILE D 21 " (cutoff:3.500A) removed outlier: 9.956A pdb=" N GLY D 23 " --> pdb=" O ASP A 20 " (cutoff:3.500A) removed outlier: 8.799A pdb=" N ALA A 22 " --> pdb=" O GLY D 23 " (cutoff:3.500A) removed outlier: 10.358A pdb=" N GLY D 25 " --> pdb=" O ALA A 22 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N HIS A 24 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 9.053A pdb=" N GLU D 27 " --> pdb=" O HIS A 24 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLN A 26 " --> pdb=" O GLU D 27 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N LEU D 29 " --> pdb=" O GLN A 26 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL A 28 " --> pdb=" O LEU D 29 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N ARG D 31 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE A 30 " --> pdb=" O ARG D 31 " (cutoff:3.500A) removed outlier: 9.155A pdb=" N GLU D 18 " --> pdb=" O ALA G 19 " (cutoff:3.500A) removed outlier: 9.733A pdb=" N ILE G 21 " --> pdb=" O GLU D 18 " (cutoff:3.500A) removed outlier: 8.982A pdb=" N ASP D 20 " --> pdb=" O ILE G 21 " (cutoff:3.500A) removed outlier: 9.955A pdb=" N GLY G 23 " --> pdb=" O ASP D 20 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N ALA D 22 " --> pdb=" O GLY G 23 " (cutoff:3.500A) removed outlier: 10.359A pdb=" N GLY G 25 " --> pdb=" O ALA D 22 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N HIS D 24 " --> pdb=" O GLY G 25 " (cutoff:3.500A) removed outlier: 9.052A pdb=" N GLU G 27 " --> pdb=" O HIS D 24 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLN D 26 " --> pdb=" O GLU G 27 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N LEU G 29 " --> pdb=" O GLN D 26 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL D 28 " --> pdb=" O LEU G 29 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ARG G 31 " --> pdb=" O VAL D 28 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE D 30 " --> pdb=" O ARG G 31 " (cutoff:3.500A) removed outlier: 9.155A pdb=" N GLU G 18 " --> pdb=" O ALA J 19 " (cutoff:3.500A) removed outlier: 9.733A pdb=" N ILE J 21 " --> pdb=" O GLU G 18 " (cutoff:3.500A) removed outlier: 8.981A pdb=" N ASP G 20 " --> pdb=" O ILE J 21 " (cutoff:3.500A) removed outlier: 9.956A pdb=" N GLY J 23 " --> pdb=" O ASP G 20 " (cutoff:3.500A) removed outlier: 8.799A pdb=" N ALA G 22 " --> pdb=" O GLY J 23 " (cutoff:3.500A) removed outlier: 10.359A pdb=" N GLY J 25 " --> pdb=" O ALA G 22 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N HIS G 24 " --> pdb=" O GLY J 25 " (cutoff:3.500A) removed outlier: 9.052A pdb=" N GLU J 27 " --> pdb=" O HIS G 24 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLN G 26 " --> pdb=" O GLU J 27 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N LEU J 29 " --> pdb=" O GLN G 26 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL G 28 " --> pdb=" O LEU J 29 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N ARG J 31 " --> pdb=" O VAL G 28 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE G 30 " --> pdb=" O ARG J 31 " (cutoff:3.500A) removed outlier: 9.156A pdb=" N GLU J 18 " --> pdb=" O ALA M 19 " (cutoff:3.500A) removed outlier: 9.733A pdb=" N ILE M 21 " --> pdb=" O GLU J 18 " (cutoff:3.500A) removed outlier: 8.982A pdb=" N ASP J 20 " --> pdb=" O ILE M 21 " (cutoff:3.500A) removed outlier: 9.956A pdb=" N GLY M 23 " --> pdb=" O ASP J 20 " (cutoff:3.500A) removed outlier: 8.799A pdb=" N ALA J 22 " --> pdb=" O GLY M 23 " (cutoff:3.500A) removed outlier: 10.358A pdb=" N GLY M 25 " --> pdb=" O ALA J 22 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N HIS J 24 " --> pdb=" O GLY M 25 " (cutoff:3.500A) removed outlier: 9.052A pdb=" N GLU M 27 " --> pdb=" O HIS J 24 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLN J 26 " --> pdb=" O GLU M 27 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N LEU M 29 " --> pdb=" O GLN J 26 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL J 28 " --> pdb=" O LEU M 29 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N ARG M 31 " --> pdb=" O VAL J 28 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE J 30 " --> pdb=" O ARG M 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 9 through 13 Processing sheet with id=AA4, first strand: chain 'B' and resid 16 through 24 Processing sheet with id=AA5, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AA6, first strand: chain 'C' and resid 9 through 14 80 hydrogen bonds defined for protein. 240 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: 0.21 Time building geometry restraints manager: 0.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 455 1.29 - 1.35: 418 1.35 - 1.42: 307 1.42 - 1.49: 365 1.49 - 1.55: 1130 Bond restraints: 2675 Sorted by residual: bond pdb=" CB GLU A 6 " pdb=" CG GLU A 6 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.29e+00 bond pdb=" CB GLU D 6 " pdb=" CG GLU D 6 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.28e+00 bond pdb=" CB GLU M 6 " pdb=" CG GLU M 6 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.27e+00 bond pdb=" CB GLU J 6 " pdb=" CG GLU J 6 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.26e+00 bond pdb=" CB GLU G 6 " pdb=" CG GLU G 6 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.23e+00 ... (remaining 2670 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 3462 1.71 - 3.41: 130 3.41 - 5.12: 18 5.12 - 6.83: 5 6.83 - 8.53: 10 Bond angle restraints: 3625 Sorted by residual: angle pdb=" N TRP M 7 " pdb=" CA TRP M 7 " pdb=" C TRP M 7 " ideal model delta sigma weight residual 110.80 118.24 -7.44 2.13e+00 2.20e-01 1.22e+01 angle pdb=" N TRP J 7 " pdb=" CA TRP J 7 " pdb=" C TRP J 7 " ideal model delta sigma weight residual 110.80 118.24 -7.44 2.13e+00 2.20e-01 1.22e+01 angle pdb=" N TRP A 7 " pdb=" CA TRP A 7 " pdb=" C TRP A 7 " ideal model delta sigma weight residual 110.80 118.17 -7.37 2.13e+00 2.20e-01 1.20e+01 angle pdb=" N TRP G 7 " pdb=" CA TRP G 7 " pdb=" C TRP G 7 " ideal model delta sigma weight residual 110.80 118.14 -7.34 2.13e+00 2.20e-01 1.19e+01 angle pdb=" N TRP D 7 " pdb=" CA TRP D 7 " pdb=" C TRP D 7 " ideal model delta sigma weight residual 110.80 118.14 -7.34 2.13e+00 2.20e-01 1.19e+01 ... (remaining 3620 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.24: 1241 15.24 - 30.47: 161 30.47 - 45.70: 58 45.70 - 60.94: 10 60.94 - 76.17: 5 Dihedral angle restraints: 1475 sinusoidal: 600 harmonic: 875 Sorted by residual: dihedral pdb=" CA GLN J 8 " pdb=" C GLN J 8 " pdb=" N GLN J 9 " pdb=" CA GLN J 9 " ideal model delta harmonic sigma weight residual 180.00 161.14 18.86 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA GLN G 8 " pdb=" C GLN G 8 " pdb=" N GLN G 9 " pdb=" CA GLN G 9 " ideal model delta harmonic sigma weight residual 180.00 161.15 18.85 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA GLN D 8 " pdb=" C GLN D 8 " pdb=" N GLN D 9 " pdb=" CA GLN D 9 " ideal model delta harmonic sigma weight residual 180.00 161.15 18.85 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 1472 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 169 0.027 - 0.054: 92 0.054 - 0.081: 48 0.081 - 0.108: 55 0.108 - 0.135: 26 Chirality restraints: 390 Sorted by residual: chirality pdb=" CA TRP D 7 " pdb=" N TRP D 7 " pdb=" C TRP D 7 " pdb=" CB TRP D 7 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CA TRP J 7 " pdb=" N TRP J 7 " pdb=" C TRP J 7 " pdb=" CB TRP J 7 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.52e-01 chirality pdb=" CA TRP M 7 " pdb=" N TRP M 7 " pdb=" C TRP M 7 " pdb=" CB TRP M 7 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.46e-01 ... (remaining 387 not shown) Planarity restraints: 455 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 27 " -0.004 2.00e-02 2.50e+03 8.59e-03 7.38e-01 pdb=" CD GLU B 27 " 0.015 2.00e-02 2.50e+03 pdb=" OE1 GLU B 27 " -0.005 2.00e-02 2.50e+03 pdb=" OE2 GLU B 27 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN I 12 " -0.004 2.00e-02 2.50e+03 8.53e-03 7.27e-01 pdb=" CG ASN I 12 " 0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN I 12 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN I 12 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU E 27 " -0.004 2.00e-02 2.50e+03 8.52e-03 7.26e-01 pdb=" CD GLU E 27 " 0.015 2.00e-02 2.50e+03 pdb=" OE1 GLU E 27 " -0.005 2.00e-02 2.50e+03 pdb=" OE2 GLU E 27 " -0.005 2.00e-02 2.50e+03 ... (remaining 452 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 755 2.85 - 3.36: 1898 3.36 - 3.87: 4529 3.87 - 4.39: 5031 4.39 - 4.90: 10214 Nonbonded interactions: 22427 Sorted by model distance: nonbonded pdb=" OE1 GLU J 6 " pdb=" CD1 TRP J 7 " model vdw 2.333 3.260 nonbonded pdb=" OE1 GLU A 6 " pdb=" CD1 TRP A 7 " model vdw 2.333 3.260 nonbonded pdb=" OE1 GLU G 6 " pdb=" CD1 TRP G 7 " model vdw 2.333 3.260 nonbonded pdb=" OE1 GLU D 6 " pdb=" CD1 TRP D 7 " model vdw 2.333 3.260 nonbonded pdb=" OE1 GLU M 6 " pdb=" CD1 TRP M 7 " model vdw 2.333 3.260 ... (remaining 22422 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 'D' selection = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'O' } 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: 0.000 Normalize map: mean=0, sd=1: 8.840 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: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 3.460 Find NCS groups from input model: 0.030 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:6.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 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 : 0.004 0.034 2675 Z= 0.180 Angle : 0.824 8.535 3625 Z= 0.434 Chirality : 0.057 0.135 390 Planarity : 0.002 0.009 455 Dihedral : 16.733 76.170 905 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 20.75 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.03 (0.45), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.30 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 31 PHE 0.002 0.001 PHE H 33 TRP 0.011 0.001 TRP H 7 HIS 0.002 0.001 HIS E 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.18 ( 2675) covalent geometry : angle 0.82406 / 0.43 ( 3625) hydrogen bonds : bond 0.12756 / 8.35 ( 80) hydrogen bonds : angle 8.07496 / 5.78 ( 240) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.123 Fit side-chains revert: symmetry clash REVERT: A 31 ARG cc_start: 0.7516 (mtt180) cc_final: 0.5351 (ppt170) REVERT: B 8 GLN cc_start: 0.7945 (pt0) cc_final: 0.6976 (tp-100) REVERT: B 31 ARG cc_start: 0.7721 (mtt90) cc_final: 0.7275 (mmp80) REVERT: M 31 ARG cc_start: 0.7072 (mtt180) cc_final: 0.6087 (mmp-170) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.5783 time to fit residues: 48.3209 Evaluate side-chains 55 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 26 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 GLN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 8 GLN L 8 GLN ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 8 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.089927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.078873 restraints weight = 5837.740| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 2.93 r_work: 0.3961 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 2675 Z= 0.205 Angle : 0.705 6.932 3625 Z= 0.358 Chirality : 0.055 0.125 390 Planarity : 0.004 0.042 455 Dihedral : 6.005 17.654 315 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.40 % Allowed : 26.42 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.86 (0.46), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 31 PHE 0.004 0.001 PHE G 33 TRP 0.007 0.001 TRP N 7 HIS 0.002 0.001 HIS E 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.20 ( 2675) covalent geometry : angle 0.70540 / 0.36 ( 3625) hydrogen bonds : bond 0.03161 / 2.10 ( 80) hydrogen bonds : angle 5.29479 / 3.69 ( 240) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.066 Fit side-chains REVERT: A 16 LYS cc_start: 0.8705 (tttt) cc_final: 0.7172 (pmtt) REVERT: A 31 ARG cc_start: 0.7452 (mtt180) cc_final: 0.4996 (ppt170) REVERT: B 8 GLN cc_start: 0.8650 (pt0) cc_final: 0.6828 (tp-100) REVERT: B 31 ARG cc_start: 0.7589 (mtt90) cc_final: 0.6776 (mmp-170) REVERT: E 20 ASP cc_start: 0.8274 (p0) cc_final: 0.8058 (p0) REVERT: G 18 GLU cc_start: 0.7654 (mp0) cc_final: 0.7358 (mp0) REVERT: K 8 GLN cc_start: 0.8718 (pp30) cc_final: 0.8169 (pp30) REVERT: M 16 LYS cc_start: 0.8069 (tttt) cc_final: 0.7757 (tttm) REVERT: M 18 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7259 (mp0) outliers start: 9 outliers final: 1 residues processed: 68 average time/residue: 0.5669 time to fit residues: 39.2362 Evaluate side-chains 53 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 9 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 5 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 GLN I 8 GLN ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 GLN ** L 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 8 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.088689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.077516 restraints weight = 5996.637| |-----------------------------------------------------------------------------| r_work (start): 0.4051 rms_B_bonded: 3.06 r_work: 0.3953 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 2675 Z= 0.211 Angle : 0.723 7.644 3625 Z= 0.357 Chirality : 0.054 0.135 390 Planarity : 0.003 0.019 455 Dihedral : 5.839 16.812 315 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 7.17 % Allowed : 26.04 % Favored : 66.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.93 (0.46), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.23 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 31 PHE 0.002 0.001 PHE K 33 TRP 0.008 0.001 TRP N 7 HIS 0.002 0.001 HIS A 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.21 ( 2675) covalent geometry : angle 0.72262 / 0.36 ( 3625) hydrogen bonds : bond 0.02816 / 1.88 ( 80) hydrogen bonds : angle 4.93447 / 3.48 ( 240) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 49 time to evaluate : 0.067 Fit side-chains REVERT: A 16 LYS cc_start: 0.8739 (tttt) cc_final: 0.7190 (pmtt) REVERT: A 31 ARG cc_start: 0.7494 (mtt180) cc_final: 0.5249 (ppt170) REVERT: B 8 GLN cc_start: 0.8582 (pt0) cc_final: 0.6770 (tp-100) REVERT: B 31 ARG cc_start: 0.7624 (mtt90) cc_final: 0.6603 (mmp-170) REVERT: E 9 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.8354 (tt0) REVERT: G 18 GLU cc_start: 0.7738 (mp0) cc_final: 0.7227 (mp0) REVERT: K 8 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8012 (pp30) REVERT: M 18 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7482 (mp0) outliers start: 19 outliers final: 1 residues processed: 66 average time/residue: 0.4673 time to fit residues: 31.4811 Evaluate side-chains 48 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 9 GLN Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain K residue 8 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 19 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 8 GLN L 8 GLN O 8 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.087699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.076599 restraints weight = 6085.424| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 3.06 r_work: 0.3914 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 2675 Z= 0.269 Angle : 0.761 8.312 3625 Z= 0.381 Chirality : 0.056 0.147 390 Planarity : 0.002 0.014 455 Dihedral : 6.253 17.233 315 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 5.28 % Allowed : 27.17 % Favored : 67.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.45), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG N 31 PHE 0.003 0.001 PHE M 33 TRP 0.007 0.001 TRP N 7 HIS 0.003 0.001 HIS J 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00606 / 0.27 ( 2675) covalent geometry : angle 0.76065 / 0.38 ( 3625) hydrogen bonds : bond 0.02801 / 1.88 ( 80) hydrogen bonds : angle 4.78402 / 3.40 ( 240) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.091 Fit side-chains REVERT: A 16 LYS cc_start: 0.8797 (tttt) cc_final: 0.7354 (pmtt) REVERT: B 8 GLN cc_start: 0.8317 (pt0) cc_final: 0.6860 (tp-100) REVERT: B 31 ARG cc_start: 0.7760 (mtt90) cc_final: 0.6488 (tpm170) REVERT: E 9 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8399 (tt0) REVERT: G 18 GLU cc_start: 0.7789 (mp0) cc_final: 0.7299 (mp0) REVERT: H 18 GLU cc_start: 0.8431 (tt0) cc_final: 0.8186 (mt-10) REVERT: H 20 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.8008 (p0) REVERT: K 8 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.7964 (pp30) REVERT: M 18 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7483 (mp0) REVERT: N 6 GLU cc_start: 0.3294 (pm20) cc_final: 0.2984 (pm20) outliers start: 14 outliers final: 4 residues processed: 59 average time/residue: 0.4654 time to fit residues: 28.0345 Evaluate side-chains 51 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain E residue 8 GLN Chi-restraints excluded: chain E residue 9 GLN Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain H residue 20 ASP Chi-restraints excluded: chain K residue 8 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 4 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 8 GLN ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 GLN ** L 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 8 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.086903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.075819 restraints weight = 6133.749| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 3.08 r_work: 0.3900 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.050 2675 Z= 0.338 Angle : 0.800 8.716 3625 Z= 0.407 Chirality : 0.057 0.162 390 Planarity : 0.002 0.014 455 Dihedral : 6.531 17.758 315 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 5.66 % Allowed : 24.91 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.06 (0.43), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.33), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 31 PHE 0.004 0.001 PHE M 33 TRP 0.010 0.001 TRP D 7 HIS 0.003 0.002 HIS G 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00769 / 0.34 ( 2675) covalent geometry : angle 0.80022 / 0.41 ( 3625) hydrogen bonds : bond 0.03074 / 2.07 ( 80) hydrogen bonds : angle 4.81457 / 3.41 ( 240) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.090 Fit side-chains REVERT: A 16 LYS cc_start: 0.8818 (tttt) cc_final: 0.7340 (pmtt) REVERT: B 8 GLN cc_start: 0.8362 (pt0) cc_final: 0.6818 (tp-100) REVERT: B 31 ARG cc_start: 0.7825 (mtt90) cc_final: 0.6539 (tpm170) REVERT: D 18 GLU cc_start: 0.7721 (mp0) cc_final: 0.7467 (mp0) REVERT: G 18 GLU cc_start: 0.7882 (mp0) cc_final: 0.7339 (mp0) REVERT: H 18 GLU cc_start: 0.8501 (tt0) cc_final: 0.8134 (mt-10) REVERT: H 20 ASP cc_start: 0.8245 (OUTLIER) cc_final: 0.8031 (p0) REVERT: K 8 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.7921 (pp30) REVERT: M 18 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7450 (mp0) REVERT: N 6 GLU cc_start: 0.2954 (pm20) cc_final: 0.2668 (pm20) outliers start: 15 outliers final: 6 residues processed: 58 average time/residue: 0.4999 time to fit residues: 29.6319 Evaluate side-chains 49 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain E residue 8 GLN Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain H residue 20 ASP Chi-restraints excluded: chain K residue 8 GLN Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain O residue 8 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 17 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 12 ASN H 12 ASN I 8 GLN ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 GLN ** L 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 8 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.090584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.079601 restraints weight = 5921.946| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 3.04 r_work: 0.3970 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2675 Z= 0.141 Angle : 0.727 8.598 3625 Z= 0.351 Chirality : 0.054 0.135 390 Planarity : 0.003 0.052 455 Dihedral : 5.855 15.726 315 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.77 % Allowed : 27.55 % Favored : 68.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.05 (0.45), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 31 PHE 0.002 0.000 PHE D 33 TRP 0.006 0.001 TRP H 14 HIS 0.001 0.001 HIS A 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 2675) covalent geometry : angle 0.72711 / 0.35 ( 3625) hydrogen bonds : bond 0.02503 / 1.69 ( 80) hydrogen bonds : angle 4.71787 / 3.36 ( 240) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.114 Fit side-chains REVERT: A 16 LYS cc_start: 0.8718 (tttt) cc_final: 0.7270 (pmtt) REVERT: B 8 GLN cc_start: 0.8389 (pt0) cc_final: 0.7067 (tp-100) REVERT: B 31 ARG cc_start: 0.7747 (mtt90) cc_final: 0.6695 (mmp-170) REVERT: G 18 GLU cc_start: 0.7864 (mp0) cc_final: 0.7341 (mp0) REVERT: H 8 GLN cc_start: 0.8434 (pt0) cc_final: 0.8211 (tt0) REVERT: H 18 GLU cc_start: 0.8418 (tt0) cc_final: 0.8175 (mt-10) REVERT: H 20 ASP cc_start: 0.8167 (OUTLIER) cc_final: 0.7911 (p0) REVERT: K 8 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8119 (pp30) REVERT: M 18 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7440 (mp0) outliers start: 10 outliers final: 1 residues processed: 54 average time/residue: 0.5844 time to fit residues: 32.1977 Evaluate side-chains 46 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain H residue 20 ASP Chi-restraints excluded: chain K residue 8 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 0 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 8 GLN ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 GLN ** L 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** 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 = 0.4227 r_free = 0.4227 target = 0.089280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.078514 restraints weight = 6012.610| |-----------------------------------------------------------------------------| r_work (start): 0.4025 rms_B_bonded: 2.96 r_work: 0.3932 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2675 Z= 0.166 Angle : 0.735 8.849 3625 Z= 0.358 Chirality : 0.054 0.132 390 Planarity : 0.003 0.045 455 Dihedral : 5.756 15.205 315 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.40 % Allowed : 28.68 % Favored : 67.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.98 (0.45), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 31 PHE 0.002 0.001 PHE A 33 TRP 0.006 0.001 TRP N 7 HIS 0.002 0.001 HIS A 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 ( 2675) covalent geometry : angle 0.73494 / 0.36 ( 3625) hydrogen bonds : bond 0.02499 / 1.69 ( 80) hydrogen bonds : angle 4.63545 / 3.28 ( 240) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.096 Fit side-chains REVERT: A 16 LYS cc_start: 0.8744 (tttt) cc_final: 0.7274 (pmtt) REVERT: B 8 GLN cc_start: 0.8422 (pt0) cc_final: 0.7110 (tp-100) REVERT: B 31 ARG cc_start: 0.7630 (mtt90) cc_final: 0.6772 (mmp-170) REVERT: G 18 GLU cc_start: 0.7861 (mp0) cc_final: 0.7341 (mp0) REVERT: H 8 GLN cc_start: 0.8487 (pt0) cc_final: 0.8262 (tt0) REVERT: H 18 GLU cc_start: 0.8449 (tt0) cc_final: 0.8185 (mt-10) REVERT: H 20 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7839 (p0) REVERT: K 8 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8173 (pp30) REVERT: M 18 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7437 (mp0) outliers start: 9 outliers final: 4 residues processed: 52 average time/residue: 0.5046 time to fit residues: 26.7333 Evaluate side-chains 49 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain H residue 20 ASP Chi-restraints excluded: chain I residue 10 VAL Chi-restraints excluded: chain K residue 8 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 12 ASN I 8 GLN ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 GLN ** L 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.087971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.077018 restraints weight = 6139.584| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 3.06 r_work: 0.3922 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 2675 Z= 0.234 Angle : 0.773 9.165 3625 Z= 0.383 Chirality : 0.054 0.134 390 Planarity : 0.003 0.036 455 Dihedral : 6.062 17.081 315 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 3.02 % Allowed : 29.81 % Favored : 67.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.01 (0.45), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 31 PHE 0.002 0.001 PHE A 33 TRP 0.008 0.001 TRP A 7 HIS 0.002 0.001 HIS J 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.23 ( 2675) covalent geometry : angle 0.77282 / 0.38 ( 3625) hydrogen bonds : bond 0.02682 / 1.80 ( 80) hydrogen bonds : angle 4.65389 / 3.28 ( 240) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.063 Fit side-chains REVERT: A 16 LYS cc_start: 0.8757 (tttt) cc_final: 0.7183 (pmtt) REVERT: B 8 GLN cc_start: 0.8437 (pt0) cc_final: 0.6900 (tp-100) REVERT: B 31 ARG cc_start: 0.7740 (mtt90) cc_final: 0.6737 (mmp-170) REVERT: G 18 GLU cc_start: 0.7806 (mp0) cc_final: 0.7237 (mp0) REVERT: H 18 GLU cc_start: 0.8452 (tt0) cc_final: 0.8154 (mt-10) REVERT: H 20 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7899 (p0) REVERT: K 8 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8214 (pp30) REVERT: M 18 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7425 (mp0) outliers start: 8 outliers final: 4 residues processed: 48 average time/residue: 0.4792 time to fit residues: 23.5031 Evaluate side-chains 47 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain H residue 20 ASP Chi-restraints excluded: chain I residue 10 VAL Chi-restraints excluded: chain K residue 8 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 2 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 12 ASN I 8 GLN ** K 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 GLN ** L 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.090402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.079484 restraints weight = 6100.437| |-----------------------------------------------------------------------------| r_work (start): 0.4056 rms_B_bonded: 3.01 r_work: 0.3967 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2675 Z= 0.142 Angle : 0.756 9.204 3625 Z= 0.366 Chirality : 0.054 0.134 390 Planarity : 0.002 0.037 455 Dihedral : 5.538 15.169 315 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.64 % Allowed : 30.19 % Favored : 67.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.97 (0.46), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 31 PHE 0.001 0.000 PHE D 33 TRP 0.005 0.001 TRP N 14 HIS 0.001 0.000 HIS N 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 2675) covalent geometry : angle 0.75649 / 0.37 ( 3625) hydrogen bonds : bond 0.02388 / 1.61 ( 80) hydrogen bonds : angle 4.58816 / 3.24 ( 240) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.066 Fit side-chains REVERT: A 16 LYS cc_start: 0.8708 (tttt) cc_final: 0.7190 (pmtt) REVERT: B 8 GLN cc_start: 0.8384 (pt0) cc_final: 0.7118 (tp-100) REVERT: B 31 ARG cc_start: 0.7648 (mtt90) cc_final: 0.6866 (mmp-170) REVERT: G 18 GLU cc_start: 0.7878 (mp0) cc_final: 0.7294 (mp0) REVERT: H 18 GLU cc_start: 0.8447 (tt0) cc_final: 0.8234 (mt-10) REVERT: K 8 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.8436 (pp30) REVERT: M 18 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7383 (mp0) outliers start: 7 outliers final: 3 residues processed: 56 average time/residue: 0.5095 time to fit residues: 29.0790 Evaluate side-chains 48 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain I residue 10 VAL Chi-restraints excluded: chain K residue 8 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 6.9990 chunk 11 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 18 optimal weight: 0.0170 chunk 1 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 overall best weight: 3.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 12 ASN I 8 GLN L 8 GLN ** L 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.086758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.075772 restraints weight = 6427.526| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 3.12 r_work: 0.3903 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.054 2675 Z= 0.326 Angle : 0.842 9.282 3625 Z= 0.425 Chirality : 0.056 0.142 390 Planarity : 0.003 0.029 455 Dihedral : 6.275 18.226 315 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 3.02 % Allowed : 29.81 % Favored : 67.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.97 (0.45), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 31 PHE 0.004 0.001 PHE M 33 TRP 0.012 0.001 TRP A 7 HIS 0.003 0.002 HIS A 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00754 / 0.33 ( 2675) covalent geometry : angle 0.84159 / 0.42 ( 3625) hydrogen bonds : bond 0.02966 / 1.93 ( 80) hydrogen bonds : angle 4.68934 / 3.29 ( 240) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.066 Fit side-chains REVERT: A 16 LYS cc_start: 0.8815 (tttt) cc_final: 0.7328 (pmtt) REVERT: B 8 GLN cc_start: 0.8457 (pt0) cc_final: 0.6946 (tp-100) REVERT: B 31 ARG cc_start: 0.7752 (mtt90) cc_final: 0.6774 (mmp-170) REVERT: G 18 GLU cc_start: 0.7826 (mp0) cc_final: 0.7183 (mp0) REVERT: H 18 GLU cc_start: 0.8528 (tt0) cc_final: 0.8189 (mt-10) REVERT: J 18 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7319 (mp0) REVERT: K 8 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.8147 (pp30) REVERT: M 18 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7446 (mp0) outliers start: 8 outliers final: 4 residues processed: 47 average time/residue: 0.5568 time to fit residues: 26.6648 Evaluate side-chains 45 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain I residue 10 VAL Chi-restraints excluded: chain K residue 8 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 3 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 12 ASN I 8 GLN L 8 GLN ** L 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.090998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.080155 restraints weight = 6030.595| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 2.99 r_work: 0.3974 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2675 Z= 0.141 Angle : 0.783 9.316 3625 Z= 0.379 Chirality : 0.054 0.134 390 Planarity : 0.003 0.035 455 Dihedral : 5.576 14.763 315 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.02 % Allowed : 30.19 % Favored : 66.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.46), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 31 PHE 0.001 0.000 PHE G 33 TRP 0.010 0.001 TRP H 14 HIS 0.001 0.000 HIS N 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 ( 2675) covalent geometry : angle 0.78323 / 0.38 ( 3625) hydrogen bonds : bond 0.02442 / 1.62 ( 80) hydrogen bonds : angle 4.61773 / 3.27 ( 240) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1202.10 seconds wall clock time: 21 minutes 10.14 seconds (1270.14 seconds total)