Starting phenix.real_space_refine on Fri Mar 14 04:09:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ty6_41711/03_2025/8ty6_41711.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ty6_41711/03_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_41711/03_2025/8ty6_41711.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ty6_41711/03_2025/8ty6_41711.map" model { file = "/net/cci-nas-00/data/ceres_data/8ty6_41711/03_2025/8ty6_41711.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ty6_41711/03_2025/8ty6_41711.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 6.48, per 1000 atoms: 0.67 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: 2.75 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.96 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: 2.66 Time building geometry restraints manager: 3.23 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: 0.02 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: 1.100 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: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.140 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.370 ------------------------------------------------------------------------------- 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 9876 Z= 0.146 Angle : 0.444 5.425 13428 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.005 0.001 TRP E 80 HIS 0.002 0.000 HIS F 62 PHE 0.008 0.001 PHE A 168 TYR 0.009 0.001 TYR D 169 ARG 0.002 0.000 ARG C 167 *********************** 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 : 1.424 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: 0.2759 time to fit residues: 119.1940 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 : 1.113 ------------------------------------------------------------------------------- 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 106 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 0.2980 chunk 98 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 60 optimal weight: 0.0870 chunk 73 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 overall best weight: 0.6160 ------------------------------------------------------------------------------- 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 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3807 r_free = 0.3807 target = 0.147015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.120181 restraints weight = 14648.038| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.57 r_work: 0.3313 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9876 Z= 0.178 Angle : 0.511 4.755 13428 Z= 0.266 Chirality : 0.039 0.144 1536 Planarity : 0.005 0.041 1746 Dihedral : 6.336 59.258 1362 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.65 % Allowed : 11.82 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.25), residues: 1236 helix: 2.11 (0.18), residues: 894 sheet: -1.36 (0.67), residues: 54 loop : 1.11 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 80 HIS 0.005 0.001 HIS E 120 PHE 0.009 0.001 PHE D 161 TYR 0.009 0.001 TYR D 169 ARG 0.007 0.001 ARG D 154 *********************** 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 273 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 256 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.8118 (mmt) cc_final: 0.7871 (mmt) REVERT: A 83 LEU cc_start: 0.8353 (mt) cc_final: 0.8058 (mt) REVERT: A 175 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.5966 (mp0) REVERT: A 195 ASN cc_start: 0.7803 (m-40) cc_final: 0.7176 (m110) REVERT: A 210 THR cc_start: 0.8131 (p) cc_final: 0.7671 (p) REVERT: A 213 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7679 (mt-10) REVERT: B 18 ARG cc_start: 0.6566 (ttp-170) cc_final: 0.5786 (ttt180) REVERT: B 69 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8247 (tt) REVERT: B 118 MET cc_start: 0.8527 (mtp) cc_final: 0.8182 (mtp) REVERT: B 170 LYS cc_start: 0.8354 (tttt) cc_final: 0.7962 (tppt) REVERT: B 175 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.5795 (mp0) REVERT: B 213 GLU cc_start: 0.7457 (tp30) cc_final: 0.6833 (tp30) REVERT: C 23 TRP cc_start: 0.8887 (t-100) cc_final: 0.8671 (t-100) REVERT: C 30 LYS cc_start: 0.7465 (mmtt) cc_final: 0.6958 (mttt) REVERT: C 54 THR cc_start: 0.7807 (m) cc_final: 0.7161 (p) REVERT: C 100 ARG cc_start: 0.7929 (mmp80) cc_final: 0.7728 (mmt180) REVERT: C 171 THR cc_start: 0.8383 (m) cc_final: 0.8011 (p) REVERT: C 195 ASN cc_start: 0.7560 (t0) cc_final: 0.7267 (t0) REVERT: D 25 LYS cc_start: 0.7701 (mptt) cc_final: 0.7181 (mttt) REVERT: D 70 LYS cc_start: 0.7975 (ttmm) cc_final: 0.7758 (ttpp) REVERT: E 68 MET cc_start: 0.8580 (mtm) cc_final: 0.8279 (mtp) REVERT: E 79 GLU cc_start: 0.9016 (tp30) cc_final: 0.8370 (tp30) REVERT: E 82 ARG cc_start: 0.7695 (mtp-110) cc_final: 0.7334 (ttp80) REVERT: E 175 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.5936 (mp0) REVERT: E 195 ASN cc_start: 0.8418 (t0) cc_final: 0.8168 (t0) REVERT: E 197 ASP cc_start: 0.8428 (m-30) cc_final: 0.8011 (p0) REVERT: F 4 GLN cc_start: 0.8534 (tt0) cc_final: 0.8040 (pm20) REVERT: F 69 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7775 (mt) REVERT: F 175 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.5472 (mp0) REVERT: F 189 LEU cc_start: 0.8383 (tp) cc_final: 0.8000 (tp) outliers start: 17 outliers final: 6 residues processed: 268 average time/residue: 0.3274 time to fit residues: 118.6282 Evaluate side-chains 238 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 226 time to evaluate : 1.781 ------------------------------------------------------------------------------- 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 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 146 SER 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 121 optimal weight: 4.9990 chunk 79 optimal weight: 0.4980 chunk 50 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 ASN D 139 ASN ** D 195 ASN ** 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 = 0.3783 r_free = 0.3783 target = 0.144820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.117835 restraints weight = 14995.795| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.57 r_work: 0.3288 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9876 Z= 0.242 Angle : 0.524 8.689 13428 Z= 0.265 Chirality : 0.039 0.143 1536 Planarity : 0.005 0.049 1746 Dihedral : 5.637 58.641 1353 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.62 % Allowed : 12.60 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.24), residues: 1236 helix: 2.00 (0.18), residues: 888 sheet: None (None), residues: 0 loop : 0.67 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 80 HIS 0.002 0.001 HIS E 12 PHE 0.010 0.002 PHE F 40 TYR 0.010 0.001 TYR D 169 ARG 0.008 0.001 ARG D 143 *********************** 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 264 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 237 time to evaluate : 1.605 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.8096 (mmt) cc_final: 0.7881 (mmt) REVERT: A 83 LEU cc_start: 0.8344 (mt) cc_final: 0.8031 (mt) REVERT: A 175 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6032 (mp0) REVERT: A 195 ASN cc_start: 0.7653 (m-40) cc_final: 0.7248 (m110) REVERT: A 213 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7596 (mt-10) REVERT: B 18 ARG cc_start: 0.6671 (ttp-170) cc_final: 0.5850 (ttt180) REVERT: B 69 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8200 (tt) REVERT: B 170 LYS cc_start: 0.8388 (tttt) cc_final: 0.7990 (tppt) REVERT: B 175 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.5669 (mp0) REVERT: C 23 TRP cc_start: 0.8930 (t-100) cc_final: 0.8685 (t-100) REVERT: C 30 LYS cc_start: 0.7451 (mmtt) cc_final: 0.6979 (mttt) REVERT: C 54 THR cc_start: 0.7952 (m) cc_final: 0.7184 (p) REVERT: D 25 LYS cc_start: 0.7757 (mptt) cc_final: 0.7183 (mttt) REVERT: D 70 LYS cc_start: 0.8040 (ttmm) cc_final: 0.7820 (ttpp) REVERT: E 68 MET cc_start: 0.8670 (mtm) cc_final: 0.8395 (mtp) REVERT: E 79 GLU cc_start: 0.8993 (tp30) cc_final: 0.8185 (tp30) REVERT: E 82 ARG cc_start: 0.7840 (mtp-110) cc_final: 0.7230 (ttp80) REVERT: E 175 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.6089 (mp0) REVERT: F 4 GLN cc_start: 0.8647 (tt0) cc_final: 0.8030 (pm20) REVERT: F 69 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7871 (mt) REVERT: F 175 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.5504 (mp0) REVERT: F 189 LEU cc_start: 0.8408 (tp) cc_final: 0.8065 (tp) outliers start: 27 outliers final: 9 residues processed: 252 average time/residue: 0.3662 time to fit residues: 124.9461 Evaluate side-chains 234 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 219 time to evaluate : 1.819 ------------------------------------------------------------------------------- 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 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 28 optimal weight: 1.9990 chunk 118 optimal weight: 0.0010 chunk 77 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 96 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 HIS 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 = 0.3805 r_free = 0.3805 target = 0.146322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.119513 restraints weight = 14576.012| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.55 r_work: 0.3310 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9876 Z= 0.172 Angle : 0.497 9.073 13428 Z= 0.248 Chirality : 0.039 0.157 1536 Planarity : 0.005 0.048 1746 Dihedral : 5.641 58.678 1353 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.52 % Allowed : 13.66 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.24), residues: 1236 helix: 2.04 (0.18), residues: 888 sheet: None (None), residues: 0 loop : 0.72 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 80 HIS 0.002 0.000 HIS B 12 PHE 0.009 0.001 PHE F 40 TYR 0.011 0.001 TYR E 145 ARG 0.009 0.001 ARG D 143 *********************** 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 249 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 223 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.8048 (mmt) cc_final: 0.7821 (mmt) REVERT: A 83 LEU cc_start: 0.8373 (mt) cc_final: 0.8061 (mt) REVERT: A 175 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.5986 (mp0) REVERT: A 195 ASN cc_start: 0.7690 (m-40) cc_final: 0.7255 (m110) REVERT: B 18 ARG cc_start: 0.6629 (ttp-170) cc_final: 0.5780 (ttt180) REVERT: B 69 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8239 (tt) REVERT: B 136 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7839 (tp) REVERT: B 170 LYS cc_start: 0.8414 (tttt) cc_final: 0.8005 (tppt) REVERT: B 175 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.5703 (mp0) REVERT: B 214 MET cc_start: 0.7616 (mtm) cc_final: 0.7404 (mtt) REVERT: C 23 TRP cc_start: 0.8900 (t-100) cc_final: 0.8683 (t-100) REVERT: C 30 LYS cc_start: 0.7413 (mmtt) cc_final: 0.6949 (mttt) REVERT: C 54 THR cc_start: 0.7897 (m) cc_final: 0.7139 (p) REVERT: C 100 ARG cc_start: 0.8028 (mmm160) cc_final: 0.7691 (mmt180) REVERT: D 25 LYS cc_start: 0.7761 (mptt) cc_final: 0.7196 (mttt) REVERT: D 70 LYS cc_start: 0.7965 (ttmm) cc_final: 0.7765 (ttpp) REVERT: E 68 MET cc_start: 0.8604 (mtm) cc_final: 0.8288 (mtp) REVERT: E 79 GLU cc_start: 0.8966 (tp30) cc_final: 0.8632 (tp30) REVERT: E 175 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6197 (mp0) REVERT: F 4 GLN cc_start: 0.8590 (tt0) cc_final: 0.8003 (pm20) REVERT: F 35 GLU cc_start: 0.9006 (pm20) cc_final: 0.8803 (pm20) REVERT: F 69 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7839 (mt) REVERT: F 175 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.5609 (mp0) REVERT: F 189 LEU cc_start: 0.8466 (tp) cc_final: 0.8113 (tp) outliers start: 26 outliers final: 13 residues processed: 240 average time/residue: 0.2539 time to fit residues: 81.1418 Evaluate side-chains 233 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 213 time to evaluate : 1.149 ------------------------------------------------------------------------------- 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 136 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain C residue 11 VAL 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 175 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 27 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 76 optimal weight: 0.6980 chunk 22 optimal weight: 8.9990 chunk 53 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 80 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- 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** E 21 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.143373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.116266 restraints weight = 14857.427| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.56 r_work: 0.3260 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9876 Z= 0.309 Angle : 0.551 12.066 13428 Z= 0.278 Chirality : 0.041 0.142 1536 Planarity : 0.005 0.053 1746 Dihedral : 5.749 58.895 1353 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.81 % Allowed : 14.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.24), residues: 1236 helix: 1.84 (0.18), residues: 888 sheet: None (None), residues: 0 loop : 0.66 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 80 HIS 0.014 0.001 HIS E 12 PHE 0.012 0.002 PHE F 40 TYR 0.013 0.002 TYR E 145 ARG 0.010 0.001 ARG D 143 *********************** 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 257 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 228 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8349 (mt) cc_final: 0.8041 (mt) REVERT: A 175 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6065 (mp0) REVERT: A 195 ASN cc_start: 0.7723 (m-40) cc_final: 0.7477 (m-40) REVERT: B 18 ARG cc_start: 0.6400 (ttp-170) cc_final: 0.5580 (ttt180) REVERT: B 69 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8128 (tt) REVERT: B 136 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7753 (tp) REVERT: B 170 LYS cc_start: 0.8435 (tttt) cc_final: 0.8034 (tppt) REVERT: B 175 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.5581 (mp0) REVERT: B 214 MET cc_start: 0.7695 (mtm) cc_final: 0.6958 (mtp) REVERT: C 30 LYS cc_start: 0.7512 (mmtt) cc_final: 0.7166 (mttt) REVERT: C 54 THR cc_start: 0.8131 (m) cc_final: 0.7235 (p) REVERT: D 25 LYS cc_start: 0.7807 (mptt) cc_final: 0.7183 (mttt) REVERT: D 152 ASP cc_start: 0.8088 (m-30) cc_final: 0.7768 (t0) REVERT: D 212 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7707 (tm-30) REVERT: E 79 GLU cc_start: 0.8956 (tp30) cc_final: 0.8598 (tp30) REVERT: E 175 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.6311 (mp0) REVERT: F 4 GLN cc_start: 0.8698 (tt0) cc_final: 0.8037 (pm20) REVERT: F 35 GLU cc_start: 0.9001 (pm20) cc_final: 0.8754 (pm20) REVERT: F 69 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8136 (mt) REVERT: F 136 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8839 (tp) REVERT: F 175 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.5638 (mp0) REVERT: F 189 LEU cc_start: 0.8467 (tp) cc_final: 0.8105 (tp) outliers start: 29 outliers final: 15 residues processed: 247 average time/residue: 0.2481 time to fit residues: 81.7956 Evaluate side-chains 237 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 214 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE 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 189 LEU 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 214 MET 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 49 optimal weight: 3.9990 chunk 95 optimal weight: 0.4980 chunk 108 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 3 optimal weight: 0.0370 chunk 5 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 overall best weight: 0.7062 ------------------------------------------------------------------------------- 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 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.146386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.119489 restraints weight = 14826.772| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.56 r_work: 0.3308 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9876 Z= 0.176 Angle : 0.502 12.183 13428 Z= 0.251 Chirality : 0.038 0.130 1536 Planarity : 0.005 0.049 1746 Dihedral : 5.706 59.330 1353 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.23 % Allowed : 16.38 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.24), residues: 1236 helix: 1.97 (0.18), residues: 888 sheet: None (None), residues: 0 loop : 0.73 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 80 HIS 0.009 0.001 HIS E 12 PHE 0.010 0.001 PHE F 40 TYR 0.016 0.001 TYR D 130 ARG 0.011 0.001 ARG D 154 *********************** 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 251 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 228 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8367 (mt) cc_final: 0.8069 (mt) REVERT: A 175 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.5965 (mp0) REVERT: A 195 ASN cc_start: 0.7727 (m-40) cc_final: 0.7509 (m-40) REVERT: B 18 ARG cc_start: 0.6559 (ttp-170) cc_final: 0.5678 (ttt180) REVERT: B 69 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8230 (tt) REVERT: B 136 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7826 (tp) REVERT: B 170 LYS cc_start: 0.8396 (tttt) cc_final: 0.7996 (tppt) REVERT: B 175 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.5704 (mp0) REVERT: B 213 GLU cc_start: 0.7491 (tp30) cc_final: 0.7075 (tp30) REVERT: B 214 MET cc_start: 0.7594 (mtm) cc_final: 0.6860 (mtp) REVERT: C 30 LYS cc_start: 0.7433 (mmtt) cc_final: 0.6995 (mttt) REVERT: C 54 THR cc_start: 0.8002 (m) cc_final: 0.7190 (p) REVERT: D 25 LYS cc_start: 0.7815 (mptt) cc_final: 0.7235 (mttt) REVERT: D 152 ASP cc_start: 0.8104 (m-30) cc_final: 0.7789 (t0) REVERT: D 212 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7591 (tm-30) REVERT: E 79 GLU cc_start: 0.8969 (tp30) cc_final: 0.8635 (tp30) REVERT: E 175 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6360 (mp0) REVERT: F 4 GLN cc_start: 0.8644 (tt0) cc_final: 0.8031 (pm20) REVERT: F 25 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8321 (ttpt) REVERT: F 69 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.8026 (mt) REVERT: F 175 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.5739 (mp0) REVERT: F 189 LEU cc_start: 0.8428 (tp) cc_final: 0.8062 (tp) outliers start: 23 outliers final: 13 residues processed: 245 average time/residue: 0.2507 time to fit residues: 81.8136 Evaluate side-chains 239 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 218 time to evaluate : 1.056 ------------------------------------------------------------------------------- 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 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 189 LEU 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 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 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 121 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 1 optimal weight: 0.0040 chunk 49 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.5396 ------------------------------------------------------------------------------- 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 = 0.3781 r_free = 0.3781 target = 0.144576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.117644 restraints weight = 14869.738| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.54 r_work: 0.3282 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9876 Z= 0.254 Angle : 0.534 12.411 13428 Z= 0.268 Chirality : 0.040 0.141 1536 Planarity : 0.005 0.054 1746 Dihedral : 5.711 59.156 1353 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.91 % Allowed : 15.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.24), residues: 1236 helix: 1.87 (0.18), residues: 888 sheet: None (None), residues: 0 loop : 0.69 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 23 HIS 0.007 0.001 HIS E 12 PHE 0.011 0.002 PHE F 40 TYR 0.010 0.001 TYR D 169 ARG 0.013 0.001 ARG D 154 *********************** 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 254 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 224 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8353 (mt) cc_final: 0.8045 (mt) REVERT: A 175 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6037 (mp0) REVERT: A 195 ASN cc_start: 0.7771 (OUTLIER) cc_final: 0.7551 (m-40) REVERT: B 18 ARG cc_start: 0.6420 (ttp-170) cc_final: 0.5573 (ttt180) REVERT: B 69 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8162 (tt) REVERT: B 136 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7789 (tp) REVERT: B 170 LYS cc_start: 0.8428 (tttt) cc_final: 0.8031 (tppt) REVERT: B 175 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.5642 (mp0) REVERT: B 214 MET cc_start: 0.7659 (mtm) cc_final: 0.6959 (mtp) REVERT: C 30 LYS cc_start: 0.7526 (mmtt) cc_final: 0.7177 (mttt) REVERT: C 54 THR cc_start: 0.8072 (m) cc_final: 0.7216 (p) REVERT: D 25 LYS cc_start: 0.7864 (mptt) cc_final: 0.7275 (mttt) REVERT: D 152 ASP cc_start: 0.8041 (m-30) cc_final: 0.7727 (t0) REVERT: D 212 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7614 (tm-30) REVERT: E 79 GLU cc_start: 0.8979 (tp30) cc_final: 0.8637 (tp30) REVERT: E 175 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6392 (mp0) REVERT: F 4 GLN cc_start: 0.8659 (tt0) cc_final: 0.8033 (pm20) REVERT: F 25 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8383 (ttpt) REVERT: F 69 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8133 (mt) REVERT: F 175 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.5872 (mp0) REVERT: F 189 LEU cc_start: 0.8467 (tp) cc_final: 0.8087 (tp) REVERT: F 214 MET cc_start: 0.8985 (mtm) cc_final: 0.8770 (mtm) outliers start: 30 outliers final: 12 residues processed: 243 average time/residue: 0.2607 time to fit residues: 85.2661 Evaluate side-chains 238 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 217 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 189 LEU 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 40 optimal weight: 0.0770 chunk 116 optimal weight: 0.4980 chunk 77 optimal weight: 8.9990 chunk 108 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 = 0.147078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.120323 restraints weight = 14962.054| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.56 r_work: 0.3324 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9876 Z= 0.172 Angle : 0.513 12.456 13428 Z= 0.256 Chirality : 0.038 0.138 1536 Planarity : 0.005 0.054 1746 Dihedral : 5.683 59.361 1353 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.52 % Allowed : 16.76 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.24), residues: 1236 helix: 1.96 (0.18), residues: 888 sheet: None (None), residues: 0 loop : 0.75 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 23 HIS 0.006 0.000 HIS E 12 PHE 0.010 0.001 PHE F 40 TYR 0.009 0.001 TYR E 169 ARG 0.012 0.001 ARG D 143 *********************** 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 253 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 227 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8369 (mt) cc_final: 0.8056 (mt) REVERT: A 175 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6016 (mp0) REVERT: A 195 ASN cc_start: 0.7816 (OUTLIER) cc_final: 0.7579 (m-40) REVERT: B 18 ARG cc_start: 0.6468 (ttp-170) cc_final: 0.5600 (ttt180) REVERT: B 136 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7840 (tp) REVERT: B 170 LYS cc_start: 0.8396 (tttt) cc_final: 0.7994 (tppt) REVERT: B 213 GLU cc_start: 0.7441 (tp30) cc_final: 0.7104 (tp30) REVERT: B 214 MET cc_start: 0.7602 (mtm) cc_final: 0.6918 (mtp) REVERT: C 30 LYS cc_start: 0.7396 (mmtt) cc_final: 0.6995 (mttt) REVERT: C 54 THR cc_start: 0.7967 (m) cc_final: 0.7199 (p) REVERT: D 25 LYS cc_start: 0.7795 (mptt) cc_final: 0.7208 (mttt) REVERT: D 74 ASN cc_start: 0.8434 (m110) cc_final: 0.8036 (m110) REVERT: D 152 ASP cc_start: 0.7959 (m-30) cc_final: 0.7707 (t0) REVERT: D 212 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7560 (tm-30) REVERT: E 79 GLU cc_start: 0.8989 (tp30) cc_final: 0.8656 (tp30) REVERT: E 175 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6488 (mp0) REVERT: F 4 GLN cc_start: 0.8625 (tt0) cc_final: 0.8031 (pm20) REVERT: F 175 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.6007 (mp0) REVERT: F 189 LEU cc_start: 0.8421 (tp) cc_final: 0.8041 (tp) outliers start: 26 outliers final: 12 residues processed: 246 average time/residue: 0.2500 time to fit residues: 82.6668 Evaluate side-chains 238 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 221 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 11 VAL 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 119 THR Chi-restraints excluded: chain E residue 175 GLU 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 74 optimal weight: 0.8980 chunk 80 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 86 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 ASN E 9 GLN ** 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 = 0.3791 r_free = 0.3791 target = 0.145257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.118392 restraints weight = 14836.376| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.53 r_work: 0.3298 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9876 Z= 0.258 Angle : 0.565 12.928 13428 Z= 0.282 Chirality : 0.040 0.151 1536 Planarity : 0.005 0.055 1746 Dihedral : 5.122 58.751 1346 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.94 % Allowed : 17.44 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.24), residues: 1236 helix: 1.89 (0.18), residues: 882 sheet: None (None), residues: 0 loop : 0.62 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 80 HIS 0.005 0.001 HIS E 12 PHE 0.011 0.002 PHE F 40 TYR 0.010 0.001 TYR D 169 ARG 0.014 0.001 ARG D 143 *********************** 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 241 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 221 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8339 (mt) cc_final: 0.8035 (mt) REVERT: A 175 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6012 (mp0) REVERT: A 195 ASN cc_start: 0.7864 (OUTLIER) cc_final: 0.7629 (m-40) REVERT: B 18 ARG cc_start: 0.6409 (ttp-170) cc_final: 0.5540 (ttt180) REVERT: B 136 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7791 (tp) REVERT: B 170 LYS cc_start: 0.8433 (tttt) cc_final: 0.8015 (tppt) REVERT: B 214 MET cc_start: 0.7741 (mtm) cc_final: 0.7222 (mtp) REVERT: C 30 LYS cc_start: 0.7493 (mmtt) cc_final: 0.7139 (mttt) REVERT: C 54 THR cc_start: 0.8072 (m) cc_final: 0.7212 (p) REVERT: D 25 LYS cc_start: 0.7862 (mptt) cc_final: 0.7286 (mttt) REVERT: D 152 ASP cc_start: 0.8031 (m-30) cc_final: 0.7829 (t0) REVERT: E 9 GLN cc_start: 0.6584 (OUTLIER) cc_final: 0.6335 (pm20) REVERT: E 79 GLU cc_start: 0.8982 (tp30) cc_final: 0.8652 (tp30) REVERT: E 175 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.6572 (mp0) REVERT: F 4 GLN cc_start: 0.8672 (tt0) cc_final: 0.8038 (pm20) REVERT: F 175 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.6156 (mp0) REVERT: F 189 LEU cc_start: 0.8423 (tp) cc_final: 0.8056 (tp) outliers start: 20 outliers final: 12 residues processed: 234 average time/residue: 0.2828 time to fit residues: 88.1655 Evaluate side-chains 233 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 215 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 136 LEU Chi-restraints excluded: chain C residue 11 VAL 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 9 GLN Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 175 GLU 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 18 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 40 optimal weight: 0.0010 chunk 89 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 92 optimal weight: 7.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- 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 = 0.3813 r_free = 0.3813 target = 0.147149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.120305 restraints weight = 14788.694| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.55 r_work: 0.3325 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9876 Z= 0.189 Angle : 0.557 13.689 13428 Z= 0.279 Chirality : 0.040 0.186 1536 Planarity : 0.005 0.061 1746 Dihedral : 5.086 59.015 1346 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.65 % Allowed : 17.44 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.24), residues: 1236 helix: 1.87 (0.18), residues: 888 sheet: None (None), residues: 0 loop : 0.72 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 80 HIS 0.006 0.000 HIS E 12 PHE 0.011 0.001 PHE F 40 TYR 0.009 0.001 TYR E 169 ARG 0.015 0.001 ARG D 143 ********************** 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: 17 poor density : 220 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8377 (mt) cc_final: 0.8057 (mt) REVERT: A 175 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.5979 (mp0) REVERT: A 195 ASN cc_start: 0.7850 (OUTLIER) cc_final: 0.7612 (m-40) REVERT: B 18 ARG cc_start: 0.6481 (ttp-170) cc_final: 0.5550 (ttt180) REVERT: B 136 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7836 (tp) REVERT: B 170 LYS cc_start: 0.8393 (tttt) cc_final: 0.7985 (tppt) REVERT: B 213 GLU cc_start: 0.7418 (tp30) cc_final: 0.7104 (tp30) REVERT: B 214 MET cc_start: 0.7710 (mtm) cc_final: 0.6763 (mtp) REVERT: C 30 LYS cc_start: 0.7397 (mmtt) cc_final: 0.6987 (mttt) REVERT: C 54 THR cc_start: 0.7991 (m) cc_final: 0.7177 (p) REVERT: D 25 LYS cc_start: 0.7811 (mptt) cc_final: 0.7220 (mttt) REVERT: E 25 LYS cc_start: 0.8425 (mmtp) cc_final: 0.8217 (mmtp) REVERT: E 79 GLU cc_start: 0.8980 (tp30) cc_final: 0.8651 (tp30) REVERT: E 118 MET cc_start: 0.8290 (mmm) cc_final: 0.7956 (mmm) REVERT: E 175 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.6670 (mp0) REVERT: F 4 GLN cc_start: 0.8644 (tt0) cc_final: 0.8049 (pm20) REVERT: F 175 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.6158 (mp0) REVERT: F 189 LEU cc_start: 0.8427 (tp) cc_final: 0.8049 (tp) outliers start: 17 outliers final: 11 residues processed: 231 average time/residue: 0.2668 time to fit residues: 82.9243 Evaluate side-chains 230 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 214 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 11 VAL 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 119 THR Chi-restraints excluded: chain E residue 175 GLU 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 71 optimal weight: 0.0670 chunk 113 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 114 optimal weight: 0.0050 chunk 16 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 overall best weight: 0.5132 ------------------------------------------------------------------------------- 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 = 0.3828 r_free = 0.3828 target = 0.148296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.121638 restraints weight = 14795.023| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.54 r_work: 0.3342 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9876 Z= 0.175 Angle : 0.556 13.701 13428 Z= 0.275 Chirality : 0.039 0.164 1536 Planarity : 0.005 0.067 1746 Dihedral : 5.044 58.401 1346 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.55 % Allowed : 17.83 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.24), residues: 1236 helix: 1.95 (0.18), residues: 882 sheet: None (None), residues: 0 loop : 0.54 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 23 HIS 0.006 0.000 HIS E 12 PHE 0.010 0.001 PHE F 40 TYR 0.009 0.001 TYR E 169 ARG 0.015 0.001 ARG D 154 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4543.50 seconds wall clock time: 82 minutes 10.77 seconds (4930.77 seconds total)