Starting phenix.real_space_refine on Tue Aug 4 12:05:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/27wr_81518/08_2026/27wr_81518.cif Found real_map, /net/cci-nas-00/data/ceres_data/27wr_81518/08_2026/27wr_81518.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/27wr_81518/08_2026/27wr_81518.cif" } default_model = "/net/cci-nas-00/data/ceres_data/27wr_81518/08_2026/27wr_81518.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/27wr_81518/08_2026/27wr_81518.map" default_real_map = "/net/cci-nas-00/data/ceres_data/27wr_81518/08_2026/27wr_81518.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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.005 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 1420 2.51 5 N 400 2.21 5 O 400 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 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: 2220 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 222 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "B" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 222 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Restraints were copied for chains: C, E, G, I, D, F, H, J Time building chain proxies: 0.40, per 1000 atoms: 0.18 Number of scatterers: 2220 At special positions: 0 Unit cell: (66.172, 83.88, 42.872, 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 400 8.00 N 400 7.00 C 1420 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: 0.10 Conformation dependent library (CDL) restraints added in 48.4 milliseconds 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 480 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 7 sheets defined 0.0% alpha, 42.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 13 removed outlier: 6.195A pdb=" N TRP A 7 " --> pdb=" O GLN C 8 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N VAL C 10 " --> pdb=" O TRP A 7 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLN A 9 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ASN C 12 " --> pdb=" O GLN A 9 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU A 11 " --> pdb=" O ASN C 12 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N TRP C 7 " --> pdb=" O GLN E 8 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N VAL E 10 " --> pdb=" O TRP C 7 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLN C 9 " --> pdb=" O VAL E 10 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ASN E 12 " --> pdb=" O GLN C 9 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU C 11 " --> pdb=" O ASN E 12 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N TRP E 7 " --> pdb=" O GLN G 8 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N VAL G 10 " --> pdb=" O TRP E 7 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLN E 9 " --> pdb=" O VAL G 10 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ASN G 12 " --> pdb=" O GLN E 9 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU E 11 " --> pdb=" O ASN G 12 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N TRP G 7 " --> pdb=" O GLN I 8 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N VAL I 10 " --> pdb=" O TRP G 7 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLN G 9 " --> pdb=" O VAL I 10 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ASN I 12 " --> pdb=" O GLN G 9 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU G 11 " --> pdb=" O ASN I 12 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 17 Processing sheet with id=AA3, first strand: chain 'A' and resid 20 through 24 removed outlier: 6.289A pdb=" N ILE A 21 " --> pdb=" O ALA C 22 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N HIS C 24 " --> pdb=" O ILE A 21 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLY A 23 " --> pdb=" O HIS C 24 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE C 21 " --> pdb=" O ALA E 22 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N HIS E 24 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLY C 23 " --> pdb=" O HIS E 24 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE E 21 " --> pdb=" O ALA G 22 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N HIS G 24 " --> pdb=" O ILE E 21 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLY E 23 " --> pdb=" O HIS G 24 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ILE G 21 " --> pdb=" O ALA I 22 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N HIS I 24 " --> pdb=" O ILE G 21 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLY G 23 " --> pdb=" O HIS I 24 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 27 through 29 removed outlier: 6.338A pdb=" N VAL A 28 " --> pdb=" O LEU C 29 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL C 28 " --> pdb=" O LEU E 29 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL E 28 " --> pdb=" O LEU G 29 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL G 28 " --> pdb=" O LEU I 29 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 6 through 7 Processing sheet with id=AA6, first strand: chain 'B' and resid 16 through 23 removed outlier: 6.470A pdb=" N LYS B 16 " --> pdb=" O VAL D 17 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ALA D 19 " --> pdb=" O LYS B 16 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLU B 18 " --> pdb=" O ALA D 19 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ILE D 21 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N ASP B 20 " --> pdb=" O ILE D 21 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N GLY D 23 " --> pdb=" O ASP B 20 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA B 22 " --> pdb=" O GLY D 23 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LYS D 16 " --> pdb=" O VAL F 17 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N ALA F 19 " --> pdb=" O LYS D 16 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLU D 18 " --> pdb=" O ALA F 19 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ILE F 21 " --> pdb=" O GLU D 18 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N ASP D 20 " --> pdb=" O ILE F 21 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N GLY F 23 " --> pdb=" O ASP D 20 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA D 22 " --> pdb=" O GLY F 23 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LYS F 16 " --> pdb=" O VAL H 17 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ALA H 19 " --> pdb=" O LYS F 16 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLU F 18 " --> pdb=" O ALA H 19 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ILE H 21 " --> pdb=" O GLU F 18 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N ASP F 20 " --> pdb=" O ILE H 21 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N GLY H 23 " --> pdb=" O ASP F 20 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA F 22 " --> pdb=" O GLY H 23 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LYS H 16 " --> pdb=" O VAL J 17 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N ALA J 19 " --> pdb=" O LYS H 16 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLU H 18 " --> pdb=" O ALA J 19 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ILE J 21 " --> pdb=" O GLU H 18 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N ASP H 20 " --> pdb=" O ILE J 21 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N GLY J 23 " --> pdb=" O ASP H 20 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA H 22 " --> pdb=" O GLY J 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 27 through 30 20 hydrogen bonds defined for protein. 60 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: 0.32 Time building geometry restraints manager: 0.14 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: 400 1.29 - 1.35: 360 1.35 - 1.42: 210 1.42 - 1.48: 315 1.48 - 1.55: 975 Bond restraints: 2260 Sorted by residual: bond pdb=" CB LYS A 16 " pdb=" CG LYS A 16 " ideal model delta sigma weight residual 1.520 1.494 0.026 3.00e-02 1.11e+03 7.79e-01 bond pdb=" CB LYS E 16 " pdb=" CG LYS E 16 " ideal model delta sigma weight residual 1.520 1.494 0.026 3.00e-02 1.11e+03 7.71e-01 bond pdb=" CB LYS G 16 " pdb=" CG LYS G 16 " ideal model delta sigma weight residual 1.520 1.494 0.026 3.00e-02 1.11e+03 7.36e-01 bond pdb=" CB LYS C 16 " pdb=" CG LYS C 16 " ideal model delta sigma weight residual 1.520 1.494 0.026 3.00e-02 1.11e+03 7.36e-01 bond pdb=" CB LYS I 16 " pdb=" CG LYS I 16 " ideal model delta sigma weight residual 1.520 1.495 0.025 3.00e-02 1.11e+03 7.02e-01 ... (remaining 2255 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.75: 2664 0.75 - 1.50: 317 1.50 - 2.25: 50 2.25 - 3.00: 22 3.00 - 3.75: 7 Bond angle restraints: 3060 Sorted by residual: angle pdb=" C VAL H 17 " pdb=" N GLU H 18 " pdb=" CA GLU H 18 " ideal model delta sigma weight residual 122.74 119.73 3.01 1.54e+00 4.22e-01 3.83e+00 angle pdb=" C VAL F 17 " pdb=" N GLU F 18 " pdb=" CA GLU F 18 " ideal model delta sigma weight residual 122.74 119.73 3.01 1.54e+00 4.22e-01 3.81e+00 angle pdb=" C VAL D 17 " pdb=" N GLU D 18 " pdb=" CA GLU D 18 " ideal model delta sigma weight residual 122.74 119.75 2.99 1.54e+00 4.22e-01 3.77e+00 angle pdb=" C VAL J 17 " pdb=" N GLU J 18 " pdb=" CA GLU J 18 " ideal model delta sigma weight residual 122.74 119.76 2.98 1.54e+00 4.22e-01 3.75e+00 angle pdb=" C VAL B 17 " pdb=" N GLU B 18 " pdb=" CA GLU B 18 " ideal model delta sigma weight residual 122.74 119.82 2.92 1.54e+00 4.22e-01 3.61e+00 ... (remaining 3055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.94: 1030 14.94 - 29.88: 150 29.88 - 44.82: 50 44.82 - 59.76: 15 59.76 - 74.70: 15 Dihedral angle restraints: 1260 sinusoidal: 510 harmonic: 750 Sorted by residual: dihedral pdb=" CA GLU C 18 " pdb=" C GLU C 18 " pdb=" N ALA C 19 " pdb=" CA ALA C 19 " ideal model delta harmonic sigma weight residual 180.00 161.71 18.29 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA GLU E 18 " pdb=" C GLU E 18 " pdb=" N ALA E 19 " pdb=" CA ALA E 19 " ideal model delta harmonic sigma weight residual 180.00 161.72 18.28 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA GLU I 18 " pdb=" C GLU I 18 " pdb=" N ALA I 19 " pdb=" CA ALA I 19 " ideal model delta harmonic sigma weight residual 180.00 161.75 18.25 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 1257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 176 0.026 - 0.051: 69 0.051 - 0.077: 20 0.077 - 0.103: 26 0.103 - 0.128: 39 Chirality restraints: 330 Sorted by residual: chirality pdb=" CA ILE I 30 " pdb=" N ILE I 30 " pdb=" C ILE I 30 " pdb=" CB ILE I 30 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.12e-01 chirality pdb=" CA ILE E 30 " pdb=" N ILE E 30 " pdb=" C ILE E 30 " pdb=" CB ILE E 30 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.01e-01 chirality pdb=" CA ILE C 30 " pdb=" N ILE C 30 " pdb=" C ILE C 30 " pdb=" CB ILE C 30 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.01e-01 ... (remaining 327 not shown) Planarity restraints: 390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU C 18 " -0.006 2.00e-02 2.50e+03 1.17e-02 1.37e+00 pdb=" CD GLU C 18 " 0.020 2.00e-02 2.50e+03 pdb=" OE1 GLU C 18 " -0.007 2.00e-02 2.50e+03 pdb=" OE2 GLU C 18 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU E 18 " -0.006 2.00e-02 2.50e+03 1.17e-02 1.36e+00 pdb=" CD GLU E 18 " 0.020 2.00e-02 2.50e+03 pdb=" OE1 GLU E 18 " -0.007 2.00e-02 2.50e+03 pdb=" OE2 GLU E 18 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 18 " -0.006 2.00e-02 2.50e+03 1.16e-02 1.35e+00 pdb=" CD GLU A 18 " 0.020 2.00e-02 2.50e+03 pdb=" OE1 GLU A 18 " -0.007 2.00e-02 2.50e+03 pdb=" OE2 GLU A 18 " -0.007 2.00e-02 2.50e+03 ... (remaining 387 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 140 2.75 - 3.28: 1765 3.28 - 3.82: 3896 3.82 - 4.36: 4398 4.36 - 4.90: 8748 Nonbonded interactions: 18947 Sorted by model distance: nonbonded pdb=" O ARG D 31 " pdb=" CD1 LEU D 32 " model vdw 2.208 3.460 nonbonded pdb=" O ARG F 31 " pdb=" CD1 LEU F 32 " model vdw 2.208 3.460 nonbonded pdb=" O ARG H 31 " pdb=" CD1 LEU H 32 " model vdw 2.208 3.460 nonbonded pdb=" O ARG J 31 " pdb=" CD1 LEU J 32 " model vdw 2.209 3.460 nonbonded pdb=" O ARG B 31 " pdb=" CD1 LEU B 32 " model vdw 2.209 3.460 ... (remaining 18942 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 0.320 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: 0.060 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 3.230 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 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: 0.010 Load rotamer database and sin/cos tables:9.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 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 : 0.005 0.026 2260 Z= 0.223 Angle : 0.568 3.753 3060 Z= 0.321 Chirality : 0.054 0.128 330 Planarity : 0.002 0.012 390 Dihedral : 18.414 74.699 780 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 25.00 % Favored : 75.00 % 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: -4.12 (0.34), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.26), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 31 TRP 0.006 0.001 TRP C 14 HIS 0.002 0.001 HIS C 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.22 ( 2260) covalent geometry : angle 0.56759 / 0.32 ( 3060) hydrogen bonds : bond 0.05963 / 3.90 ( 20) hydrogen bonds : angle 4.53365 / 2.71 ( 60) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.066 Fit side-chains REVERT: A 31 ARG cc_start: 0.7869 (mtt-85) cc_final: 0.6979 (pmt170) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.6186 time to fit residues: 48.9901 Evaluate side-chains 51 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.093 ------------------------------------------------------------------------------- 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: 10.0000 chunk 13 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 chunk 6 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 8 GLN B 26 GLN C 8 GLN ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 GLN G 8 GLN I 8 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.126188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.119836 restraints weight = 3769.977| |-----------------------------------------------------------------------------| r_work (start): 0.4307 rms_B_bonded: 2.24 r_work: 0.4201 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.4097 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.4097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 2260 Z= 0.271 Angle : 0.584 4.151 3060 Z= 0.313 Chirality : 0.054 0.131 330 Planarity : 0.002 0.014 390 Dihedral : 5.645 16.830 280 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 7.73 % Allowed : 32.73 % Favored : 59.55 % 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: -4.17 (0.36), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (0.27), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 31 TRP 0.007 0.001 TRP G 14 HIS 0.002 0.001 HIS H 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00603 / 0.27 ( 2260) covalent geometry : angle 0.58405 / 0.31 ( 3060) hydrogen bonds : bond 0.01700 / 1.11 ( 20) hydrogen bonds : angle 3.54745 / 2.08 ( 60) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.055 Fit side-chains REVERT: A 31 ARG cc_start: 0.8410 (mtt-85) cc_final: 0.7230 (pmt170) REVERT: B 20 ASP cc_start: 0.8562 (t0) cc_final: 0.8311 (t70) REVERT: C 16 LYS cc_start: 0.8127 (ttmt) cc_final: 0.7819 (ttmt) REVERT: C 18 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.7813 (mp0) REVERT: G 31 ARG cc_start: 0.8290 (tpp-160) cc_final: 0.7997 (mmm-85) REVERT: I 16 LYS cc_start: 0.8072 (ttpt) cc_final: 0.7251 (tptt) outliers start: 17 outliers final: 3 residues processed: 70 average time/residue: 0.4790 time to fit residues: 34.1159 Evaluate side-chains 56 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain J residue 32 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 11 optimal weight: 5.9990 chunk 9 optimal weight: 20.0000 chunk 12 optimal weight: 20.0000 chunk 19 optimal weight: 5.9990 chunk 4 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 16 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 8 optimal weight: 0.0770 overall best weight: 5.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 8 GLN E 8 GLN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 8 GLN ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 8 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.101912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.095650 restraints weight = 4540.611| |-----------------------------------------------------------------------------| r_work (start): 0.4319 rms_B_bonded: 2.63 r_work: 0.4180 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 2260 Z= 0.205 Angle : 0.575 4.952 3060 Z= 0.303 Chirality : 0.055 0.137 330 Planarity : 0.002 0.010 390 Dihedral : 5.558 18.990 280 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 9.55 % Allowed : 28.18 % Favored : 62.27 % 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: -4.05 (0.36), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.08 (0.28), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 31 TRP 0.008 0.001 TRP E 14 HIS 0.002 0.001 HIS F 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.21 ( 2260) covalent geometry : angle 0.57483 / 0.30 ( 3060) hydrogen bonds : bond 0.01915 / 1.25 ( 20) hydrogen bonds : angle 3.49631 / 2.05 ( 60) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 0.058 Fit side-chains REVERT: A 6 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.6640 (pm20) REVERT: A 9 GLN cc_start: 0.9007 (tt0) cc_final: 0.8678 (tt0) REVERT: A 31 ARG cc_start: 0.8289 (mtt-85) cc_final: 0.7128 (pmt170) REVERT: B 20 ASP cc_start: 0.8444 (t0) cc_final: 0.8168 (t70) REVERT: B 31 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.7194 (mtt180) REVERT: C 16 LYS cc_start: 0.8066 (ttmt) cc_final: 0.7691 (ttmt) REVERT: C 18 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7694 (mp0) REVERT: D 8 GLN cc_start: 0.8565 (mt0) cc_final: 0.8327 (mt0) REVERT: G 31 ARG cc_start: 0.8213 (tpp-160) cc_final: 0.7994 (mmm-85) REVERT: I 16 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7733 (tppt) REVERT: I 30 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8307 (mm) outliers start: 21 outliers final: 2 residues processed: 73 average time/residue: 0.7024 time to fit residues: 52.0383 Evaluate side-chains 59 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLU Chi-restraints excluded: chain B residue 31 ARG Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain I residue 16 LYS Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain J residue 6 GLU Chi-restraints excluded: chain J residue 32 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 0 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 17 optimal weight: 20.0000 chunk 11 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 14 optimal weight: 7.9990 chunk 18 optimal weight: 0.0040 chunk 5 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 overall best weight: 4.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 8 GLN I 8 GLN ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 26 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 = 0.4471 r_free = 0.4471 target = 0.128293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.122001 restraints weight = 3812.429| |-----------------------------------------------------------------------------| r_work (start): 0.4373 rms_B_bonded: 2.25 r_work: 0.4262 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.4160 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.4160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2260 Z= 0.183 Angle : 0.569 5.136 3060 Z= 0.295 Chirality : 0.055 0.139 330 Planarity : 0.002 0.008 390 Dihedral : 5.406 18.042 280 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 6.82 % Allowed : 31.36 % Favored : 61.82 % 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: -3.96 (0.38), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.29), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 31 TRP 0.008 0.001 TRP C 14 HIS 0.001 0.001 HIS F 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 ( 2260) covalent geometry : angle 0.56869 / 0.30 ( 3060) hydrogen bonds : bond 0.01870 / 1.18 ( 20) hydrogen bonds : angle 3.48127 / 2.04 ( 60) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.128 Fit side-chains REVERT: A 6 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.6632 (pm20) REVERT: A 31 ARG cc_start: 0.8462 (mtt-85) cc_final: 0.7206 (pmt170) REVERT: B 20 ASP cc_start: 0.8530 (t0) cc_final: 0.8264 (t70) REVERT: B 31 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.7241 (mtt180) REVERT: C 16 LYS cc_start: 0.8117 (ttmt) cc_final: 0.7782 (ttmt) REVERT: C 18 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.7808 (mp0) REVERT: E 18 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8207 (mp0) REVERT: G 31 ARG cc_start: 0.8205 (tpp-160) cc_final: 0.7899 (mpt-90) REVERT: I 16 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7875 (tppt) outliers start: 15 outliers final: 4 residues processed: 63 average time/residue: 0.7234 time to fit residues: 46.3268 Evaluate side-chains 56 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLU Chi-restraints excluded: chain B residue 31 ARG Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain E residue 18 GLU Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain I residue 16 LYS Chi-restraints excluded: chain J residue 32 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 5 optimal weight: 20.0000 chunk 14 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 4 optimal weight: 20.0000 chunk 19 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 26 GLN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 8 GLN ** H 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 8 GLN ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 26 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 = 0.4475 r_free = 0.4475 target = 0.128380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.122139 restraints weight = 3756.142| |-----------------------------------------------------------------------------| r_work (start): 0.4379 rms_B_bonded: 2.21 r_work: 0.4271 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.4168 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.4168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 2260 Z= 0.208 Angle : 0.574 5.124 3060 Z= 0.296 Chirality : 0.055 0.142 330 Planarity : 0.002 0.007 390 Dihedral : 5.419 16.744 280 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 6.36 % Allowed : 33.64 % Favored : 60.00 % 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: -3.97 (0.39), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.30), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 31 TRP 0.006 0.001 TRP E 14 HIS 0.002 0.001 HIS D 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.21 ( 2260) covalent geometry : angle 0.57443 / 0.30 ( 3060) hydrogen bonds : bond 0.01987 / 1.26 ( 20) hydrogen bonds : angle 3.47745 / 2.04 ( 60) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.096 Fit side-chains REVERT: A 6 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.6674 (pm20) REVERT: A 31 ARG cc_start: 0.8478 (mtt-85) cc_final: 0.7230 (pmt170) REVERT: B 20 ASP cc_start: 0.8551 (t0) cc_final: 0.8291 (t70) REVERT: B 31 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.7295 (mtt180) REVERT: C 16 LYS cc_start: 0.8142 (ttmt) cc_final: 0.7803 (ttmt) REVERT: C 18 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.7756 (mp0) REVERT: D 8 GLN cc_start: 0.8712 (mt0) cc_final: 0.8507 (mt0) REVERT: G 6 GLU cc_start: 0.7438 (tt0) cc_final: 0.7184 (tm-30) REVERT: G 31 ARG cc_start: 0.8214 (tpp-160) cc_final: 0.7921 (mpt-90) REVERT: I 16 LYS cc_start: 0.8304 (ttpt) cc_final: 0.7877 (tppt) outliers start: 14 outliers final: 5 residues processed: 63 average time/residue: 0.6935 time to fit residues: 44.3632 Evaluate side-chains 56 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLU Chi-restraints excluded: chain B residue 31 ARG Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain J residue 6 GLU Chi-restraints excluded: chain J residue 32 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 15 optimal weight: 20.0000 chunk 13 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 chunk 8 optimal weight: 20.0000 chunk 10 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 26 GLN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 GLN ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 8 GLN ** H 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 8 GLN ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.125657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.119362 restraints weight = 3795.760| |-----------------------------------------------------------------------------| r_work (start): 0.4336 rms_B_bonded: 2.22 r_work: 0.4228 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.4121 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 2260 Z= 0.266 Angle : 0.612 5.348 3060 Z= 0.317 Chirality : 0.056 0.140 330 Planarity : 0.002 0.014 390 Dihedral : 5.623 18.893 280 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 8.18 % Allowed : 31.82 % Favored : 60.00 % 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: -4.04 (0.38), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.07 (0.29), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 31 TRP 0.007 0.001 TRP G 14 HIS 0.002 0.001 HIS D 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00603 / 0.27 ( 2260) covalent geometry : angle 0.61171 / 0.32 ( 3060) hydrogen bonds : bond 0.02182 / 1.49 ( 20) hydrogen bonds : angle 3.47920 / 2.04 ( 60) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 51 time to evaluate : 0.062 Fit side-chains REVERT: A 6 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.6787 (pm20) REVERT: A 31 ARG cc_start: 0.8500 (mtt-85) cc_final: 0.7260 (pmt170) REVERT: B 20 ASP cc_start: 0.8571 (t0) cc_final: 0.8287 (t0) REVERT: B 31 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.7301 (mtt180) REVERT: C 6 GLU cc_start: 0.7653 (tm-30) cc_final: 0.7366 (tm-30) REVERT: C 7 TRP cc_start: 0.8410 (m-90) cc_final: 0.8010 (m-90) REVERT: C 16 LYS cc_start: 0.8171 (ttmt) cc_final: 0.7841 (ttmt) REVERT: C 18 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.7641 (mp0) REVERT: D 8 GLN cc_start: 0.8702 (mt0) cc_final: 0.8418 (mt0) REVERT: E 6 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7544 (tm-30) REVERT: G 31 ARG cc_start: 0.8246 (tpp-160) cc_final: 0.7959 (mpt-90) REVERT: I 16 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7807 (tppt) outliers start: 18 outliers final: 11 residues processed: 61 average time/residue: 0.7004 time to fit residues: 43.4003 Evaluate side-chains 64 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLU Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 31 ARG Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain I residue 16 LYS Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain J residue 6 GLU Chi-restraints excluded: chain J residue 32 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 20.0000 chunk 8 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 3 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 9 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 26 GLN C 8 GLN E 8 GLN ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 8 GLN ** H 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 8 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.128336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.122142 restraints weight = 3812.863| |-----------------------------------------------------------------------------| r_work (start): 0.4385 rms_B_bonded: 2.18 r_work: 0.4275 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.4171 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2260 Z= 0.192 Angle : 0.576 5.455 3060 Z= 0.292 Chirality : 0.056 0.136 330 Planarity : 0.002 0.012 390 Dihedral : 5.468 19.186 280 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 6.82 % Allowed : 32.27 % Favored : 60.91 % 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: -3.96 (0.39), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.29), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 31 TRP 0.007 0.001 TRP I 14 HIS 0.002 0.001 HIS D 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 ( 2260) covalent geometry : angle 0.57601 / 0.29 ( 3060) hydrogen bonds : bond 0.01846 / 1.22 ( 20) hydrogen bonds : angle 3.50993 / 2.07 ( 60) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 0.095 Fit side-chains REVERT: A 6 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.6797 (pm20) REVERT: A 31 ARG cc_start: 0.8428 (mtt-85) cc_final: 0.7243 (pmt170) REVERT: B 20 ASP cc_start: 0.8575 (t0) cc_final: 0.8293 (t0) REVERT: B 31 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.7393 (mtt180) REVERT: C 6 GLU cc_start: 0.7676 (tm-30) cc_final: 0.7382 (tm-30) REVERT: C 7 TRP cc_start: 0.8396 (m-90) cc_final: 0.7980 (m-90) REVERT: C 16 LYS cc_start: 0.8173 (ttmt) cc_final: 0.7864 (ttmt) REVERT: C 18 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.7699 (mp0) REVERT: E 6 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7551 (tm-30) REVERT: G 6 GLU cc_start: 0.7414 (tt0) cc_final: 0.7156 (tm-30) REVERT: G 31 ARG cc_start: 0.8157 (tpp-160) cc_final: 0.7896 (mpt-90) REVERT: I 16 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7919 (tppt) outliers start: 15 outliers final: 10 residues processed: 60 average time/residue: 0.7100 time to fit residues: 43.2717 Evaluate side-chains 62 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLU Chi-restraints excluded: chain B residue 31 ARG Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain I residue 16 LYS Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain J residue 6 GLU Chi-restraints excluded: chain J residue 32 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 5 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN B 26 GLN C 8 GLN ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 8 GLN ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 8 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.127414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.121356 restraints weight = 3770.411| |-----------------------------------------------------------------------------| r_work (start): 0.4374 rms_B_bonded: 2.14 r_work: 0.4268 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.4166 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 2260 Z= 0.218 Angle : 0.584 5.037 3060 Z= 0.299 Chirality : 0.056 0.139 330 Planarity : 0.002 0.011 390 Dihedral : 5.496 17.944 280 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 7.27 % Allowed : 31.82 % Favored : 60.91 % 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: -3.96 (0.38), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.29), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 31 TRP 0.008 0.001 TRP I 14 HIS 0.002 0.001 HIS D 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.22 ( 2260) covalent geometry : angle 0.58448 / 0.30 ( 3060) hydrogen bonds : bond 0.01919 / 1.26 ( 20) hydrogen bonds : angle 3.48919 / 2.06 ( 60) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.056 Fit side-chains REVERT: A 6 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.6800 (pm20) REVERT: A 31 ARG cc_start: 0.8434 (mtt-85) cc_final: 0.7264 (pmt170) REVERT: B 20 ASP cc_start: 0.8587 (t0) cc_final: 0.8304 (t0) REVERT: B 31 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7412 (mtt180) REVERT: C 6 GLU cc_start: 0.7701 (tm-30) cc_final: 0.7417 (tm-30) REVERT: C 7 TRP cc_start: 0.8391 (m-90) cc_final: 0.8155 (m-90) REVERT: C 16 LYS cc_start: 0.8164 (ttmt) cc_final: 0.7857 (ttmt) REVERT: C 18 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.7610 (mp0) REVERT: E 6 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7775 (tm-30) REVERT: G 31 ARG cc_start: 0.8157 (tpp-160) cc_final: 0.7907 (mpt-90) REVERT: I 16 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7886 (tppt) outliers start: 16 outliers final: 10 residues processed: 60 average time/residue: 0.5629 time to fit residues: 34.3282 Evaluate side-chains 61 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLU Chi-restraints excluded: chain B residue 31 ARG Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain I residue 16 LYS Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain J residue 6 GLU Chi-restraints excluded: chain J residue 32 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 0 optimal weight: 20.0000 chunk 12 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 26 GLN C 8 GLN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 8 GLN ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 8 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.126772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.120671 restraints weight = 3833.872| |-----------------------------------------------------------------------------| r_work (start): 0.4369 rms_B_bonded: 2.17 r_work: 0.4262 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.4161 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.4161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 2260 Z= 0.230 Angle : 0.598 6.100 3060 Z= 0.305 Chirality : 0.056 0.140 330 Planarity : 0.002 0.013 390 Dihedral : 5.558 17.922 280 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 6.82 % Allowed : 33.64 % Favored : 59.55 % 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: -3.98 (0.38), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.03 (0.29), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 31 TRP 0.007 0.001 TRP D 7 HIS 0.002 0.001 HIS D 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.23 ( 2260) covalent geometry : angle 0.59758 / 0.31 ( 3060) hydrogen bonds : bond 0.01915 / 1.25 ( 20) hydrogen bonds : angle 3.50432 / 2.07 ( 60) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.056 Fit side-chains REVERT: A 31 ARG cc_start: 0.8447 (mtt-85) cc_final: 0.7264 (pmt170) REVERT: B 20 ASP cc_start: 0.8563 (t0) cc_final: 0.8282 (t0) REVERT: B 31 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.7404 (mtt180) REVERT: C 6 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7417 (tm-30) REVERT: C 7 TRP cc_start: 0.8404 (m-90) cc_final: 0.8164 (m-90) REVERT: C 16 LYS cc_start: 0.8164 (ttmt) cc_final: 0.7857 (ttmt) REVERT: C 18 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.7607 (mp0) REVERT: E 6 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7674 (tm-30) REVERT: G 6 GLU cc_start: 0.7585 (tt0) cc_final: 0.7347 (tm-30) REVERT: G 31 ARG cc_start: 0.8168 (tpp-160) cc_final: 0.7918 (mpt-90) REVERT: I 16 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7888 (tppt) outliers start: 15 outliers final: 10 residues processed: 56 average time/residue: 0.5554 time to fit residues: 31.5706 Evaluate side-chains 59 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 ARG Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain I residue 16 LYS Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain J residue 6 GLU Chi-restraints excluded: chain J residue 32 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 9 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 7 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 0 optimal weight: 0.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 26 GLN C 8 GLN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 GLN ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 8 GLN H 26 GLN I 8 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.129514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.123614 restraints weight = 3936.244| |-----------------------------------------------------------------------------| r_work (start): 0.4403 rms_B_bonded: 2.20 r_work: 0.4299 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.4196 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2260 Z= 0.168 Angle : 0.577 6.238 3060 Z= 0.291 Chirality : 0.056 0.133 330 Planarity : 0.002 0.011 390 Dihedral : 5.377 17.932 280 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 6.36 % Allowed : 33.64 % Favored : 60.00 % 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: -3.84 (0.39), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.30), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 31 TRP 0.008 0.001 TRP C 14 HIS 0.001 0.001 HIS D 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 ( 2260) covalent geometry : angle 0.57693 / 0.29 ( 3060) hydrogen bonds : bond 0.01739 / 1.13 ( 20) hydrogen bonds : angle 3.52054 / 2.09 ( 60) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.067 Fit side-chains REVERT: A 31 ARG cc_start: 0.8432 (mtt-85) cc_final: 0.7176 (pmt170) REVERT: B 20 ASP cc_start: 0.8528 (t0) cc_final: 0.8214 (t0) REVERT: B 31 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.7294 (mtt180) REVERT: C 6 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7448 (tm-30) REVERT: C 7 TRP cc_start: 0.8365 (m-90) cc_final: 0.8098 (m-90) REVERT: C 16 LYS cc_start: 0.8161 (ttmt) cc_final: 0.7828 (ttmt) REVERT: C 18 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.7599 (mp0) REVERT: E 6 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7514 (tm-30) REVERT: G 6 GLU cc_start: 0.7418 (tt0) cc_final: 0.7200 (tm-30) REVERT: G 31 ARG cc_start: 0.8152 (tpp-160) cc_final: 0.7887 (mpt-90) REVERT: I 16 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7864 (tppt) REVERT: I 30 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.8241 (mm) outliers start: 14 outliers final: 7 residues processed: 56 average time/residue: 0.7024 time to fit residues: 39.9287 Evaluate side-chains 57 residues out of total 220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 ARG Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain I residue 16 LYS Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain J residue 6 GLU Chi-restraints excluded: chain J residue 32 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 4 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 13 optimal weight: 30.0000 chunk 5 optimal weight: 10.0000 chunk 16 optimal weight: 20.0000 chunk 18 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN C 8 GLN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 8 GLN ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 8 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.127097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.121144 restraints weight = 4001.813| |-----------------------------------------------------------------------------| r_work (start): 0.4367 rms_B_bonded: 2.21 r_work: 0.4264 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.4160 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.4160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 2260 Z= 0.230 Angle : 0.611 5.990 3060 Z= 0.312 Chirality : 0.056 0.136 330 Planarity : 0.002 0.012 390 Dihedral : 5.571 17.785 280 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 5.91 % Allowed : 34.55 % Favored : 59.55 % 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: -3.87 (0.39), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.94 (0.30), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 31 TRP 0.009 0.001 TRP G 7 HIS 0.002 0.001 HIS D 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.23 ( 2260) covalent geometry : angle 0.61125 / 0.31 ( 3060) hydrogen bonds : bond 0.01999 / 1.29 ( 20) hydrogen bonds : angle 3.50032 / 2.06 ( 60) =============================================================================== Job complete usr+sys time: 1104.33 seconds wall clock time: 19 minutes 26.69 seconds (1166.69 seconds total)