Starting phenix.real_space_refine on Sat Aug 23 03:53:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ty6_41711/08_2025/8ty6_41711.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ty6_41711/08_2025/8ty6_41711.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ty6_41711/08_2025/8ty6_41711.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ty6_41711/08_2025/8ty6_41711.map" model { file = "/net/cci-nas-00/data/ceres_data/8ty6_41711/08_2025/8ty6_41711.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ty6_41711/08_2025/8ty6_41711.cif" } resolution = 3.3 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= 0.039 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 84 5.16 5 C 6096 2.51 5 N 1692 2.21 5 O 1806 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s 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: 9678 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1613 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1613 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1613 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1613 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "E" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1613 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "F" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1613 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 2.27, per 1000 atoms: 0.23 Number of scatterers: 9678 At special positions: 0 Unit cell: (106.92, 117.72, 73.44, 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 84 16.00 O 1806 8.00 N 1692 7.00 C 6096 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS F 45 " distance=2.03 Simple disulfide: pdb=" SG CYS A 45 " - pdb=" SG CYS B 14 " distance=2.03 Simple disulfide: pdb=" SG CYS B 45 " - pdb=" SG CYS C 14 " distance=2.03 Simple disulfide: pdb=" SG CYS C 45 " - pdb=" SG CYS D 14 " distance=2.03 Simple disulfide: pdb=" SG CYS D 45 " - pdb=" SG CYS E 14 " distance=2.03 Simple disulfide: pdb=" SG CYS E 45 " - pdb=" SG CYS F 14 " distance=2.03 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: 0.96 Conformation dependent library (CDL) restraints added in 324.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2376 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 6 sheets defined 72.5% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 16 through 31 Processing helix chain 'A' and resid 35 through 44 Processing helix chain 'A' and resid 48 through 58 Processing helix chain 'A' and resid 62 through 84 Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 110 through 120 Processing helix chain 'A' and resid 125 through 145 Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 160 through 177 Processing helix chain 'A' and resid 183 through 193 Processing helix chain 'A' and resid 195 through 206 removed outlier: 3.602A pdb=" N ILE A 201 " --> pdb=" O ASP A 197 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 218 Processing helix chain 'B' and resid 16 through 31 removed outlier: 3.601A pdb=" N ALA B 31 " --> pdb=" O VAL B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 44 removed outlier: 3.508A pdb=" N MET B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 58 Processing helix chain 'B' and resid 62 through 84 Processing helix chain 'B' and resid 100 through 105 Processing helix chain 'B' and resid 110 through 119 Processing helix chain 'B' and resid 125 through 145 Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 160 through 177 Processing helix chain 'B' and resid 183 through 194 Processing helix chain 'B' and resid 195 through 206 Processing helix chain 'B' and resid 210 through 219 Processing helix chain 'C' and resid 16 through 31 removed outlier: 3.562A pdb=" N LEU C 20 " --> pdb=" O SER C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 44 Processing helix chain 'C' and resid 48 through 58 Processing helix chain 'C' and resid 62 through 84 Processing helix chain 'C' and resid 100 through 106 Processing helix chain 'C' and resid 110 through 120 Processing helix chain 'C' and resid 125 through 145 Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'C' and resid 160 through 177 removed outlier: 3.518A pdb=" N GLN C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 193 Processing helix chain 'C' and resid 195 through 206 removed outlier: 3.550A pdb=" N ILE C 201 " --> pdb=" O ASP C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 218 Processing helix chain 'D' and resid 16 through 31 Processing helix chain 'D' and resid 35 through 44 removed outlier: 3.634A pdb=" N MET D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 58 Processing helix chain 'D' and resid 62 through 84 Processing helix chain 'D' and resid 100 through 105 Processing helix chain 'D' and resid 110 through 119 Processing helix chain 'D' and resid 125 through 145 Processing helix chain 'D' and resid 160 through 177 Processing helix chain 'D' and resid 183 through 193 Processing helix chain 'D' and resid 195 through 206 removed outlier: 3.756A pdb=" N ILE D 201 " --> pdb=" O ASP D 197 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY D 206 " --> pdb=" O LEU D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 219 Processing helix chain 'E' and resid 16 through 31 Processing helix chain 'E' and resid 35 through 44 Processing helix chain 'E' and resid 48 through 58 Processing helix chain 'E' and resid 62 through 84 Processing helix chain 'E' and resid 100 through 105 Processing helix chain 'E' and resid 110 through 119 Processing helix chain 'E' and resid 125 through 145 Processing helix chain 'E' and resid 149 through 153 Processing helix chain 'E' and resid 160 through 177 Processing helix chain 'E' and resid 183 through 193 Processing helix chain 'E' and resid 195 through 206 removed outlier: 3.828A pdb=" N ILE E 201 " --> pdb=" O ASP E 197 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY E 206 " --> pdb=" O LEU E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 218 Processing helix chain 'F' and resid 16 through 31 Processing helix chain 'F' and resid 35 through 44 Processing helix chain 'F' and resid 48 through 58 Processing helix chain 'F' and resid 62 through 84 Processing helix chain 'F' and resid 100 through 105 Processing helix chain 'F' and resid 110 through 118 Processing helix chain 'F' and resid 125 through 145 Processing helix chain 'F' and resid 149 through 153 removed outlier: 3.707A pdb=" N ILE F 153 " --> pdb=" O ILE F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 177 Processing helix chain 'F' and resid 183 through 193 Processing helix chain 'F' and resid 195 through 206 removed outlier: 3.581A pdb=" N ILE F 201 " --> pdb=" O ASP F 197 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY F 206 " --> pdb=" O LEU F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 219 removed outlier: 3.563A pdb=" N GLN F 219 " --> pdb=" O MET F 215 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 4 Processing sheet with id=AA2, first strand: chain 'B' and resid 3 through 4 Processing sheet with id=AA3, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=AA4, first strand: chain 'D' and resid 3 through 4 Processing sheet with id=AA5, first strand: chain 'E' and resid 2 through 4 Processing sheet with id=AA6, first strand: chain 'F' and resid 2 through 4 630 hydrogen bonds defined for protein. 1857 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: 1.29 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3252 1.34 - 1.46: 1919 1.46 - 1.58: 4561 1.58 - 1.70: 0 1.70 - 1.81: 144 Bond restraints: 9876 Sorted by residual: bond pdb=" N ALA B 31 " pdb=" CA ALA B 31 " ideal model delta sigma weight residual 1.457 1.469 -0.012 1.29e-02 6.01e+03 8.62e-01 bond pdb=" C VAL B 181 " pdb=" O VAL B 181 " ideal model delta sigma weight residual 1.236 1.226 0.010 1.19e-02 7.06e+03 7.01e-01 bond pdb=" N ALA F 31 " pdb=" CA ALA F 31 " ideal model delta sigma weight residual 1.457 1.468 -0.011 1.29e-02 6.01e+03 6.68e-01 bond pdb=" CA ILE B 37 " pdb=" CB ILE B 37 " ideal model delta sigma weight residual 1.539 1.543 -0.004 5.40e-03 3.43e+04 5.76e-01 bond pdb=" CA ILE C 37 " pdb=" CB ILE C 37 " ideal model delta sigma weight residual 1.539 1.535 0.004 5.40e-03 3.43e+04 4.70e-01 ... (remaining 9871 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 13101 1.09 - 2.17: 222 2.17 - 3.25: 81 3.25 - 4.34: 16 4.34 - 5.42: 8 Bond angle restraints: 13428 Sorted by residual: angle pdb=" C ALA B 31 " pdb=" CA ALA B 31 " pdb=" CB ALA B 31 " ideal model delta sigma weight residual 110.42 115.84 -5.42 1.99e+00 2.53e-01 7.43e+00 angle pdb=" C ALA F 31 " pdb=" CA ALA F 31 " pdb=" CB ALA F 31 " ideal model delta sigma weight residual 110.42 115.73 -5.31 1.99e+00 2.53e-01 7.11e+00 angle pdb=" N ALA B 31 " pdb=" CA ALA B 31 " pdb=" C ALA B 31 " ideal model delta sigma weight residual 110.80 106.71 4.09 2.13e+00 2.20e-01 3.69e+00 angle pdb=" N ALA F 31 " pdb=" CA ALA F 31 " pdb=" C ALA F 31 " ideal model delta sigma weight residual 110.80 106.88 3.92 2.13e+00 2.20e-01 3.38e+00 angle pdb=" N GLU C 175 " pdb=" CA GLU C 175 " pdb=" C GLU C 175 " ideal model delta sigma weight residual 110.97 112.93 -1.96 1.09e+00 8.42e-01 3.24e+00 ... (remaining 13423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.28: 5652 16.28 - 32.55: 310 32.55 - 48.83: 97 48.83 - 65.11: 23 65.11 - 81.39: 2 Dihedral angle restraints: 6084 sinusoidal: 2436 harmonic: 3648 Sorted by residual: dihedral pdb=" CA LEU A 202 " pdb=" CB LEU A 202 " pdb=" CG LEU A 202 " pdb=" CD1 LEU A 202 " ideal model delta sinusoidal sigma weight residual -60.00 -0.07 -59.93 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA LEU C 202 " pdb=" CB LEU C 202 " pdb=" CG LEU C 202 " pdb=" CD1 LEU C 202 " ideal model delta sinusoidal sigma weight residual 60.00 0.48 59.52 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ARG A 100 " pdb=" CB ARG A 100 " pdb=" CG ARG A 100 " pdb=" CD ARG A 100 " ideal model delta sinusoidal sigma weight residual -180.00 -120.57 -59.43 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 6081 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1057 0.030 - 0.059: 325 0.059 - 0.089: 98 0.089 - 0.118: 50 0.118 - 0.148: 6 Chirality restraints: 1536 Sorted by residual: chirality pdb=" CA ILE D 124 " pdb=" N ILE D 124 " pdb=" C ILE D 124 " pdb=" CB ILE D 124 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.46e-01 chirality pdb=" CA ILE A 124 " pdb=" N ILE A 124 " pdb=" C ILE A 124 " pdb=" CB ILE A 124 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.30e-01 chirality pdb=" CA ILE E 124 " pdb=" N ILE E 124 " pdb=" C ILE E 124 " pdb=" CB ILE E 124 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.16e-01 ... (remaining 1533 not shown) Planarity restraints: 1746 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 48 " -0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO B 49 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO B 49 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 49 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER F 33 " 0.019 5.00e-02 4.00e+02 2.89e-02 1.33e+00 pdb=" N PRO F 34 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO F 34 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO F 34 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 48 " -0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO A 49 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 49 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 49 " -0.016 5.00e-02 4.00e+02 ... (remaining 1743 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 151 2.70 - 3.25: 9675 3.25 - 3.80: 15358 3.80 - 4.35: 18843 4.35 - 4.90: 32496 Nonbonded interactions: 76523 Sorted by model distance: nonbonded pdb=" OG1 THR C 48 " pdb=" OD1 ASP C 51 " model vdw 2.144 3.040 nonbonded pdb=" OG1 THR B 48 " pdb=" OD1 ASP B 51 " model vdw 2.161 3.040 nonbonded pdb=" OG1 THR A 48 " pdb=" OD1 ASP A 51 " model vdw 2.173 3.040 nonbonded pdb=" OG1 THR D 48 " pdb=" OD1 ASP D 51 " model vdw 2.178 3.040 nonbonded pdb=" OG1 THR F 48 " pdb=" OD1 ASP F 51 " model vdw 2.193 3.040 ... (remaining 76518 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' } 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: 0.960 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.840 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 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 : 0.002 0.030 9882 Z= 0.104 Angle : 0.444 5.425 13440 Z= 0.230 Chirality : 0.036 0.148 1536 Planarity : 0.004 0.030 1746 Dihedral : 11.547 81.386 3690 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.71 % Allowed : 5.72 % Favored : 91.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.36 (0.25), residues: 1236 helix: 2.02 (0.18), residues: 894 sheet: -1.53 (0.69), residues: 54 loop : 0.97 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 167 TYR 0.009 0.001 TYR D 169 PHE 0.008 0.001 PHE A 168 TRP 0.005 0.001 TRP E 80 HIS 0.002 0.000 HIS F 62 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 9876) covalent geometry : angle 0.44398 (13428) SS BOND : bond 0.00079 ( 6) SS BOND : angle 0.41212 ( 12) hydrogen bonds : bond 0.14926 ( 630) hydrogen bonds : angle 4.78274 ( 1857) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 305 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8247 (mt) cc_final: 0.7990 (mt) REVERT: A 118 MET cc_start: 0.8981 (mtp) cc_final: 0.8777 (mtp) REVERT: A 120 HIS cc_start: 0.7826 (t-90) cc_final: 0.7157 (t-90) REVERT: A 175 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.6546 (mp0) REVERT: A 195 ASN cc_start: 0.7819 (m-40) cc_final: 0.7562 (m110) REVERT: A 213 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7543 (mt-10) REVERT: B 18 ARG cc_start: 0.6755 (ttp-170) cc_final: 0.6189 (ttt180) REVERT: B 69 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8473 (tt) REVERT: B 170 LYS cc_start: 0.8577 (tttt) cc_final: 0.8253 (tppt) REVERT: B 175 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.6098 (mp0) REVERT: B 214 MET cc_start: 0.8251 (mtt) cc_final: 0.7924 (mtt) REVERT: C 23 TRP cc_start: 0.8888 (t-100) cc_final: 0.8633 (t-100) REVERT: C 30 LYS cc_start: 0.7334 (mmtt) cc_final: 0.7090 (mttt) REVERT: C 149 SER cc_start: 0.8929 (t) cc_final: 0.8727 (t) REVERT: D 25 LYS cc_start: 0.7964 (mptt) cc_final: 0.7604 (mttt) REVERT: D 70 LYS cc_start: 0.8152 (ttmm) cc_final: 0.7938 (ttpp) REVERT: D 218 CYS cc_start: 0.7734 (m) cc_final: 0.7288 (m) REVERT: E 10 MET cc_start: 0.7149 (mmt) cc_final: 0.6777 (mmt) REVERT: E 68 MET cc_start: 0.8752 (mtm) cc_final: 0.8439 (mtp) REVERT: E 175 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.6643 (mp0) REVERT: E 214 MET cc_start: 0.8596 (mtt) cc_final: 0.8210 (mtm) REVERT: F 4 GLN cc_start: 0.8331 (tt0) cc_final: 0.8061 (pm20) REVERT: F 69 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7959 (mt) REVERT: F 171 THR cc_start: 0.8315 (m) cc_final: 0.6444 (m) REVERT: F 175 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.5530 (mp0) REVERT: F 189 LEU cc_start: 0.8423 (tp) cc_final: 0.8096 (tp) REVERT: F 202 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8776 (mp) outliers start: 28 outliers final: 6 residues processed: 330 average time/residue: 0.1038 time to fit residues: 45.1505 Evaluate side-chains 245 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 232 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 175 GLU Chi-restraints excluded: chain F residue 202 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 0.0040 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 0.2980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 0.4980 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 HIS B 21 ASN B 67 GLN B 139 ASN D 219 GLN E 120 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.145235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.118358 restraints weight = 14774.445| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.56 r_work: 0.3293 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9882 Z= 0.143 Angle : 0.521 4.783 13440 Z= 0.271 Chirality : 0.039 0.160 1536 Planarity : 0.005 0.044 1746 Dihedral : 6.326 59.296 1362 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.36 % Allowed : 12.02 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.42 (0.24), residues: 1236 helix: 2.05 (0.18), residues: 894 sheet: -1.46 (0.67), residues: 54 loop : 1.02 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 154 TYR 0.010 0.001 TYR D 169 PHE 0.008 0.001 PHE A 168 TRP 0.009 0.001 TRP E 80 HIS 0.005 0.001 HIS E 120 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 9876) covalent geometry : angle 0.52098 (13428) SS BOND : bond 0.00941 ( 6) SS BOND : angle 0.80004 ( 12) hydrogen bonds : bond 0.04487 ( 630) hydrogen bonds : angle 4.02599 ( 1857) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 253 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.8126 (mmt) cc_final: 0.7874 (mmt) REVERT: A 83 LEU cc_start: 0.8341 (mt) cc_final: 0.8042 (mt) REVERT: A 120 HIS cc_start: 0.7867 (t-90) cc_final: 0.7218 (t-90) REVERT: A 175 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6048 (mp0) REVERT: A 195 ASN cc_start: 0.7768 (m-40) cc_final: 0.7136 (m110) REVERT: A 210 THR cc_start: 0.8168 (p) cc_final: 0.7721 (p) REVERT: A 213 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7696 (mt-10) REVERT: B 18 ARG cc_start: 0.6647 (ttp-170) cc_final: 0.5841 (ttt180) REVERT: B 69 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8218 (tt) REVERT: B 170 LYS cc_start: 0.8388 (tttt) cc_final: 0.7995 (tppt) REVERT: B 175 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.5787 (mp0) REVERT: B 213 GLU cc_start: 0.7433 (tp30) cc_final: 0.6826 (tp30) REVERT: C 23 TRP cc_start: 0.8886 (t-100) cc_final: 0.8663 (t-100) REVERT: C 30 LYS cc_start: 0.7469 (mmtt) cc_final: 0.6996 (mttt) REVERT: C 54 THR cc_start: 0.7919 (m) cc_final: 0.7179 (p) REVERT: C 100 ARG cc_start: 0.7981 (mmp80) cc_final: 0.7776 (mmt180) REVERT: D 25 LYS cc_start: 0.7730 (mptt) cc_final: 0.7218 (mttt) REVERT: D 70 LYS cc_start: 0.8059 (ttmm) cc_final: 0.7829 (ttpp) REVERT: D 214 MET cc_start: 0.7927 (mtt) cc_final: 0.7589 (mpp) REVERT: E 68 MET cc_start: 0.8661 (mtm) cc_final: 0.8369 (mtp) REVERT: E 79 GLU cc_start: 0.8983 (tp30) cc_final: 0.8292 (tp30) REVERT: E 82 ARG cc_start: 0.7688 (mtp-110) cc_final: 0.7269 (ttp80) REVERT: E 175 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.5959 (mp0) REVERT: F 4 GLN cc_start: 0.8563 (tt0) cc_final: 0.8046 (pm20) REVERT: F 69 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7854 (mt) REVERT: F 175 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.5443 (mp0) REVERT: F 189 LEU cc_start: 0.8389 (tp) cc_final: 0.8028 (tp) outliers start: 14 outliers final: 6 residues processed: 264 average time/residue: 0.1119 time to fit residues: 39.1930 Evaluate side-chains 242 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 230 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 175 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 105 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 72 optimal weight: 8.9990 chunk 112 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 ASN C 12 HIS D 139 ASN D 195 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.146069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.119132 restraints weight = 14893.795| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.58 r_work: 0.3306 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9882 Z= 0.119 Angle : 0.499 8.551 13440 Z= 0.253 Chirality : 0.038 0.135 1536 Planarity : 0.005 0.047 1746 Dihedral : 5.684 59.043 1355 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.42 % Allowed : 12.89 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.50 (0.24), residues: 1236 helix: 2.07 (0.18), residues: 888 sheet: None (None), residues: 0 loop : 0.71 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 143 TYR 0.009 0.001 TYR D 169 PHE 0.009 0.002 PHE F 40 TRP 0.008 0.001 TRP E 80 HIS 0.002 0.000 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9876) covalent geometry : angle 0.49912 (13428) SS BOND : bond 0.00328 ( 6) SS BOND : angle 0.62786 ( 12) hydrogen bonds : bond 0.03797 ( 630) hydrogen bonds : angle 3.86901 ( 1857) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 241 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.8048 (mmt) cc_final: 0.7828 (mmt) REVERT: A 83 LEU cc_start: 0.8391 (mt) cc_final: 0.8092 (mt) REVERT: A 175 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.5992 (mp0) REVERT: A 195 ASN cc_start: 0.7658 (m-40) cc_final: 0.7270 (m110) REVERT: A 210 THR cc_start: 0.8161 (p) cc_final: 0.7676 (p) REVERT: A 213 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7667 (mt-10) REVERT: B 18 ARG cc_start: 0.6660 (ttp-170) cc_final: 0.5854 (ttt180) REVERT: B 69 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8243 (tt) REVERT: B 118 MET cc_start: 0.8529 (mtp) cc_final: 0.8183 (mtp) REVERT: B 170 LYS cc_start: 0.8365 (tttt) cc_final: 0.7990 (tppt) REVERT: B 175 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.5636 (mp0) REVERT: B 215 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.8026 (mtp) REVERT: C 23 TRP cc_start: 0.8906 (t-100) cc_final: 0.8676 (t-100) REVERT: C 30 LYS cc_start: 0.7426 (mmtt) cc_final: 0.6943 (mttt) REVERT: C 54 THR cc_start: 0.7889 (m) cc_final: 0.7137 (p) REVERT: C 100 ARG cc_start: 0.7966 (mmp80) cc_final: 0.7755 (mmt180) REVERT: D 25 LYS cc_start: 0.7725 (mptt) cc_final: 0.7171 (mttt) REVERT: D 70 LYS cc_start: 0.7955 (ttmm) cc_final: 0.7741 (ttpp) REVERT: E 68 MET cc_start: 0.8635 (mtm) cc_final: 0.8309 (mtp) REVERT: E 79 GLU cc_start: 0.8983 (tp30) cc_final: 0.8156 (tp30) REVERT: E 82 ARG cc_start: 0.7812 (mtp-110) cc_final: 0.7220 (ttp80) REVERT: E 175 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.6093 (mp0) REVERT: F 4 GLN cc_start: 0.8595 (tt0) cc_final: 0.8039 (pm20) REVERT: F 69 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7848 (mt) REVERT: F 175 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.5449 (mp0) REVERT: F 189 LEU cc_start: 0.8404 (tp) cc_final: 0.8044 (tp) outliers start: 25 outliers final: 9 residues processed: 256 average time/residue: 0.1159 time to fit residues: 39.8050 Evaluate side-chains 238 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 222 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 175 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 65 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 chunk 3 optimal weight: 0.0020 chunk 19 optimal weight: 7.9990 chunk 59 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 125 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 overall best weight: 1.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 139 ASN E 21 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.144206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.117309 restraints weight = 14812.886| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.56 r_work: 0.3277 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9882 Z= 0.159 Angle : 0.527 8.795 13440 Z= 0.265 Chirality : 0.040 0.147 1536 Planarity : 0.005 0.051 1746 Dihedral : 5.733 58.509 1355 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.33 % Allowed : 14.92 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.37 (0.24), residues: 1236 helix: 1.96 (0.18), residues: 888 sheet: None (None), residues: 0 loop : 0.72 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 143 TYR 0.013 0.002 TYR E 145 PHE 0.010 0.002 PHE F 40 TRP 0.009 0.001 TRP E 80 HIS 0.002 0.000 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 9876) covalent geometry : angle 0.52683 (13428) SS BOND : bond 0.00139 ( 6) SS BOND : angle 0.74735 ( 12) hydrogen bonds : bond 0.03970 ( 630) hydrogen bonds : angle 3.91413 ( 1857) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 221 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.8070 (mmt) cc_final: 0.7860 (mmt) REVERT: A 83 LEU cc_start: 0.8306 (mt) cc_final: 0.7983 (mt) REVERT: A 175 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6045 (mp0) REVERT: A 195 ASN cc_start: 0.7735 (m-40) cc_final: 0.7298 (m110) REVERT: B 18 ARG cc_start: 0.6534 (ttp-170) cc_final: 0.5666 (ttt180) REVERT: B 69 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8133 (tt) REVERT: B 136 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7823 (tp) REVERT: B 170 LYS cc_start: 0.8448 (tttt) cc_final: 0.8031 (tppt) REVERT: B 175 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.5681 (mp0) REVERT: B 214 MET cc_start: 0.7629 (mtm) cc_final: 0.6829 (mtp) REVERT: B 215 MET cc_start: 0.8245 (ttt) cc_final: 0.8038 (mtp) REVERT: C 23 TRP cc_start: 0.8926 (t-100) cc_final: 0.8697 (t-100) REVERT: C 30 LYS cc_start: 0.7477 (mmtt) cc_final: 0.7011 (mttt) REVERT: C 54 THR cc_start: 0.8069 (m) cc_final: 0.7240 (p) REVERT: C 100 ARG cc_start: 0.7949 (mmp80) cc_final: 0.7693 (mmt180) REVERT: D 25 LYS cc_start: 0.7777 (mptt) cc_final: 0.7198 (mttt) REVERT: E 68 MET cc_start: 0.8655 (mtm) cc_final: 0.8367 (mtp) REVERT: E 79 GLU cc_start: 0.9001 (tp30) cc_final: 0.8215 (tp30) REVERT: E 82 ARG cc_start: 0.7889 (mtp-110) cc_final: 0.7205 (ttp80) REVERT: E 175 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6152 (mp0) REVERT: F 4 GLN cc_start: 0.8686 (tt0) cc_final: 0.8045 (pm20) REVERT: F 69 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7903 (mt) REVERT: F 175 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.5545 (mp0) REVERT: F 189 LEU cc_start: 0.8402 (tp) cc_final: 0.8040 (tp) outliers start: 24 outliers final: 14 residues processed: 238 average time/residue: 0.1192 time to fit residues: 37.8572 Evaluate side-chains 234 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 213 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain E residue 199 LYS Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 146 SER Chi-restraints excluded: chain F residue 175 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 76 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 119 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 67 GLN D 139 ASN E 21 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.144246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.117158 restraints weight = 14985.456| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.58 r_work: 0.3273 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9882 Z= 0.158 Angle : 0.525 11.184 13440 Z= 0.264 Chirality : 0.040 0.149 1536 Planarity : 0.005 0.056 1746 Dihedral : 5.785 58.678 1355 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.20 % Allowed : 14.83 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.29 (0.24), residues: 1236 helix: 1.90 (0.18), residues: 888 sheet: None (None), residues: 0 loop : 0.70 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 154 TYR 0.011 0.001 TYR E 145 PHE 0.011 0.002 PHE F 40 TRP 0.009 0.001 TRP E 80 HIS 0.002 0.000 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 9876) covalent geometry : angle 0.52487 (13428) SS BOND : bond 0.00219 ( 6) SS BOND : angle 0.98514 ( 12) hydrogen bonds : bond 0.03934 ( 630) hydrogen bonds : angle 3.90884 ( 1857) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 223 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8306 (mt) cc_final: 0.7988 (mt) REVERT: A 175 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6051 (mp0) REVERT: A 195 ASN cc_start: 0.7755 (m-40) cc_final: 0.7513 (m-40) REVERT: B 18 ARG cc_start: 0.6375 (ttp-170) cc_final: 0.5548 (ttt180) REVERT: B 69 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8164 (tt) REVERT: B 136 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7757 (tp) REVERT: B 170 LYS cc_start: 0.8428 (tttt) cc_final: 0.8029 (tppt) REVERT: B 175 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.5640 (mp0) REVERT: C 30 LYS cc_start: 0.7430 (mmtt) cc_final: 0.7014 (mttt) REVERT: C 54 THR cc_start: 0.8063 (m) cc_final: 0.7194 (p) REVERT: C 100 ARG cc_start: 0.7925 (mmp80) cc_final: 0.7720 (mmt180) REVERT: D 25 LYS cc_start: 0.7801 (mptt) cc_final: 0.7185 (mttt) REVERT: D 152 ASP cc_start: 0.8127 (m-30) cc_final: 0.7817 (t0) REVERT: E 68 MET cc_start: 0.8676 (mtm) cc_final: 0.8369 (mtp) REVERT: E 79 GLU cc_start: 0.8991 (tp30) cc_final: 0.8656 (tp30) REVERT: E 175 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6260 (mp0) REVERT: F 4 GLN cc_start: 0.8709 (tt0) cc_final: 0.8022 (pm20) REVERT: F 69 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8089 (mt) REVERT: F 136 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8834 (tp) REVERT: F 175 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.5606 (mp0) REVERT: F 189 LEU cc_start: 0.8461 (tp) cc_final: 0.8100 (tp) outliers start: 33 outliers final: 15 residues processed: 247 average time/residue: 0.1210 time to fit residues: 39.9175 Evaluate side-chains 234 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 211 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain E residue 199 LYS Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 146 SER Chi-restraints excluded: chain F residue 175 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 87 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 chunk 113 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 192 GLN D 139 ASN E 21 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.146180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.119205 restraints weight = 14827.058| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.59 r_work: 0.3308 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9882 Z= 0.119 Angle : 0.518 11.203 13440 Z= 0.257 Chirality : 0.039 0.138 1536 Planarity : 0.005 0.052 1746 Dihedral : 5.744 59.301 1355 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.91 % Allowed : 15.50 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.36 (0.24), residues: 1236 helix: 1.94 (0.18), residues: 888 sheet: None (None), residues: 0 loop : 0.74 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 154 TYR 0.009 0.001 TYR D 130 PHE 0.010 0.001 PHE F 40 TRP 0.009 0.001 TRP C 23 HIS 0.002 0.000 HIS B 12 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 9876) covalent geometry : angle 0.51730 (13428) SS BOND : bond 0.00099 ( 6) SS BOND : angle 0.82175 ( 12) hydrogen bonds : bond 0.03616 ( 630) hydrogen bonds : angle 3.78480 ( 1857) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 229 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8363 (mt) cc_final: 0.8063 (mt) REVERT: A 175 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.5981 (mp0) REVERT: A 195 ASN cc_start: 0.7727 (OUTLIER) cc_final: 0.7502 (m-40) REVERT: B 18 ARG cc_start: 0.6378 (ttp-170) cc_final: 0.5557 (ttt180) REVERT: B 69 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8301 (tt) REVERT: B 118 MET cc_start: 0.8440 (mtp) cc_final: 0.8129 (mtp) REVERT: B 136 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7835 (tp) REVERT: B 170 LYS cc_start: 0.8414 (tttt) cc_final: 0.8006 (tppt) REVERT: B 175 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.5713 (mp0) REVERT: B 213 GLU cc_start: 0.7385 (tp30) cc_final: 0.6946 (tp30) REVERT: C 30 LYS cc_start: 0.7417 (mmtt) cc_final: 0.7011 (mttt) REVERT: C 54 THR cc_start: 0.7985 (m) cc_final: 0.7183 (p) REVERT: D 25 LYS cc_start: 0.7806 (mptt) cc_final: 0.7214 (mttt) REVERT: D 74 ASN cc_start: 0.8440 (m110) cc_final: 0.8050 (m110) REVERT: D 152 ASP cc_start: 0.8025 (m-30) cc_final: 0.7723 (t0) REVERT: D 212 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7650 (tm-30) REVERT: E 68 MET cc_start: 0.8640 (mtm) cc_final: 0.8373 (mtp) REVERT: E 79 GLU cc_start: 0.8991 (tp30) cc_final: 0.8656 (tp30) REVERT: E 175 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6359 (mp0) REVERT: F 4 GLN cc_start: 0.8666 (tt0) cc_final: 0.8020 (pm20) REVERT: F 69 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.8005 (mt) REVERT: F 136 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8839 (tp) REVERT: F 175 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.5789 (mp0) REVERT: F 189 LEU cc_start: 0.8429 (tp) cc_final: 0.8059 (tp) outliers start: 30 outliers final: 15 residues processed: 250 average time/residue: 0.1044 time to fit residues: 35.1825 Evaluate side-chains 242 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 218 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 193 ASN Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 146 SER Chi-restraints excluded: chain F residue 175 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 8 optimal weight: 0.4980 chunk 116 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 139 ASN ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.142971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.115966 restraints weight = 14860.289| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.56 r_work: 0.3260 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9882 Z= 0.205 Angle : 0.582 12.259 13440 Z= 0.292 Chirality : 0.041 0.149 1536 Planarity : 0.005 0.057 1746 Dihedral : 5.838 59.288 1355 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.81 % Allowed : 15.89 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.04 (0.24), residues: 1236 helix: 1.71 (0.18), residues: 888 sheet: None (None), residues: 0 loop : 0.60 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 154 TYR 0.014 0.002 TYR D 130 PHE 0.013 0.002 PHE F 40 TRP 0.010 0.001 TRP C 80 HIS 0.014 0.001 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00507 ( 9876) covalent geometry : angle 0.58138 (13428) SS BOND : bond 0.00220 ( 6) SS BOND : angle 1.33043 ( 12) hydrogen bonds : bond 0.04308 ( 630) hydrogen bonds : angle 4.02787 ( 1857) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 219 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8365 (mt) cc_final: 0.8057 (mt) REVERT: A 175 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6082 (mp0) REVERT: A 195 ASN cc_start: 0.7822 (m-40) cc_final: 0.7584 (m-40) REVERT: B 18 ARG cc_start: 0.6414 (ttp-170) cc_final: 0.5540 (ttt180) REVERT: B 69 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8225 (tt) REVERT: B 136 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7743 (tp) REVERT: B 170 LYS cc_start: 0.8466 (tttt) cc_final: 0.8051 (tppt) REVERT: B 175 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.5617 (mp0) REVERT: C 30 LYS cc_start: 0.7519 (mmtt) cc_final: 0.7168 (mttt) REVERT: C 54 THR cc_start: 0.8174 (m) cc_final: 0.7271 (p) REVERT: D 25 LYS cc_start: 0.7830 (mptt) cc_final: 0.7215 (mttt) REVERT: D 152 ASP cc_start: 0.8100 (m-30) cc_final: 0.7892 (t0) REVERT: E 79 GLU cc_start: 0.8978 (tp30) cc_final: 0.8627 (tp30) REVERT: E 175 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.6434 (mp0) REVERT: F 4 GLN cc_start: 0.8774 (tt0) cc_final: 0.8076 (pm20) REVERT: F 69 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8168 (mt) REVERT: F 175 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.5923 (mp0) REVERT: F 189 LEU cc_start: 0.8484 (tp) cc_final: 0.8121 (tp) outliers start: 29 outliers final: 17 residues processed: 241 average time/residue: 0.1207 time to fit residues: 38.9347 Evaluate side-chains 236 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 212 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain E residue 199 LYS Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 146 SER Chi-restraints excluded: chain F residue 175 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 29 optimal weight: 0.0770 chunk 64 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 77 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 ASN D 139 ASN ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.146836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.119962 restraints weight = 14821.866| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.58 r_work: 0.3317 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9882 Z= 0.113 Angle : 0.536 13.502 13440 Z= 0.264 Chirality : 0.039 0.147 1536 Planarity : 0.005 0.055 1746 Dihedral : 5.724 59.840 1355 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.33 % Allowed : 17.15 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.25 (0.24), residues: 1236 helix: 1.87 (0.18), residues: 888 sheet: None (None), residues: 0 loop : 0.68 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 143 TYR 0.010 0.001 TYR E 169 PHE 0.010 0.001 PHE F 40 TRP 0.007 0.001 TRP E 23 HIS 0.009 0.001 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 9876) covalent geometry : angle 0.53567 (13428) SS BOND : bond 0.00101 ( 6) SS BOND : angle 0.75924 ( 12) hydrogen bonds : bond 0.03521 ( 630) hydrogen bonds : angle 3.81162 ( 1857) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 223 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8378 (mt) cc_final: 0.8057 (mt) REVERT: A 175 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.5949 (mp0) REVERT: A 195 ASN cc_start: 0.7852 (OUTLIER) cc_final: 0.7608 (m-40) REVERT: B 18 ARG cc_start: 0.6338 (ttp-170) cc_final: 0.5490 (ttt180) REVERT: B 69 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8307 (tt) REVERT: B 118 MET cc_start: 0.8508 (mtp) cc_final: 0.8221 (mtp) REVERT: B 136 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7808 (tp) REVERT: B 170 LYS cc_start: 0.8391 (tttt) cc_final: 0.7989 (tppt) REVERT: C 30 LYS cc_start: 0.7368 (mmtt) cc_final: 0.6954 (mttt) REVERT: C 54 THR cc_start: 0.7976 (m) cc_final: 0.7181 (p) REVERT: D 25 LYS cc_start: 0.7800 (mptt) cc_final: 0.7206 (mttt) REVERT: D 152 ASP cc_start: 0.7996 (m-30) cc_final: 0.7789 (t0) REVERT: E 79 GLU cc_start: 0.9000 (tp30) cc_final: 0.8667 (tp30) REVERT: E 172 LEU cc_start: 0.8360 (tp) cc_final: 0.8023 (tp) REVERT: E 175 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.6522 (mp0) REVERT: E 197 ASP cc_start: 0.8358 (m-30) cc_final: 0.7942 (p0) REVERT: F 4 GLN cc_start: 0.8769 (tt0) cc_final: 0.8088 (pm20) REVERT: F 82 ARG cc_start: 0.8425 (mtm110) cc_final: 0.8063 (ttp80) REVERT: F 175 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.6030 (mp0) REVERT: F 189 LEU cc_start: 0.8482 (tp) cc_final: 0.8095 (tp) outliers start: 24 outliers final: 13 residues processed: 243 average time/residue: 0.1197 time to fit residues: 39.1087 Evaluate side-chains 233 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 214 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 193 ASN Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 146 SER Chi-restraints excluded: chain F residue 175 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 93 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 139 ASN ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.147025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.120313 restraints weight = 14783.495| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.56 r_work: 0.3322 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9882 Z= 0.122 Angle : 0.545 13.724 13440 Z= 0.269 Chirality : 0.039 0.149 1536 Planarity : 0.005 0.059 1746 Dihedral : 5.265 59.258 1350 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.94 % Allowed : 17.83 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.24 (0.24), residues: 1236 helix: 1.86 (0.18), residues: 888 sheet: None (None), residues: 0 loop : 0.69 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 143 TYR 0.009 0.001 TYR E 169 PHE 0.011 0.001 PHE F 40 TRP 0.006 0.001 TRP C 80 HIS 0.006 0.000 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 9876) covalent geometry : angle 0.54503 (13428) SS BOND : bond 0.00114 ( 6) SS BOND : angle 0.89742 ( 12) hydrogen bonds : bond 0.03570 ( 630) hydrogen bonds : angle 3.82109 ( 1857) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 220 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8371 (mt) cc_final: 0.8078 (mt) REVERT: A 175 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.5938 (mp0) REVERT: A 195 ASN cc_start: 0.7834 (OUTLIER) cc_final: 0.7591 (m-40) REVERT: B 18 ARG cc_start: 0.6411 (ttp-170) cc_final: 0.5514 (ttt180) REVERT: B 136 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7842 (tp) REVERT: B 170 LYS cc_start: 0.8393 (tttt) cc_final: 0.8000 (tppt) REVERT: C 30 LYS cc_start: 0.7364 (mmtt) cc_final: 0.6974 (mttt) REVERT: C 54 THR cc_start: 0.7982 (m) cc_final: 0.7206 (p) REVERT: D 25 LYS cc_start: 0.7818 (mptt) cc_final: 0.7232 (mttt) REVERT: D 152 ASP cc_start: 0.8034 (m-30) cc_final: 0.7832 (t0) REVERT: E 23 TRP cc_start: 0.8627 (t-100) cc_final: 0.8283 (t-100) REVERT: E 79 GLU cc_start: 0.8993 (tp30) cc_final: 0.8670 (tp30) REVERT: E 175 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.6610 (mp0) REVERT: E 197 ASP cc_start: 0.8398 (m-30) cc_final: 0.8004 (p0) REVERT: F 4 GLN cc_start: 0.8771 (tt0) cc_final: 0.8095 (pm20) REVERT: F 175 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.6047 (mp0) REVERT: F 189 LEU cc_start: 0.8484 (tp) cc_final: 0.8096 (tp) outliers start: 20 outliers final: 13 residues processed: 236 average time/residue: 0.1201 time to fit residues: 38.1838 Evaluate side-chains 229 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 211 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 193 ASN Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 146 SER Chi-restraints excluded: chain F residue 175 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 70 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 ASN ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.143788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.116955 restraints weight = 14842.746| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.51 r_work: 0.3276 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9882 Z= 0.204 Angle : 0.614 13.681 13440 Z= 0.306 Chirality : 0.042 0.162 1536 Planarity : 0.006 0.067 1746 Dihedral : 5.262 59.081 1348 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.94 % Allowed : 17.54 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.94 (0.24), residues: 1236 helix: 1.64 (0.18), residues: 888 sheet: None (None), residues: 0 loop : 0.56 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 143 TYR 0.011 0.002 TYR E 145 PHE 0.012 0.002 PHE F 40 TRP 0.009 0.001 TRP E 80 HIS 0.004 0.001 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00506 ( 9876) covalent geometry : angle 0.61241 (13428) SS BOND : bond 0.00379 ( 6) SS BOND : angle 1.39938 ( 12) hydrogen bonds : bond 0.04236 ( 630) hydrogen bonds : angle 4.04981 ( 1857) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 217 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8331 (mt) cc_final: 0.8013 (mt) REVERT: A 175 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6153 (mp0) REVERT: A 195 ASN cc_start: 0.7904 (m-40) cc_final: 0.7642 (m-40) REVERT: B 18 ARG cc_start: 0.6401 (ttp-170) cc_final: 0.5349 (ttt180) REVERT: B 118 MET cc_start: 0.8623 (mtp) cc_final: 0.8315 (mtp) REVERT: B 136 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7735 (tp) REVERT: B 170 LYS cc_start: 0.8456 (tttt) cc_final: 0.8036 (tppt) REVERT: C 30 LYS cc_start: 0.7470 (mmtt) cc_final: 0.7128 (mttt) REVERT: C 54 THR cc_start: 0.8181 (m) cc_final: 0.7319 (p) REVERT: D 25 LYS cc_start: 0.7832 (mptt) cc_final: 0.7219 (mttt) REVERT: D 152 ASP cc_start: 0.8087 (m-30) cc_final: 0.7880 (t0) REVERT: E 79 GLU cc_start: 0.8945 (tp30) cc_final: 0.8596 (tp30) REVERT: E 175 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.6469 (mp0) REVERT: E 197 ASP cc_start: 0.8190 (m-30) cc_final: 0.7794 (p0) REVERT: F 4 GLN cc_start: 0.8729 (tt0) cc_final: 0.7997 (pm20) REVERT: F 175 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.6120 (mp0) REVERT: F 189 LEU cc_start: 0.8477 (tp) cc_final: 0.8111 (tp) outliers start: 20 outliers final: 14 residues processed: 233 average time/residue: 0.1192 time to fit residues: 37.3994 Evaluate side-chains 230 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 212 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 146 SER Chi-restraints excluded: chain F residue 175 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 53 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 42 optimal weight: 0.0020 chunk 73 optimal weight: 0.6980 chunk 77 optimal weight: 8.9990 chunk 8 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.147323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.120653 restraints weight = 14807.521| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.53 r_work: 0.3329 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9882 Z= 0.114 Angle : 0.555 13.952 13440 Z= 0.273 Chirality : 0.039 0.139 1536 Planarity : 0.005 0.061 1746 Dihedral : 5.122 59.512 1348 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.45 % Allowed : 18.12 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.13 (0.24), residues: 1236 helix: 1.78 (0.18), residues: 888 sheet: None (None), residues: 0 loop : 0.65 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 154 TYR 0.010 0.001 TYR E 169 PHE 0.011 0.001 PHE F 40 TRP 0.007 0.001 TRP A 117 HIS 0.005 0.001 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 9876) covalent geometry : angle 0.55440 (13428) SS BOND : bond 0.00162 ( 6) SS BOND : angle 0.81169 ( 12) hydrogen bonds : bond 0.03547 ( 630) hydrogen bonds : angle 3.84938 ( 1857) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2117.65 seconds wall clock time: 37 minutes 5.22 seconds (2225.22 seconds total)