Starting phenix.real_space_refine on Wed Feb 4 01:41:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wzc_66388/02_2026/9wzc_66388.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wzc_66388/02_2026/9wzc_66388.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wzc_66388/02_2026/9wzc_66388.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wzc_66388/02_2026/9wzc_66388.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wzc_66388/02_2026/9wzc_66388.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wzc_66388/02_2026/9wzc_66388.map" } resolution = 2.45 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= 0.002 sd= 0.021 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 24 5.16 5 C 5292 2.51 5 N 1440 2.21 5 O 1500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8256 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 688 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 688 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 688 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 688 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 688 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 688 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 688 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 688 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 688 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 688 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 688 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 688 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.93, per 1000 atoms: 0.23 Number of scatterers: 8256 At special positions: 0 Unit cell: (84.84, 85.68, 94.92, 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 24 16.00 O 1500 8.00 N 1440 7.00 C 5292 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 260.9 milliseconds 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1968 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 0 sheets defined 92.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 112 through 118 removed outlier: 3.981A pdb=" N ASP A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 126 Processing helix chain 'A' and resid 128 through 137 removed outlier: 4.002A pdb=" N LEU A 132 " --> pdb=" O ASN A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 151 Processing helix chain 'A' and resid 154 through 164 Processing helix chain 'A' and resid 165 through 169 Processing helix chain 'A' and resid 170 through 185 Processing helix chain 'A' and resid 185 through 194 Processing helix chain 'B' and resid 113 through 118 Processing helix chain 'B' and resid 118 through 126 Processing helix chain 'B' and resid 128 through 137 removed outlier: 4.009A pdb=" N LEU B 132 " --> pdb=" O ASN B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 151 Processing helix chain 'B' and resid 154 through 164 Processing helix chain 'B' and resid 165 through 169 Processing helix chain 'B' and resid 170 through 185 Processing helix chain 'B' and resid 185 through 194 Processing helix chain 'C' and resid 113 through 118 Processing helix chain 'C' and resid 118 through 126 Processing helix chain 'C' and resid 128 through 137 removed outlier: 3.771A pdb=" N LEU C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 151 Processing helix chain 'C' and resid 154 through 164 Processing helix chain 'C' and resid 165 through 169 Processing helix chain 'C' and resid 170 through 185 Processing helix chain 'C' and resid 185 through 194 Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 118 through 126 Processing helix chain 'D' and resid 128 through 137 removed outlier: 4.070A pdb=" N LEU D 132 " --> pdb=" O ASN D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 151 Processing helix chain 'D' and resid 154 through 164 Processing helix chain 'D' and resid 165 through 169 Processing helix chain 'D' and resid 170 through 185 Processing helix chain 'D' and resid 185 through 194 Processing helix chain 'E' and resid 113 through 118 Processing helix chain 'E' and resid 118 through 126 Processing helix chain 'E' and resid 128 through 137 removed outlier: 3.842A pdb=" N LEU E 132 " --> pdb=" O ASN E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 151 Processing helix chain 'E' and resid 154 through 164 Processing helix chain 'E' and resid 165 through 169 Processing helix chain 'E' and resid 170 through 185 Processing helix chain 'E' and resid 185 through 194 Processing helix chain 'F' and resid 113 through 118 Processing helix chain 'F' and resid 118 through 126 Processing helix chain 'F' and resid 128 through 137 removed outlier: 4.079A pdb=" N LEU F 132 " --> pdb=" O ASN F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 151 Processing helix chain 'F' and resid 154 through 164 Processing helix chain 'F' and resid 165 through 169 Processing helix chain 'F' and resid 170 through 185 Processing helix chain 'F' and resid 185 through 194 removed outlier: 3.632A pdb=" N VAL F 189 " --> pdb=" O GLN F 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 118 Processing helix chain 'G' and resid 118 through 126 Processing helix chain 'G' and resid 128 through 137 removed outlier: 3.993A pdb=" N LEU G 132 " --> pdb=" O ASN G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 151 Processing helix chain 'G' and resid 154 through 164 Processing helix chain 'G' and resid 165 through 169 Processing helix chain 'G' and resid 170 through 185 Processing helix chain 'G' and resid 185 through 194 Processing helix chain 'H' and resid 113 through 118 Processing helix chain 'H' and resid 118 through 126 Processing helix chain 'H' and resid 128 through 137 removed outlier: 4.185A pdb=" N LEU H 132 " --> pdb=" O ASN H 128 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 151 Processing helix chain 'H' and resid 154 through 164 Processing helix chain 'H' and resid 165 through 169 Processing helix chain 'H' and resid 170 through 185 Processing helix chain 'H' and resid 185 through 194 Processing helix chain 'I' and resid 113 through 118 Processing helix chain 'I' and resid 118 through 126 Processing helix chain 'I' and resid 128 through 137 removed outlier: 4.226A pdb=" N LEU I 132 " --> pdb=" O ASN I 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 151 Processing helix chain 'I' and resid 154 through 164 Processing helix chain 'I' and resid 165 through 169 Processing helix chain 'I' and resid 170 through 185 Processing helix chain 'I' and resid 185 through 194 Processing helix chain 'J' and resid 113 through 118 Processing helix chain 'J' and resid 118 through 126 Processing helix chain 'J' and resid 128 through 137 removed outlier: 4.001A pdb=" N LEU J 132 " --> pdb=" O ASN J 128 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 151 Processing helix chain 'J' and resid 154 through 164 Processing helix chain 'J' and resid 165 through 169 Processing helix chain 'J' and resid 170 through 185 Processing helix chain 'J' and resid 185 through 194 Processing helix chain 'K' and resid 113 through 118 Processing helix chain 'K' and resid 118 through 126 Processing helix chain 'K' and resid 128 through 137 removed outlier: 4.041A pdb=" N LEU K 132 " --> pdb=" O ASN K 128 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 151 Processing helix chain 'K' and resid 154 through 164 Processing helix chain 'K' and resid 165 through 169 Processing helix chain 'K' and resid 170 through 185 Processing helix chain 'K' and resid 185 through 194 Processing helix chain 'L' and resid 113 through 118 Processing helix chain 'L' and resid 118 through 126 Processing helix chain 'L' and resid 128 through 137 removed outlier: 4.103A pdb=" N LEU L 132 " --> pdb=" O ASN L 128 " (cutoff:3.500A) Processing helix chain 'L' and resid 142 through 151 Processing helix chain 'L' and resid 154 through 164 Processing helix chain 'L' and resid 165 through 169 Processing helix chain 'L' and resid 170 through 185 Processing helix chain 'L' and resid 185 through 194 539 hydrogen bonds defined for protein. 1545 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: 1.22 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2686 1.34 - 1.46: 1457 1.46 - 1.57: 4269 1.57 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 8448 Sorted by residual: bond pdb=" C THR I 166 " pdb=" N PRO I 167 " ideal model delta sigma weight residual 1.335 1.360 -0.025 1.28e-02 6.10e+03 3.88e+00 bond pdb=" CB GLU G 152 " pdb=" CG GLU G 152 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 5.68e-01 bond pdb=" CG GLU F 190 " pdb=" CD GLU F 190 " ideal model delta sigma weight residual 1.516 1.498 0.018 2.50e-02 1.60e+03 5.04e-01 bond pdb=" CB GLU F 152 " pdb=" CG GLU F 152 " ideal model delta sigma weight residual 1.520 1.541 -0.021 3.00e-02 1.11e+03 4.98e-01 bond pdb=" CB ASP G 191 " pdb=" CG ASP G 191 " ideal model delta sigma weight residual 1.516 1.533 -0.017 2.50e-02 1.60e+03 4.56e-01 ... (remaining 8443 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 11300 1.83 - 3.65: 115 3.65 - 5.47: 36 5.47 - 7.30: 9 7.30 - 9.12: 12 Bond angle restraints: 11472 Sorted by residual: angle pdb=" N VAL F 140 " pdb=" CA VAL F 140 " pdb=" C VAL F 140 " ideal model delta sigma weight residual 113.71 109.73 3.98 9.50e-01 1.11e+00 1.76e+01 angle pdb=" N THR F 166 " pdb=" CA THR F 166 " pdb=" C THR F 166 " ideal model delta sigma weight residual 109.81 115.81 -6.00 2.21e+00 2.05e-01 7.36e+00 angle pdb=" CA LEU J 112 " pdb=" CB LEU J 112 " pdb=" CG LEU J 112 " ideal model delta sigma weight residual 116.30 125.42 -9.12 3.50e+00 8.16e-02 6.80e+00 angle pdb=" C PHE H 165 " pdb=" N THR H 166 " pdb=" CA THR H 166 " ideal model delta sigma weight residual 120.06 123.16 -3.10 1.19e+00 7.06e-01 6.77e+00 angle pdb=" N THR G 166 " pdb=" CA THR G 166 " pdb=" C THR G 166 " ideal model delta sigma weight residual 109.81 115.55 -5.74 2.21e+00 2.05e-01 6.74e+00 ... (remaining 11467 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.07: 4504 15.07 - 30.14: 413 30.14 - 45.21: 120 45.21 - 60.28: 34 60.28 - 75.35: 5 Dihedral angle restraints: 5076 sinusoidal: 2088 harmonic: 2988 Sorted by residual: dihedral pdb=" CA ASP F 143 " pdb=" CB ASP F 143 " pdb=" CG ASP F 143 " pdb=" OD1 ASP F 143 " ideal model delta sinusoidal sigma weight residual -30.00 -88.19 58.19 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CA ASP A 143 " pdb=" CB ASP A 143 " pdb=" CG ASP A 143 " pdb=" OD1 ASP A 143 " ideal model delta sinusoidal sigma weight residual -30.00 -86.27 56.27 1 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CA GLN C 185 " pdb=" CB GLN C 185 " pdb=" CG GLN C 185 " pdb=" CD GLN C 185 " ideal model delta sinusoidal sigma weight residual 60.00 119.87 -59.87 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 5073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 907 0.029 - 0.058: 217 0.058 - 0.088: 69 0.088 - 0.117: 68 0.117 - 0.146: 11 Chirality restraints: 1272 Sorted by residual: chirality pdb=" CA PRO B 153 " pdb=" N PRO B 153 " pdb=" C PRO B 153 " pdb=" CB PRO B 153 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.34e-01 chirality pdb=" CA THR F 166 " pdb=" N THR F 166 " pdb=" C THR F 166 " pdb=" CB THR F 166 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA THR I 166 " pdb=" N THR I 166 " pdb=" C THR I 166 " pdb=" CB THR I 166 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 1269 not shown) Planarity restraints: 1452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU F 190 " 0.008 2.00e-02 2.50e+03 1.71e-02 2.91e+00 pdb=" CD GLU F 190 " -0.030 2.00e-02 2.50e+03 pdb=" OE1 GLU F 190 " 0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU F 190 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR E 166 " 0.027 5.00e-02 4.00e+02 4.11e-02 2.70e+00 pdb=" N PRO E 167 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO E 167 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 167 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR J 166 " 0.027 5.00e-02 4.00e+02 4.08e-02 2.67e+00 pdb=" N PRO J 167 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO J 167 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO J 167 " 0.023 5.00e-02 4.00e+02 ... (remaining 1449 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 192 2.71 - 3.26: 7974 3.26 - 3.81: 13589 3.81 - 4.35: 16960 4.35 - 4.90: 29439 Nonbonded interactions: 68154 Sorted by model distance: nonbonded pdb=" O LYS F 161 " pdb=" OG SER F 164 " model vdw 2.165 3.040 nonbonded pdb=" OE2 GLU A 144 " pdb=" NH2 ARG G 160 " model vdw 2.177 3.120 nonbonded pdb=" OE2 GLU G 144 " pdb=" NH2 ARG H 160 " model vdw 2.191 3.120 nonbonded pdb=" NH2 ARG A 160 " pdb=" OE2 GLU J 144 " model vdw 2.214 3.120 nonbonded pdb=" O PHE I 163 " pdb=" OG1 THR I 166 " model vdw 2.219 3.040 ... (remaining 68149 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 1.550 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.980 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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:9.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 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 : 0.003 0.028 8448 Z= 0.117 Angle : 0.609 9.125 11472 Z= 0.306 Chirality : 0.037 0.146 1272 Planarity : 0.004 0.041 1452 Dihedral : 13.309 75.351 3108 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.91 (0.29), residues: 972 helix: 2.63 (0.20), residues: 792 sheet: None (None), residues: 0 loop : -1.52 (0.42), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 182 TYR 0.020 0.001 TYR F 146 PHE 0.018 0.001 PHE F 163 TRP 0.006 0.001 TRP K 131 HIS 0.002 0.000 HIS F 113 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 8448) covalent geometry : angle 0.60918 (11472) hydrogen bonds : bond 0.14555 ( 539) hydrogen bonds : angle 4.17511 ( 1545) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: A 147 GLN cc_start: 0.9062 (mt0) cc_final: 0.8702 (mt0) REVERT: A 179 GLN cc_start: 0.8546 (tp40) cc_final: 0.8201 (tp-100) REVERT: A 190 GLU cc_start: 0.8369 (tp30) cc_final: 0.7914 (tp30) REVERT: B 190 GLU cc_start: 0.8530 (mp0) cc_final: 0.8129 (mp0) REVERT: C 139 LYS cc_start: 0.9450 (mtmm) cc_final: 0.9199 (ptpp) REVERT: C 143 ASP cc_start: 0.8635 (t70) cc_final: 0.8098 (t70) REVERT: C 147 GLN cc_start: 0.9179 (mt0) cc_final: 0.8806 (mt0) REVERT: D 191 ASP cc_start: 0.9211 (t0) cc_final: 0.8988 (t0) REVERT: F 190 GLU cc_start: 0.8452 (mp0) cc_final: 0.8056 (mp0) REVERT: G 128 ASN cc_start: 0.8500 (t0) cc_final: 0.7613 (p0) REVERT: G 190 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7934 (tm-30) REVERT: G 191 ASP cc_start: 0.9328 (t0) cc_final: 0.9124 (t0) REVERT: H 139 LYS cc_start: 0.9464 (mtmm) cc_final: 0.9237 (ptpp) REVERT: H 147 GLN cc_start: 0.9128 (mt0) cc_final: 0.8818 (mt0) REVERT: H 190 GLU cc_start: 0.8377 (tp30) cc_final: 0.8039 (tp30) REVERT: I 128 ASN cc_start: 0.8611 (t0) cc_final: 0.8277 (t0) REVERT: I 190 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7866 (tm-30) REVERT: J 128 ASN cc_start: 0.8505 (t0) cc_final: 0.8010 (t0) REVERT: J 190 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7709 (tm-30) REVERT: J 191 ASP cc_start: 0.9261 (t0) cc_final: 0.8934 (t0) REVERT: K 128 ASN cc_start: 0.8462 (t0) cc_final: 0.7966 (t0) REVERT: L 128 ASN cc_start: 0.8667 (t0) cc_final: 0.7922 (p0) REVERT: L 190 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7866 (tp30) outliers start: 0 outliers final: 0 residues processed: 303 average time/residue: 0.7275 time to fit residues: 230.0106 Evaluate side-chains 268 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.0670 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 overall best weight: 1.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN A 147 GLN B 117 GLN B 128 ASN B 147 GLN B 179 GLN C 117 GLN C 145 GLN C 179 GLN D 128 ASN D 145 GLN D 147 GLN D 179 GLN D 185 GLN E 117 GLN E 147 GLN F 113 HIS F 117 GLN F 128 ASN F 147 GLN F 185 GLN G 147 GLN H 145 GLN I 179 GLN J 117 GLN K 117 GLN K 145 GLN K 147 GLN L 113 HIS L 147 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.057844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 19)----------------| | r_work = 0.2463 r_free = 0.2463 target = 0.049573 restraints weight = 18189.675| |-----------------------------------------------------------------------------| r_work (start): 0.2461 rms_B_bonded: 2.47 r_work: 0.2312 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2186 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9015 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8448 Z= 0.112 Angle : 0.540 6.161 11472 Z= 0.267 Chirality : 0.036 0.124 1272 Planarity : 0.005 0.045 1452 Dihedral : 3.406 10.235 1092 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.46 % Allowed : 10.81 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.92 (0.29), residues: 972 helix: 2.64 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -1.89 (0.41), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 194 TYR 0.016 0.001 TYR F 146 PHE 0.009 0.001 PHE I 114 TRP 0.003 0.000 TRP D 131 HIS 0.001 0.000 HIS J 113 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 8448) covalent geometry : angle 0.53996 (11472) hydrogen bonds : bond 0.03077 ( 539) hydrogen bonds : angle 3.41544 ( 1545) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 281 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 GLU cc_start: 0.8907 (tp30) cc_final: 0.8567 (tp30) REVERT: C 139 LYS cc_start: 0.9546 (mtmm) cc_final: 0.9269 (ptpp) REVERT: C 147 GLN cc_start: 0.9287 (mt0) cc_final: 0.8984 (mt0) REVERT: C 152 GLU cc_start: 0.9271 (mm-30) cc_final: 0.8996 (mm-30) REVERT: D 190 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8555 (pp20) REVERT: D 191 ASP cc_start: 0.9336 (t0) cc_final: 0.9129 (t0) REVERT: G 147 GLN cc_start: 0.9205 (mt0) cc_final: 0.8869 (mt0) REVERT: G 190 GLU cc_start: 0.8842 (tm-30) cc_final: 0.8588 (tm-30) REVERT: G 191 ASP cc_start: 0.9426 (t0) cc_final: 0.9205 (t0) REVERT: H 143 ASP cc_start: 0.8762 (t70) cc_final: 0.8337 (t70) REVERT: H 147 GLN cc_start: 0.9208 (mt0) cc_final: 0.8964 (mt0) REVERT: H 190 GLU cc_start: 0.8949 (tp30) cc_final: 0.8652 (tp30) REVERT: I 128 ASN cc_start: 0.8907 (t0) cc_final: 0.8524 (t0) REVERT: K 128 ASN cc_start: 0.8738 (t0) cc_final: 0.8342 (t0) REVERT: K 130 GLU cc_start: 0.6011 (OUTLIER) cc_final: 0.5721 (tt0) REVERT: L 128 ASN cc_start: 0.8963 (t0) cc_final: 0.8672 (t0) REVERT: L 190 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8450 (tp30) outliers start: 13 outliers final: 6 residues processed: 286 average time/residue: 0.6872 time to fit residues: 205.2252 Evaluate side-chains 275 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 267 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain F residue 157 SER Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain H residue 186 SER Chi-restraints excluded: chain K residue 130 GLU Chi-restraints excluded: chain L residue 186 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 84 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN A 147 GLN B 117 GLN B 147 GLN C 117 GLN D 128 ASN D 147 GLN E 147 GLN E 179 GLN F 117 GLN F 128 ASN F 185 GLN G 128 ASN H 179 GLN J 117 GLN J 128 ASN K 117 GLN K 147 GLN K 179 GLN L 147 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.055793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2415 r_free = 0.2415 target = 0.047207 restraints weight = 18063.257| |-----------------------------------------------------------------------------| r_work (start): 0.2414 rms_B_bonded: 2.42 r_work: 0.2267 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2141 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9038 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8448 Z= 0.137 Angle : 0.566 5.562 11472 Z= 0.280 Chirality : 0.037 0.119 1272 Planarity : 0.005 0.047 1452 Dihedral : 3.386 9.987 1092 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.14 % Allowed : 12.95 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.94 (0.29), residues: 972 helix: 2.67 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -1.94 (0.42), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 194 TYR 0.013 0.001 TYR F 146 PHE 0.009 0.001 PHE I 114 TRP 0.003 0.000 TRP K 131 HIS 0.002 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 8448) covalent geometry : angle 0.56569 (11472) hydrogen bonds : bond 0.03204 ( 539) hydrogen bonds : angle 3.27899 ( 1545) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 275 time to evaluate : 0.359 Fit side-chains REVERT: A 147 GLN cc_start: 0.9163 (mt0) cc_final: 0.8899 (mt0) REVERT: A 190 GLU cc_start: 0.8951 (tp30) cc_final: 0.8598 (tp30) REVERT: B 183 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8251 (mp0) REVERT: B 191 ASP cc_start: 0.9366 (t0) cc_final: 0.9088 (t0) REVERT: C 143 ASP cc_start: 0.8930 (t70) cc_final: 0.8572 (t70) REVERT: C 147 GLN cc_start: 0.9289 (mt0) cc_final: 0.9023 (mt0) REVERT: C 190 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8641 (mm-30) REVERT: D 190 GLU cc_start: 0.8800 (pp20) cc_final: 0.8557 (pp20) REVERT: G 147 GLN cc_start: 0.9203 (mt0) cc_final: 0.8914 (mt0) REVERT: G 190 GLU cc_start: 0.8906 (tm-30) cc_final: 0.8671 (tm-30) REVERT: G 191 ASP cc_start: 0.9442 (t0) cc_final: 0.9229 (t0) REVERT: H 143 ASP cc_start: 0.8800 (t70) cc_final: 0.8413 (t70) REVERT: H 190 GLU cc_start: 0.8961 (tp30) cc_final: 0.8683 (tp30) REVERT: I 193 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8415 (mt-10) REVERT: K 130 GLU cc_start: 0.6355 (OUTLIER) cc_final: 0.5864 (tm-30) REVERT: L 190 GLU cc_start: 0.8842 (tm-30) cc_final: 0.8501 (tp30) outliers start: 19 outliers final: 6 residues processed: 283 average time/residue: 0.6406 time to fit residues: 189.8901 Evaluate side-chains 275 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 268 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain F residue 157 SER Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain K residue 130 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 78 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 92 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 117 GLN B 128 ASN B 147 GLN C 117 GLN C 179 GLN C 185 GLN D 128 ASN D 147 GLN D 185 GLN E 147 GLN F 117 GLN G 117 GLN G 185 GLN H 128 ASN I 185 GLN J 117 GLN J 128 ASN K 117 GLN K 147 GLN L 128 ASN L 147 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.054286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2379 r_free = 0.2379 target = 0.045980 restraints weight = 18726.292| |-----------------------------------------------------------------------------| r_work (start): 0.2380 rms_B_bonded: 2.50 r_work: 0.2232 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2108 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9077 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8448 Z= 0.175 Angle : 0.577 10.044 11472 Z= 0.286 Chirality : 0.038 0.124 1272 Planarity : 0.006 0.048 1452 Dihedral : 3.565 10.672 1092 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.25 % Allowed : 12.61 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.85 (0.29), residues: 972 helix: 2.63 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -2.11 (0.42), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 194 TYR 0.011 0.001 TYR F 146 PHE 0.008 0.001 PHE I 114 TRP 0.002 0.001 TRP A 171 HIS 0.002 0.001 HIS J 113 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 8448) covalent geometry : angle 0.57746 (11472) hydrogen bonds : bond 0.03499 ( 539) hydrogen bonds : angle 3.34469 ( 1545) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 270 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 147 GLN cc_start: 0.9181 (mt0) cc_final: 0.8881 (mt0) REVERT: A 190 GLU cc_start: 0.8905 (tp30) cc_final: 0.8591 (tp30) REVERT: B 191 ASP cc_start: 0.9384 (t0) cc_final: 0.9116 (t0) REVERT: C 147 GLN cc_start: 0.9299 (mt0) cc_final: 0.9010 (mt0) REVERT: C 152 GLU cc_start: 0.9285 (mm-30) cc_final: 0.9063 (mm-30) REVERT: C 190 GLU cc_start: 0.8960 (mm-30) cc_final: 0.8750 (mm-30) REVERT: D 190 GLU cc_start: 0.8857 (pp20) cc_final: 0.8651 (pp20) REVERT: D 191 ASP cc_start: 0.9380 (t0) cc_final: 0.9141 (t0) REVERT: F 191 ASP cc_start: 0.9375 (t0) cc_final: 0.9104 (t0) REVERT: G 147 GLN cc_start: 0.9197 (mt0) cc_final: 0.8834 (mt0) REVERT: G 190 GLU cc_start: 0.8953 (tm-30) cc_final: 0.8668 (tp30) REVERT: H 147 GLN cc_start: 0.9207 (mt0) cc_final: 0.9007 (mt0) REVERT: H 190 GLU cc_start: 0.8988 (tp30) cc_final: 0.8734 (tp30) REVERT: K 130 GLU cc_start: 0.6546 (OUTLIER) cc_final: 0.6178 (tm-30) REVERT: L 190 GLU cc_start: 0.8869 (tm-30) cc_final: 0.8526 (tp30) outliers start: 20 outliers final: 7 residues processed: 285 average time/residue: 0.6339 time to fit residues: 189.2917 Evaluate side-chains 274 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 266 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 194 ARG Chi-restraints excluded: chain F residue 157 SER Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain H residue 186 SER Chi-restraints excluded: chain K residue 130 GLU Chi-restraints excluded: chain L residue 186 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 70 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 86 optimal weight: 7.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 117 GLN B 147 GLN C 117 GLN D 128 ASN D 147 GLN E 117 GLN E 147 GLN E 179 GLN F 117 GLN G 117 GLN G 185 GLN H 128 ASN H 179 GLN I 185 GLN J 117 GLN K 128 ASN K 147 GLN K 179 GLN L 128 ASN L 147 GLN L 179 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.057287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2454 r_free = 0.2454 target = 0.048785 restraints weight = 18374.199| |-----------------------------------------------------------------------------| r_work (start): 0.2455 rms_B_bonded: 2.46 r_work: 0.2308 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2184 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9030 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8448 Z= 0.109 Angle : 0.584 8.155 11472 Z= 0.282 Chirality : 0.036 0.117 1272 Planarity : 0.005 0.049 1452 Dihedral : 3.419 28.622 1092 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.80 % Allowed : 14.75 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.89 (0.29), residues: 972 helix: 2.65 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -2.01 (0.43), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG F 194 TYR 0.011 0.001 TYR F 146 PHE 0.009 0.001 PHE I 114 TRP 0.002 0.000 TRP K 131 HIS 0.001 0.000 HIS D 113 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 8448) covalent geometry : angle 0.58373 (11472) hydrogen bonds : bond 0.02645 ( 539) hydrogen bonds : angle 3.20937 ( 1545) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 274 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 GLU cc_start: 0.8893 (tp30) cc_final: 0.8494 (tp30) REVERT: B 191 ASP cc_start: 0.9371 (t0) cc_final: 0.9084 (t0) REVERT: C 143 ASP cc_start: 0.8874 (t70) cc_final: 0.8501 (t70) REVERT: C 147 GLN cc_start: 0.9281 (mt0) cc_final: 0.8980 (mt0) REVERT: C 190 GLU cc_start: 0.8981 (mm-30) cc_final: 0.8709 (mm-30) REVERT: G 147 GLN cc_start: 0.9204 (mt0) cc_final: 0.8830 (mt0) REVERT: G 190 GLU cc_start: 0.8916 (tm-30) cc_final: 0.8656 (tp30) REVERT: G 191 ASP cc_start: 0.9398 (t0) cc_final: 0.9098 (t0) REVERT: H 147 GLN cc_start: 0.9243 (mt0) cc_final: 0.8955 (mt0) REVERT: H 190 GLU cc_start: 0.8985 (tp30) cc_final: 0.8740 (tp30) REVERT: K 130 GLU cc_start: 0.6322 (OUTLIER) cc_final: 0.5983 (tm-30) REVERT: L 190 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8523 (tp30) outliers start: 16 outliers final: 6 residues processed: 282 average time/residue: 0.5790 time to fit residues: 171.0134 Evaluate side-chains 274 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 267 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain F residue 157 SER Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain H residue 186 SER Chi-restraints excluded: chain K residue 130 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 93 optimal weight: 0.0980 chunk 14 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 75 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN A 147 GLN A 185 GLN B 117 GLN B 147 GLN C 117 GLN C 179 GLN D 147 GLN E 117 GLN E 147 GLN F 117 GLN G 117 GLN G 185 GLN H 128 ASN I 185 GLN J 117 GLN K 147 GLN L 147 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.059930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2544 r_free = 0.2544 target = 0.051275 restraints weight = 18085.287| |-----------------------------------------------------------------------------| r_work (start): 0.2542 rms_B_bonded: 2.48 r_work: 0.2405 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2284 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9134 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8448 Z= 0.104 Angle : 0.541 6.802 11472 Z= 0.266 Chirality : 0.035 0.118 1272 Planarity : 0.006 0.052 1452 Dihedral : 3.305 21.884 1092 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.80 % Allowed : 15.20 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.93 (0.29), residues: 972 helix: 2.66 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -1.93 (0.44), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG I 194 TYR 0.010 0.001 TYR F 146 PHE 0.009 0.001 PHE I 114 TRP 0.002 0.000 TRP E 171 HIS 0.001 0.000 HIS B 113 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 8448) covalent geometry : angle 0.54095 (11472) hydrogen bonds : bond 0.02493 ( 539) hydrogen bonds : angle 3.15724 ( 1545) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 270 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: A 147 GLN cc_start: 0.9239 (mt0) cc_final: 0.8973 (mt0) REVERT: A 190 GLU cc_start: 0.8944 (tp30) cc_final: 0.8642 (tp30) REVERT: B 160 ARG cc_start: 0.9211 (mtm-85) cc_final: 0.8904 (mtt90) REVERT: B 191 ASP cc_start: 0.9390 (t0) cc_final: 0.9063 (t0) REVERT: C 139 LYS cc_start: 0.9606 (mtmm) cc_final: 0.9318 (mttp) REVERT: C 147 GLN cc_start: 0.9342 (mt0) cc_final: 0.9052 (mt0) REVERT: C 190 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8787 (mm-30) REVERT: G 147 GLN cc_start: 0.9276 (mt0) cc_final: 0.8874 (mt0) REVERT: G 190 GLU cc_start: 0.8967 (tm-30) cc_final: 0.8699 (tp30) REVERT: H 147 GLN cc_start: 0.9319 (mt0) cc_final: 0.9058 (mt0) REVERT: H 190 GLU cc_start: 0.8954 (tp30) cc_final: 0.8668 (tp30) REVERT: K 130 GLU cc_start: 0.6524 (OUTLIER) cc_final: 0.6161 (tm-30) REVERT: L 190 GLU cc_start: 0.8888 (tm-30) cc_final: 0.8542 (tp30) outliers start: 16 outliers final: 8 residues processed: 278 average time/residue: 0.6421 time to fit residues: 186.5794 Evaluate side-chains 275 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 266 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain F residue 157 SER Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain H residue 186 SER Chi-restraints excluded: chain K residue 130 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 16 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN A 185 GLN B 147 GLN C 117 GLN D 147 GLN E 147 GLN E 179 GLN F 117 GLN G 117 GLN H 117 GLN H 179 GLN H 185 GLN I 185 GLN J 117 GLN K 117 GLN K 147 GLN K 179 GLN L 147 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.057547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2469 r_free = 0.2469 target = 0.049223 restraints weight = 18571.727| |-----------------------------------------------------------------------------| r_work (start): 0.2464 rms_B_bonded: 2.45 r_work: 0.2319 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2196 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9045 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8448 Z= 0.120 Angle : 0.583 7.022 11472 Z= 0.281 Chirality : 0.036 0.119 1272 Planarity : 0.006 0.066 1452 Dihedral : 3.283 18.128 1092 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.80 % Allowed : 15.77 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.95 (0.29), residues: 972 helix: 2.67 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -1.91 (0.44), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 194 TYR 0.010 0.001 TYR F 146 PHE 0.009 0.001 PHE I 114 TRP 0.002 0.000 TRP I 171 HIS 0.001 0.000 HIS H 113 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 8448) covalent geometry : angle 0.58280 (11472) hydrogen bonds : bond 0.02593 ( 539) hydrogen bonds : angle 3.16249 ( 1545) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 271 time to evaluate : 0.204 Fit side-chains revert: symmetry clash REVERT: A 147 GLN cc_start: 0.9204 (mt0) cc_final: 0.8933 (mt0) REVERT: B 160 ARG cc_start: 0.9119 (mtm-85) cc_final: 0.8864 (mtt90) REVERT: B 191 ASP cc_start: 0.9361 (t0) cc_final: 0.9032 (t0) REVERT: C 147 GLN cc_start: 0.9293 (mt0) cc_final: 0.8988 (mt0) REVERT: C 190 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8733 (mm-30) REVERT: G 147 GLN cc_start: 0.9229 (mt0) cc_final: 0.8921 (mt0) REVERT: G 190 GLU cc_start: 0.8922 (tm-30) cc_final: 0.8657 (tp30) REVERT: G 191 ASP cc_start: 0.9372 (t0) cc_final: 0.9110 (t0) REVERT: H 147 GLN cc_start: 0.9297 (mt0) cc_final: 0.9001 (mt0) REVERT: H 190 GLU cc_start: 0.8965 (tp30) cc_final: 0.8683 (tp30) REVERT: K 130 GLU cc_start: 0.6421 (OUTLIER) cc_final: 0.6044 (tm-30) REVERT: L 190 GLU cc_start: 0.8861 (tm-30) cc_final: 0.8523 (tp30) outliers start: 16 outliers final: 8 residues processed: 280 average time/residue: 0.5917 time to fit residues: 173.4016 Evaluate side-chains 276 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 267 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain F residue 157 SER Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain H residue 186 SER Chi-restraints excluded: chain K residue 130 GLU Chi-restraints excluded: chain L residue 186 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 73 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 27 optimal weight: 0.0970 chunk 84 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 86 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN A 185 GLN B 147 GLN C 117 GLN D 147 GLN E 147 GLN F 117 GLN G 117 GLN H 117 GLN H 128 ASN H 185 GLN I 128 ASN I 147 GLN I 185 GLN J 117 GLN K 117 GLN K 128 ASN K 147 GLN L 147 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.060254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.051444 restraints weight = 18151.590| |-----------------------------------------------------------------------------| r_work (start): 0.2570 rms_B_bonded: 2.49 r_work: 0.2433 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2310 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9123 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8448 Z= 0.107 Angle : 0.569 8.459 11472 Z= 0.277 Chirality : 0.035 0.119 1272 Planarity : 0.006 0.067 1452 Dihedral : 3.205 14.488 1092 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.13 % Allowed : 16.67 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.00 (0.29), residues: 972 helix: 2.70 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -1.85 (0.45), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 194 TYR 0.009 0.001 TYR F 146 PHE 0.009 0.001 PHE I 114 TRP 0.002 0.000 TRP F 131 HIS 0.002 0.000 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 8448) covalent geometry : angle 0.56859 (11472) hydrogen bonds : bond 0.02372 ( 539) hydrogen bonds : angle 3.14812 ( 1545) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 270 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: A 147 GLN cc_start: 0.9263 (mt0) cc_final: 0.8941 (mt0) REVERT: B 160 ARG cc_start: 0.9198 (mtm-85) cc_final: 0.8910 (mtt90) REVERT: B 191 ASP cc_start: 0.9372 (t0) cc_final: 0.9027 (t0) REVERT: C 147 GLN cc_start: 0.9335 (mt0) cc_final: 0.9044 (mt0) REVERT: C 190 GLU cc_start: 0.9041 (mm-30) cc_final: 0.8782 (mm-30) REVERT: G 147 GLN cc_start: 0.9275 (mt0) cc_final: 0.8943 (mt0) REVERT: G 190 GLU cc_start: 0.8983 (tm-30) cc_final: 0.8700 (tp30) REVERT: H 143 ASP cc_start: 0.8990 (t70) cc_final: 0.8708 (t70) REVERT: H 147 GLN cc_start: 0.9316 (mt0) cc_final: 0.9024 (mt0) REVERT: H 190 GLU cc_start: 0.8945 (tp30) cc_final: 0.8675 (tp30) REVERT: K 130 GLU cc_start: 0.6492 (OUTLIER) cc_final: 0.6073 (tm-30) REVERT: L 190 GLU cc_start: 0.8912 (tm-30) cc_final: 0.8565 (tp30) outliers start: 10 outliers final: 4 residues processed: 277 average time/residue: 0.5956 time to fit residues: 172.6920 Evaluate side-chains 267 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 262 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain F residue 157 SER Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain K residue 130 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 9 optimal weight: 0.0980 chunk 95 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN B 147 GLN C 117 GLN D 147 GLN E 147 GLN F 117 GLN G 117 GLN H 117 GLN H 179 GLN I 147 GLN I 185 GLN J 117 GLN J 147 GLN K 117 GLN K 128 ASN K 147 GLN K 179 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.057664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2473 r_free = 0.2473 target = 0.049372 restraints weight = 18612.585| |-----------------------------------------------------------------------------| r_work (start): 0.2465 rms_B_bonded: 2.45 r_work: 0.2319 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2197 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9041 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8448 Z= 0.127 Angle : 0.613 8.679 11472 Z= 0.295 Chirality : 0.036 0.120 1272 Planarity : 0.005 0.056 1452 Dihedral : 3.220 13.537 1092 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.01 % Allowed : 16.89 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.99 (0.29), residues: 972 helix: 2.69 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -1.87 (0.45), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG F 194 TYR 0.013 0.001 TYR A 146 PHE 0.009 0.001 PHE I 114 TRP 0.002 0.000 TRP F 171 HIS 0.001 0.000 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 8448) covalent geometry : angle 0.61269 (11472) hydrogen bonds : bond 0.02590 ( 539) hydrogen bonds : angle 3.16441 ( 1545) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 265 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: B 160 ARG cc_start: 0.9123 (mtm-85) cc_final: 0.8868 (mtt90) REVERT: B 191 ASP cc_start: 0.9347 (t0) cc_final: 0.9020 (t0) REVERT: C 143 ASP cc_start: 0.8921 (t70) cc_final: 0.8526 (t70) REVERT: C 147 GLN cc_start: 0.9297 (mt0) cc_final: 0.8993 (mt0) REVERT: C 190 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8732 (mm-30) REVERT: G 147 GLN cc_start: 0.9236 (mt0) cc_final: 0.8888 (mt0) REVERT: G 190 GLU cc_start: 0.8930 (tm-30) cc_final: 0.8655 (tp30) REVERT: G 191 ASP cc_start: 0.9386 (t0) cc_final: 0.9121 (t0) REVERT: H 143 ASP cc_start: 0.8942 (t70) cc_final: 0.8693 (t70) REVERT: H 147 GLN cc_start: 0.9283 (mt0) cc_final: 0.9014 (mt0) REVERT: H 190 GLU cc_start: 0.8947 (tp30) cc_final: 0.8672 (tp30) REVERT: K 130 GLU cc_start: 0.6388 (OUTLIER) cc_final: 0.5961 (tm-30) REVERT: L 190 GLU cc_start: 0.8871 (tm-30) cc_final: 0.8527 (tp30) outliers start: 9 outliers final: 4 residues processed: 269 average time/residue: 0.6102 time to fit residues: 171.5173 Evaluate side-chains 268 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 263 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain F residue 157 SER Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain H residue 186 SER Chi-restraints excluded: chain K residue 130 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 85 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 72 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 38 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN A 147 GLN B 147 GLN C 117 GLN D 147 GLN E 147 GLN E 179 GLN F 117 GLN G 117 GLN G 185 GLN H 117 GLN I 147 GLN I 185 GLN J 117 GLN K 117 GLN K 128 ASN K 147 GLN L 147 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.058788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.050191 restraints weight = 18006.585| |-----------------------------------------------------------------------------| r_work (start): 0.2526 rms_B_bonded: 2.48 r_work: 0.2388 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2267 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9152 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8448 Z= 0.130 Angle : 0.605 8.737 11472 Z= 0.296 Chirality : 0.036 0.122 1272 Planarity : 0.006 0.069 1452 Dihedral : 3.344 12.642 1092 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.01 % Allowed : 17.23 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.92 (0.29), residues: 972 helix: 2.65 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -1.92 (0.45), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG I 194 TYR 0.012 0.001 TYR A 146 PHE 0.009 0.001 PHE I 114 TRP 0.002 0.000 TRP G 169 HIS 0.001 0.000 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 8448) covalent geometry : angle 0.60498 (11472) hydrogen bonds : bond 0.02757 ( 539) hydrogen bonds : angle 3.20127 ( 1545) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 262 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 GLN cc_start: 0.9225 (mt0) cc_final: 0.9004 (mt0) REVERT: B 160 ARG cc_start: 0.9236 (mtm-85) cc_final: 0.8948 (mtt90) REVERT: B 191 ASP cc_start: 0.9402 (t0) cc_final: 0.9051 (t0) REVERT: C 147 GLN cc_start: 0.9354 (mt0) cc_final: 0.9032 (mt0) REVERT: C 190 GLU cc_start: 0.9025 (mm-30) cc_final: 0.8782 (mm-30) REVERT: G 147 GLN cc_start: 0.9312 (mt0) cc_final: 0.8963 (mt0) REVERT: G 190 GLU cc_start: 0.8987 (tm-30) cc_final: 0.8701 (tp30) REVERT: H 143 ASP cc_start: 0.8990 (t70) cc_final: 0.8731 (t70) REVERT: H 147 GLN cc_start: 0.9328 (mt0) cc_final: 0.9054 (mt0) REVERT: H 190 GLU cc_start: 0.8938 (tp30) cc_final: 0.8651 (tp30) REVERT: K 130 GLU cc_start: 0.6646 (OUTLIER) cc_final: 0.6201 (tm-30) REVERT: L 190 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8553 (tp30) outliers start: 9 outliers final: 4 residues processed: 269 average time/residue: 0.6107 time to fit residues: 172.0157 Evaluate side-chains 267 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 262 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain F residue 157 SER Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain H residue 186 SER Chi-restraints excluded: chain K residue 130 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 92 optimal weight: 0.4980 chunk 18 optimal weight: 7.9990 chunk 1 optimal weight: 0.1980 chunk 77 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 chunk 88 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN B 147 GLN C 117 GLN D 147 GLN E 147 GLN E 179 GLN F 117 GLN G 117 GLN G 185 GLN H 117 GLN H 179 GLN I 147 GLN I 185 GLN J 117 GLN K 117 GLN K 128 ASN K 147 GLN K 179 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.059067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2496 r_free = 0.2496 target = 0.050465 restraints weight = 18295.494| |-----------------------------------------------------------------------------| r_work (start): 0.2492 rms_B_bonded: 2.49 r_work: 0.2346 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2224 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9016 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8448 Z= 0.111 Angle : 0.603 8.401 11472 Z= 0.290 Chirality : 0.035 0.119 1272 Planarity : 0.006 0.059 1452 Dihedral : 3.197 10.161 1092 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.68 % Allowed : 17.12 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.90 (0.29), residues: 972 helix: 2.63 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -1.89 (0.46), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 194 TYR 0.012 0.001 TYR A 146 PHE 0.009 0.001 PHE I 114 TRP 0.002 0.000 TRP K 131 HIS 0.002 0.000 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8448) covalent geometry : angle 0.60267 (11472) hydrogen bonds : bond 0.02380 ( 539) hydrogen bonds : angle 3.17296 ( 1545) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3650.49 seconds wall clock time: 62 minutes 34.00 seconds (3754.00 seconds total)