Starting phenix.real_space_refine on Fri Aug 22 16:52:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qhs_18416/08_2025/8qhs_18416.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qhs_18416/08_2025/8qhs_18416.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qhs_18416/08_2025/8qhs_18416.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qhs_18416/08_2025/8qhs_18416.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qhs_18416/08_2025/8qhs_18416.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qhs_18416/08_2025/8qhs_18416.map" } resolution = 2.3 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= 0.001 sd= 0.055 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 3725 2.51 5 N 935 2.21 5 O 1522 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6212 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1175 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 3, 'TRANS': 153} Chain breaks: 1 Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "C" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 64 Classifications: {'water': 64} Link IDs: {None: 63} Chain: "F" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 69 Classifications: {'water': 69} Link IDs: {None: 68} Restraints were copied for chains: C, D, E, F Time building chain proxies: 1.17, per 1000 atoms: 0.19 Number of scatterers: 6212 At special positions: 0 Unit cell: (72.688, 99.12, 159.418, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 1522 8.00 N 935 7.00 C 3725 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 9 " - pdb=" SG CYS C 104 " distance=3.00 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: 0.48 Conformation dependent library (CDL) restraints added in 333.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1400 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 3 sheets defined 14.1% alpha, 26.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 2 through 7 removed outlier: 3.514A pdb=" N ASN A 6 " --> pdb=" O ALA A 2 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU A 7 " --> pdb=" O PHE A 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2 through 7' Processing helix chain 'A' and resid 20 through 22 No H-bonds generated for 'chain 'A' and resid 20 through 22' Processing helix chain 'A' and resid 87 through 100 Processing helix chain 'C' and resid 3 through 7 removed outlier: 3.906A pdb=" N LEU C 7 " --> pdb=" O PHE C 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3 through 7' Processing helix chain 'C' and resid 20 through 22 No H-bonds generated for 'chain 'C' and resid 20 through 22' Processing helix chain 'C' and resid 87 through 100 Processing helix chain 'D' and resid 3 through 7 removed outlier: 3.907A pdb=" N LEU D 7 " --> pdb=" O PHE D 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3 through 7' Processing helix chain 'D' and resid 20 through 22 No H-bonds generated for 'chain 'D' and resid 20 through 22' Processing helix chain 'D' and resid 87 through 100 Processing helix chain 'E' and resid 3 through 7 removed outlier: 3.906A pdb=" N LEU E 7 " --> pdb=" O PHE E 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 3 through 7' Processing helix chain 'E' and resid 20 through 22 No H-bonds generated for 'chain 'E' and resid 20 through 22' Processing helix chain 'E' and resid 87 through 100 Processing helix chain 'F' and resid 3 through 7 removed outlier: 3.907A pdb=" N LEU F 7 " --> pdb=" O PHE F 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 3 through 7' Processing helix chain 'F' and resid 20 through 22 No H-bonds generated for 'chain 'F' and resid 20 through 22' Processing helix chain 'F' and resid 87 through 100 Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 29 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 36 through 38 current: chain 'A' and resid 68 through 82 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 68 through 82 current: chain 'A' and resid 114 through 129 removed outlier: 6.281A pdb=" N LYS A 141 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N TYR A 126 " --> pdb=" O SER A 139 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N SER A 139 " --> pdb=" O TYR A 126 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N PHE A 128 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THR A 137 " --> pdb=" O PHE A 128 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 137 through 144 current: chain 'D' and resid 36 through 38 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 36 through 38 current: chain 'D' and resid 68 through 82 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 68 through 82 current: chain 'D' and resid 114 through 129 removed outlier: 6.281A pdb=" N LYS D 141 " --> pdb=" O ALA D 124 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR D 126 " --> pdb=" O SER D 139 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N SER D 139 " --> pdb=" O TYR D 126 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N PHE D 128 " --> pdb=" O THR D 137 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THR D 137 " --> pdb=" O PHE D 128 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 24 through 29 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 36 through 38 current: chain 'C' and resid 68 through 82 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 68 through 82 current: chain 'C' and resid 114 through 129 removed outlier: 6.282A pdb=" N LYS C 141 " --> pdb=" O ALA C 124 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR C 126 " --> pdb=" O SER C 139 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N SER C 139 " --> pdb=" O TYR C 126 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N PHE C 128 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THR C 137 " --> pdb=" O PHE C 128 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 137 through 144 current: chain 'E' and resid 36 through 38 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 36 through 38 current: chain 'E' and resid 68 through 82 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 68 through 82 current: chain 'E' and resid 114 through 129 removed outlier: 6.281A pdb=" N LYS E 141 " --> pdb=" O ALA E 124 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N TYR E 126 " --> pdb=" O SER E 139 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N SER E 139 " --> pdb=" O TYR E 126 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N PHE E 128 " --> pdb=" O THR E 137 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THR E 137 " --> pdb=" O PHE E 128 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 24 through 29 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 36 through 38 current: chain 'F' and resid 68 through 82 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 68 through 82 current: chain 'F' and resid 114 through 129 removed outlier: 6.281A pdb=" N LYS F 141 " --> pdb=" O ALA F 124 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR F 126 " --> pdb=" O SER F 139 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N SER F 139 " --> pdb=" O TYR F 126 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N PHE F 128 " --> pdb=" O THR F 137 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THR F 137 " --> pdb=" O PHE F 128 " (cutoff:3.500A) 71 hydrogen bonds defined for protein. 213 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: 0.76 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1915 1.34 - 1.45: 1011 1.45 - 1.57: 2989 1.57 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 5965 Sorted by residual: bond pdb=" C ILE D 56 " pdb=" O ILE D 56 " ideal model delta sigma weight residual 1.236 1.223 0.014 1.19e-02 7.06e+03 1.31e+00 bond pdb=" N GLY C 44 " pdb=" CA GLY C 44 " ideal model delta sigma weight residual 1.454 1.443 0.011 9.90e-03 1.02e+04 1.29e+00 bond pdb=" C ILE C 56 " pdb=" O ILE C 56 " ideal model delta sigma weight residual 1.236 1.223 0.013 1.19e-02 7.06e+03 1.27e+00 bond pdb=" C ILE A 56 " pdb=" O ILE A 56 " ideal model delta sigma weight residual 1.236 1.223 0.013 1.19e-02 7.06e+03 1.25e+00 bond pdb=" C ILE E 56 " pdb=" O ILE E 56 " ideal model delta sigma weight residual 1.236 1.223 0.013 1.19e-02 7.06e+03 1.25e+00 ... (remaining 5960 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.91: 6889 0.91 - 1.82: 977 1.82 - 2.73: 114 2.73 - 3.64: 40 3.64 - 4.55: 15 Bond angle restraints: 8035 Sorted by residual: angle pdb=" C SER E 112 " pdb=" N LYS E 113 " pdb=" CA LYS E 113 " ideal model delta sigma weight residual 122.19 125.30 -3.11 1.41e+00 5.03e-01 4.87e+00 angle pdb=" C SER A 112 " pdb=" N LYS A 113 " pdb=" CA LYS A 113 " ideal model delta sigma weight residual 122.19 125.30 -3.11 1.41e+00 5.03e-01 4.87e+00 angle pdb=" C SER C 112 " pdb=" N LYS C 113 " pdb=" CA LYS C 113 " ideal model delta sigma weight residual 122.19 125.28 -3.09 1.41e+00 5.03e-01 4.80e+00 angle pdb=" C SER D 112 " pdb=" N LYS D 113 " pdb=" CA LYS D 113 " ideal model delta sigma weight residual 122.19 125.27 -3.08 1.41e+00 5.03e-01 4.76e+00 angle pdb=" C SER F 112 " pdb=" N LYS F 113 " pdb=" CA LYS F 113 " ideal model delta sigma weight residual 122.19 125.26 -3.07 1.41e+00 5.03e-01 4.75e+00 ... (remaining 8030 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.62: 3160 16.62 - 33.24: 202 33.24 - 49.85: 101 49.85 - 66.47: 55 66.47 - 83.09: 20 Dihedral angle restraints: 3538 sinusoidal: 1333 harmonic: 2205 Sorted by residual: dihedral pdb=" CA ALA F 121 " pdb=" C ALA F 121 " pdb=" N ILE F 122 " pdb=" CA ILE F 122 " ideal model delta harmonic sigma weight residual 180.00 161.28 18.72 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA ALA A 121 " pdb=" C ALA A 121 " pdb=" N ILE A 122 " pdb=" CA ILE A 122 " ideal model delta harmonic sigma weight residual 180.00 161.29 18.71 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA ALA D 121 " pdb=" C ALA D 121 " pdb=" N ILE D 122 " pdb=" CA ILE D 122 " ideal model delta harmonic sigma weight residual 180.00 161.30 18.70 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 3535 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 453 0.028 - 0.055: 257 0.055 - 0.083: 115 0.083 - 0.110: 50 0.110 - 0.138: 20 Chirality restraints: 895 Sorted by residual: chirality pdb=" CA ILE F 122 " pdb=" N ILE F 122 " pdb=" C ILE F 122 " pdb=" CB ILE F 122 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA ILE C 122 " pdb=" N ILE C 122 " pdb=" C ILE C 122 " pdb=" CB ILE C 122 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA ILE E 122 " pdb=" N ILE E 122 " pdb=" C ILE E 122 " pdb=" CB ILE E 122 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 892 not shown) Planarity restraints: 1035 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 101 " 0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO E 102 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO E 102 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO E 102 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 101 " -0.019 5.00e-02 4.00e+02 2.83e-02 1.28e+00 pdb=" N PRO D 102 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO D 102 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO D 102 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER F 101 " -0.019 5.00e-02 4.00e+02 2.82e-02 1.28e+00 pdb=" N PRO F 102 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO F 102 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO F 102 " -0.016 5.00e-02 4.00e+02 ... (remaining 1032 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 215 2.65 - 3.21: 5559 3.21 - 3.78: 10780 3.78 - 4.34: 14721 4.34 - 4.90: 22938 Nonbonded interactions: 54213 Sorted by model distance: nonbonded pdb=" OD1 ASP E 60 " pdb=" O HOH E 201 " model vdw 2.089 3.040 nonbonded pdb=" O HOH C 222 " pdb=" O HOH C 243 " model vdw 2.147 3.040 nonbonded pdb=" OD1 ASP F 150 " pdb=" OG1 THR F 152 " model vdw 2.158 3.040 nonbonded pdb=" OD1 ASP D 150 " pdb=" OG1 THR D 152 " model vdw 2.159 3.040 nonbonded pdb=" OD1 ASP C 150 " pdb=" OG1 THR C 152 " model vdw 2.159 3.040 ... (remaining 54208 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 5.070 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.690 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: 0.000 Load rotamer database and sin/cos tables:6.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 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 : 0.014 0.967 5966 Z= 0.693 Angle : 0.688 8.800 8037 Z= 0.407 Chirality : 0.045 0.138 895 Planarity : 0.003 0.028 1035 Dihedral : 17.608 83.088 2135 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 6.56 % Allowed : 6.56 % Favored : 86.89 % 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 aren not related in a simple way. whole: -0.18 (0.27), residues: 765 helix: -0.27 (0.50), residues: 70 sheet: 0.11 (0.29), residues: 290 loop : -0.15 (0.26), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG F 49 TYR 0.006 0.002 TYR F 138 PHE 0.015 0.002 PHE D 128 TRP 0.008 0.003 TRP D 75 HIS 0.005 0.003 HIS E 90 Details of bonding type rmsd covalent geometry : bond 0.00645 ( 5965) covalent geometry : angle 0.67646 ( 8035) SS BOND : bond 0.96731 ( 1) SS BOND : angle 8.14900 ( 2) hydrogen bonds : bond 0.15643 ( 71) hydrogen bonds : angle 5.38717 ( 213) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 128 time to evaluate : 0.157 Fit side-chains REVERT: C 17 LYS cc_start: 0.7992 (ttmt) cc_final: 0.6800 (ttpt) REVERT: C 145 MET cc_start: 0.9166 (mtp) cc_final: 0.8881 (mtp) REVERT: E 17 LYS cc_start: 0.7917 (ttmt) cc_final: 0.6997 (ttpt) REVERT: F 145 MET cc_start: 0.9120 (mtp) cc_final: 0.8795 (mtp) outliers start: 40 outliers final: 1 residues processed: 141 average time/residue: 0.6786 time to fit residues: 99.0684 Evaluate side-chains 96 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 108 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 159 GLN C 43 GLN C 159 GLN D 43 GLN D 159 GLN E 43 GLN E 159 GLN F 43 GLN F 159 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.122547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.104654 restraints weight = 5896.792| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.18 r_work: 0.3029 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5966 Z= 0.166 Angle : 0.481 3.905 8037 Z= 0.270 Chirality : 0.044 0.151 895 Planarity : 0.003 0.022 1035 Dihedral : 5.443 52.555 812 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.98 % Allowed : 13.77 % Favored : 85.25 % 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 aren not related in a simple way. whole: 0.53 (0.28), residues: 765 helix: 1.78 (0.63), residues: 70 sheet: 0.28 (0.30), residues: 290 loop : 0.29 (0.27), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG E 49 TYR 0.007 0.002 TYR F 83 PHE 0.017 0.002 PHE C 128 TRP 0.008 0.002 TRP E 65 HIS 0.003 0.002 HIS E 90 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 5965) covalent geometry : angle 0.48133 ( 8035) SS BOND : bond 0.00041 ( 1) SS BOND : angle 0.05777 ( 2) hydrogen bonds : bond 0.03303 ( 71) hydrogen bonds : angle 4.07781 ( 213) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 102 time to evaluate : 0.253 Fit side-chains REVERT: C 17 LYS cc_start: 0.8012 (ttmt) cc_final: 0.6751 (ttpt) REVERT: E 17 LYS cc_start: 0.7957 (ttmt) cc_final: 0.6779 (ttpt) REVERT: F 113 LYS cc_start: 0.8607 (mtmm) cc_final: 0.7883 (mptp) outliers start: 6 outliers final: 1 residues processed: 105 average time/residue: 0.7837 time to fit residues: 84.9784 Evaluate side-chains 98 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 108 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 27 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 61 optimal weight: 0.3980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.126550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.109675 restraints weight = 5913.401| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.05 r_work: 0.3047 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5966 Z= 0.140 Angle : 0.442 3.374 8037 Z= 0.249 Chirality : 0.043 0.150 895 Planarity : 0.002 0.019 1035 Dihedral : 5.156 51.592 812 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.98 % Allowed : 13.93 % Favored : 85.08 % 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 aren not related in a simple way. whole: 0.84 (0.29), residues: 765 helix: 2.29 (0.65), residues: 70 sheet: 0.37 (0.30), residues: 290 loop : 0.54 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 49 TYR 0.005 0.001 TYR C 83 PHE 0.013 0.001 PHE C 128 TRP 0.008 0.002 TRP E 65 HIS 0.003 0.002 HIS F 90 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 5965) covalent geometry : angle 0.44156 ( 8035) SS BOND : bond 0.00117 ( 1) SS BOND : angle 0.16811 ( 2) hydrogen bonds : bond 0.02735 ( 71) hydrogen bonds : angle 3.96372 ( 213) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 0.259 Fit side-chains REVERT: C 5 GLU cc_start: 0.8218 (mp0) cc_final: 0.7660 (mp0) REVERT: C 17 LYS cc_start: 0.7965 (ttmt) cc_final: 0.6754 (ttpt) REVERT: D 129 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8563 (tm-30) REVERT: E 17 LYS cc_start: 0.7950 (ttmt) cc_final: 0.6873 (ttpt) REVERT: E 129 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8444 (tp30) REVERT: F 113 LYS cc_start: 0.8576 (mtmm) cc_final: 0.8002 (mptp) outliers start: 6 outliers final: 0 residues processed: 104 average time/residue: 0.8006 time to fit residues: 86.0516 Evaluate side-chains 100 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 98 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain E residue 129 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 13 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 16 optimal weight: 0.0050 chunk 3 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.127018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.110142 restraints weight = 5920.133| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.05 r_work: 0.3042 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5966 Z= 0.136 Angle : 0.436 3.202 8037 Z= 0.247 Chirality : 0.043 0.150 895 Planarity : 0.002 0.017 1035 Dihedral : 4.747 17.941 810 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 1.48 % Allowed : 13.61 % Favored : 84.92 % 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 aren not related in a simple way. whole: 1.12 (0.29), residues: 765 helix: 2.52 (0.65), residues: 70 sheet: 0.49 (0.31), residues: 280 loop : 0.77 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 49 TYR 0.005 0.001 TYR F 83 PHE 0.013 0.001 PHE C 128 TRP 0.008 0.002 TRP E 65 HIS 0.003 0.002 HIS F 90 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 5965) covalent geometry : angle 0.43560 ( 8035) SS BOND : bond 0.00049 ( 1) SS BOND : angle 0.12544 ( 2) hydrogen bonds : bond 0.02546 ( 71) hydrogen bonds : angle 3.96749 ( 213) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.188 Fit side-chains REVERT: C 5 GLU cc_start: 0.8191 (mp0) cc_final: 0.7620 (mp0) REVERT: C 17 LYS cc_start: 0.7934 (ttmt) cc_final: 0.6722 (ttpt) REVERT: D 129 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8552 (tm-30) REVERT: E 17 LYS cc_start: 0.7932 (ttmt) cc_final: 0.6802 (ttpt) REVERT: E 129 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8459 (tp30) REVERT: F 113 LYS cc_start: 0.8573 (mtmm) cc_final: 0.7999 (mptp) outliers start: 9 outliers final: 2 residues processed: 106 average time/residue: 0.8389 time to fit residues: 91.8398 Evaluate side-chains 102 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 98 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain E residue 129 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 2 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 chunk 39 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.129074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.112199 restraints weight = 6028.545| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.06 r_work: 0.3109 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5966 Z= 0.107 Angle : 0.404 3.072 8037 Z= 0.230 Chirality : 0.043 0.143 895 Planarity : 0.002 0.017 1035 Dihedral : 4.436 16.551 810 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 1.31 % Allowed : 14.43 % Favored : 84.26 % 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 aren not related in a simple way. whole: 1.23 (0.30), residues: 765 helix: 2.74 (0.66), residues: 70 sheet: 0.51 (0.31), residues: 280 loop : 0.87 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 49 TYR 0.004 0.001 TYR F 83 PHE 0.010 0.001 PHE C 128 TRP 0.007 0.002 TRP E 65 HIS 0.002 0.001 HIS F 90 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 5965) covalent geometry : angle 0.40372 ( 8035) SS BOND : bond 0.00045 ( 1) SS BOND : angle 0.13225 ( 2) hydrogen bonds : bond 0.02074 ( 71) hydrogen bonds : angle 3.88450 ( 213) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.157 Fit side-chains REVERT: C 5 GLU cc_start: 0.8185 (mp0) cc_final: 0.7640 (mp0) REVERT: C 17 LYS cc_start: 0.7923 (ttmt) cc_final: 0.6739 (ttpt) REVERT: D 129 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8570 (tm-30) REVERT: E 17 LYS cc_start: 0.7904 (ttmt) cc_final: 0.6858 (ttpt) REVERT: E 129 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8492 (tp30) REVERT: F 113 LYS cc_start: 0.8580 (mtmm) cc_final: 0.8034 (mptp) outliers start: 8 outliers final: 3 residues processed: 106 average time/residue: 0.7858 time to fit residues: 86.1642 Evaluate side-chains 107 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 102 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain E residue 129 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 46 optimal weight: 8.9990 chunk 13 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 51 optimal weight: 0.6980 chunk 58 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 60 optimal weight: 0.0060 chunk 20 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.126670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.109604 restraints weight = 5952.623| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.07 r_work: 0.3069 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5966 Z= 0.120 Angle : 0.418 3.018 8037 Z= 0.238 Chirality : 0.043 0.146 895 Planarity : 0.002 0.017 1035 Dihedral : 4.509 17.129 810 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.13 % Allowed : 14.26 % Favored : 83.61 % 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 aren not related in a simple way. whole: 1.26 (0.30), residues: 765 helix: 2.70 (0.67), residues: 70 sheet: 0.47 (0.31), residues: 280 loop : 0.95 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 49 TYR 0.005 0.001 TYR A 138 PHE 0.011 0.001 PHE C 128 TRP 0.007 0.002 TRP E 65 HIS 0.002 0.001 HIS F 90 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 5965) covalent geometry : angle 0.41843 ( 8035) SS BOND : bond 0.00028 ( 1) SS BOND : angle 0.09264 ( 2) hydrogen bonds : bond 0.02224 ( 71) hydrogen bonds : angle 3.98407 ( 213) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.171 Fit side-chains REVERT: C 5 GLU cc_start: 0.8119 (mp0) cc_final: 0.7581 (mp0) REVERT: C 17 LYS cc_start: 0.7928 (ttmt) cc_final: 0.6729 (ttpt) REVERT: D 129 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8553 (tm-30) REVERT: E 17 LYS cc_start: 0.7904 (ttmt) cc_final: 0.6829 (ttpt) REVERT: E 129 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8476 (tp30) REVERT: F 113 LYS cc_start: 0.8591 (mtmm) cc_final: 0.8019 (mptp) outliers start: 13 outliers final: 6 residues processed: 105 average time/residue: 0.7847 time to fit residues: 85.1807 Evaluate side-chains 105 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 129 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 48 optimal weight: 0.0970 chunk 67 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.125666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.108790 restraints weight = 6021.859| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.06 r_work: 0.3040 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5966 Z= 0.147 Angle : 0.452 3.277 8037 Z= 0.255 Chirality : 0.043 0.148 895 Planarity : 0.002 0.017 1035 Dihedral : 4.724 18.381 810 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.97 % Allowed : 14.43 % Favored : 83.61 % 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 aren not related in a simple way. whole: 1.24 (0.30), residues: 765 helix: 2.60 (0.66), residues: 70 sheet: 0.46 (0.31), residues: 280 loop : 0.96 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 49 TYR 0.006 0.002 TYR F 83 PHE 0.013 0.001 PHE C 128 TRP 0.007 0.002 TRP E 65 HIS 0.003 0.002 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 5965) covalent geometry : angle 0.45255 ( 8035) SS BOND : bond 0.00003 ( 1) SS BOND : angle 0.12805 ( 2) hydrogen bonds : bond 0.02588 ( 71) hydrogen bonds : angle 4.10845 ( 213) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.270 Fit side-chains REVERT: C 5 GLU cc_start: 0.8079 (mp0) cc_final: 0.7545 (mp0) REVERT: C 17 LYS cc_start: 0.7950 (ttmt) cc_final: 0.6700 (ttpt) REVERT: D 129 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8580 (tm-30) REVERT: E 17 LYS cc_start: 0.7942 (ttmt) cc_final: 0.6843 (ttpt) REVERT: E 129 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8436 (tp30) REVERT: F 113 LYS cc_start: 0.8622 (mtmm) cc_final: 0.8067 (mptp) outliers start: 12 outliers final: 7 residues processed: 107 average time/residue: 0.7949 time to fit residues: 87.9869 Evaluate side-chains 111 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 155 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 59 optimal weight: 7.9990 chunk 9 optimal weight: 0.3980 chunk 6 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 72 optimal weight: 0.3980 chunk 3 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.124456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.107188 restraints weight = 6035.349| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.08 r_work: 0.3018 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5966 Z= 0.173 Angle : 0.480 3.525 8037 Z= 0.271 Chirality : 0.044 0.150 895 Planarity : 0.003 0.017 1035 Dihedral : 4.896 19.033 810 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.80 % Allowed : 14.92 % Favored : 83.28 % 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 aren not related in a simple way. whole: 1.20 (0.30), residues: 765 helix: 2.45 (0.65), residues: 70 sheet: 0.45 (0.31), residues: 280 loop : 0.95 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 49 TYR 0.007 0.002 TYR F 96 PHE 0.014 0.002 PHE C 128 TRP 0.007 0.002 TRP E 65 HIS 0.004 0.002 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 5965) covalent geometry : angle 0.48032 ( 8035) SS BOND : bond 0.00019 ( 1) SS BOND : angle 0.09719 ( 2) hydrogen bonds : bond 0.02874 ( 71) hydrogen bonds : angle 4.17694 ( 213) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.256 Fit side-chains REVERT: A 62 VAL cc_start: 0.8554 (m) cc_final: 0.8299 (t) REVERT: C 5 GLU cc_start: 0.8081 (mp0) cc_final: 0.7553 (mp0) REVERT: C 17 LYS cc_start: 0.7987 (ttmt) cc_final: 0.6711 (ttpt) REVERT: D 129 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8553 (tm-30) REVERT: E 17 LYS cc_start: 0.7983 (ttmt) cc_final: 0.6865 (ttpt) REVERT: E 129 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8442 (tp30) REVERT: F 113 LYS cc_start: 0.8680 (mtmm) cc_final: 0.7994 (mptp) outliers start: 11 outliers final: 7 residues processed: 108 average time/residue: 0.7983 time to fit residues: 89.1669 Evaluate side-chains 106 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 155 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 7 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 9 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 67 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.129520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.112715 restraints weight = 5991.298| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.06 r_work: 0.3078 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5966 Z= 0.105 Angle : 0.407 4.321 8037 Z= 0.233 Chirality : 0.042 0.142 895 Planarity : 0.002 0.018 1035 Dihedral : 4.381 16.301 810 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.64 % Allowed : 15.74 % Favored : 82.62 % 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 aren not related in a simple way. whole: 1.35 (0.30), residues: 765 helix: 2.82 (0.67), residues: 70 sheet: 0.49 (0.32), residues: 280 loop : 1.04 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 49 TYR 0.004 0.001 TYR A 83 PHE 0.010 0.001 PHE C 128 TRP 0.008 0.002 TRP E 65 HIS 0.002 0.001 HIS F 90 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 5965) covalent geometry : angle 0.40702 ( 8035) SS BOND : bond 0.00043 ( 1) SS BOND : angle 0.13118 ( 2) hydrogen bonds : bond 0.01971 ( 71) hydrogen bonds : angle 4.00853 ( 213) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.204 Fit side-chains REVERT: C 5 GLU cc_start: 0.8079 (mp0) cc_final: 0.7538 (mp0) REVERT: C 17 LYS cc_start: 0.7916 (ttmt) cc_final: 0.6695 (ttpt) REVERT: D 129 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8534 (tm-30) REVERT: E 17 LYS cc_start: 0.7860 (ttmt) cc_final: 0.6782 (ttpt) REVERT: E 129 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8426 (tp30) REVERT: F 113 LYS cc_start: 0.8575 (mtmm) cc_final: 0.8038 (mptp) outliers start: 10 outliers final: 6 residues processed: 106 average time/residue: 0.7988 time to fit residues: 87.3897 Evaluate side-chains 106 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 155 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 57 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 11 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.124593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.107725 restraints weight = 6003.025| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.05 r_work: 0.3025 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5966 Z= 0.183 Angle : 0.495 3.886 8037 Z= 0.278 Chirality : 0.044 0.153 895 Planarity : 0.003 0.018 1035 Dihedral : 4.912 19.235 810 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.80 % Allowed : 15.57 % Favored : 82.62 % 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 aren not related in a simple way. whole: 1.25 (0.30), residues: 765 helix: 2.50 (0.65), residues: 70 sheet: 0.43 (0.31), residues: 280 loop : 1.01 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 49 TYR 0.006 0.002 TYR F 96 PHE 0.014 0.002 PHE C 128 TRP 0.007 0.002 TRP E 75 HIS 0.004 0.002 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 5965) covalent geometry : angle 0.49474 ( 8035) SS BOND : bond 0.00034 ( 1) SS BOND : angle 0.12856 ( 2) hydrogen bonds : bond 0.02904 ( 71) hydrogen bonds : angle 4.19489 ( 213) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.201 Fit side-chains REVERT: A 62 VAL cc_start: 0.8566 (m) cc_final: 0.8317 (t) REVERT: C 5 GLU cc_start: 0.8079 (mp0) cc_final: 0.7550 (mp0) REVERT: C 17 LYS cc_start: 0.7982 (ttmt) cc_final: 0.6706 (ttpt) REVERT: D 129 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8557 (tm-30) REVERT: E 17 LYS cc_start: 0.8000 (ttmt) cc_final: 0.6881 (ttpt) REVERT: E 129 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8443 (tp30) REVERT: F 113 LYS cc_start: 0.8657 (mtmm) cc_final: 0.8006 (mptp) outliers start: 11 outliers final: 8 residues processed: 106 average time/residue: 0.7765 time to fit residues: 84.9682 Evaluate side-chains 105 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 155 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 51 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 57 optimal weight: 0.0370 chunk 5 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 44 optimal weight: 0.0980 chunk 9 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.133864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.117252 restraints weight = 5943.514| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.07 r_work: 0.3108 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5966 Z= 0.091 Angle : 0.389 3.447 8037 Z= 0.224 Chirality : 0.042 0.142 895 Planarity : 0.002 0.019 1035 Dihedral : 4.220 15.331 810 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.31 % Allowed : 15.90 % Favored : 82.79 % 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 aren not related in a simple way. whole: 1.40 (0.30), residues: 765 helix: 2.90 (0.68), residues: 70 sheet: 0.49 (0.32), residues: 280 loop : 1.10 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 49 TYR 0.004 0.001 TYR A 83 PHE 0.009 0.001 PHE D 128 TRP 0.008 0.001 TRP A 65 HIS 0.002 0.001 HIS F 90 Details of bonding type rmsd covalent geometry : bond 0.00200 ( 5965) covalent geometry : angle 0.38898 ( 8035) SS BOND : bond 0.00054 ( 1) SS BOND : angle 0.08659 ( 2) hydrogen bonds : bond 0.01744 ( 71) hydrogen bonds : angle 3.99969 ( 213) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3157.87 seconds wall clock time: 54 minutes 23.46 seconds (3263.46 seconds total)