Starting phenix.real_space_refine on Wed Mar 4 20:16:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7njy_12427/03_2026/7njy_12427.cif Found real_map, /net/cci-nas-00/data/ceres_data/7njy_12427/03_2026/7njy_12427.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7njy_12427/03_2026/7njy_12427.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7njy_12427/03_2026/7njy_12427.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7njy_12427/03_2026/7njy_12427.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7njy_12427/03_2026/7njy_12427.map" } resolution = 2.94 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= 0.000 sd= 0.001 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: 5 Type Number sf(0) Gaussians S 28 5.16 5 C 5346 2.51 5 N 1316 2.21 5 O 1399 1.98 5 H 8337 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16426 Number of models: 1 Model: "" Number of chains: 12 Chain: "L" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "M" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "N" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "O" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "P" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "Q" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "R" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "S" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "T" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "a" Number of atoms: 3767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 3767 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 10, 'TRANS': 227} Chain: "b" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 979 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "d" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 952 Classifications: {'peptide': 61} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 58} Time building chain proxies: 3.17, per 1000 atoms: 0.19 Number of scatterers: 16426 At special positions: 0 Unit cell: (94.62, 78.85, 116.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 O 1399 8.00 N 1316 7.00 C 5346 6.00 H 8337 1.00 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: 1.47 Conformation dependent library (CDL) restraints added in 567.9 milliseconds 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1904 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 2 sheets defined 87.9% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'L' and resid 4 through 46 removed outlier: 3.742A pdb=" N ILE L 8 " --> pdb=" O ASP L 4 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 81 removed outlier: 3.501A pdb=" N PHE L 54 " --> pdb=" O GLN L 50 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N THR L 55 " --> pdb=" O GLY L 51 " (cutoff:3.500A) Proline residue: L 56 - end of helix removed outlier: 4.146A pdb=" N ALA L 67 " --> pdb=" O LEU L 63 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TYR L 68 " --> pdb=" O VAL L 64 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 46 Processing helix chain 'M' and resid 49 through 80 removed outlier: 4.588A pdb=" N THR M 55 " --> pdb=" O GLY M 51 " (cutoff:3.500A) Proline residue: M 56 - end of helix removed outlier: 3.629A pdb=" N TYR M 68 " --> pdb=" O VAL M 64 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 46 removed outlier: 3.630A pdb=" N ILE N 8 " --> pdb=" O ASP N 4 " (cutoff:3.500A) Processing helix chain 'N' and resid 49 through 80 removed outlier: 4.010A pdb=" N THR N 55 " --> pdb=" O GLY N 51 " (cutoff:3.500A) Proline residue: N 56 - end of helix removed outlier: 3.694A pdb=" N ALA N 67 " --> pdb=" O LEU N 63 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR N 68 " --> pdb=" O VAL N 64 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 46 Processing helix chain 'O' and resid 49 through 80 removed outlier: 4.415A pdb=" N THR O 55 " --> pdb=" O GLY O 51 " (cutoff:3.500A) Proline residue: O 56 - end of helix removed outlier: 4.097A pdb=" N ALA O 67 " --> pdb=" O LEU O 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 46 removed outlier: 3.651A pdb=" N ILE P 8 " --> pdb=" O ASP P 4 " (cutoff:3.500A) Processing helix chain 'P' and resid 49 through 81 removed outlier: 3.834A pdb=" N PHE P 54 " --> pdb=" O GLN P 50 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N THR P 55 " --> pdb=" O GLY P 51 " (cutoff:3.500A) Proline residue: P 56 - end of helix removed outlier: 3.677A pdb=" N ALA P 67 " --> pdb=" O LEU P 63 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR P 68 " --> pdb=" O VAL P 64 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 46 removed outlier: 3.592A pdb=" N ILE Q 8 " --> pdb=" O ASP Q 4 " (cutoff:3.500A) Processing helix chain 'Q' and resid 49 through 80 removed outlier: 3.854A pdb=" N THR Q 55 " --> pdb=" O GLY Q 51 " (cutoff:3.500A) Proline residue: Q 56 - end of helix Processing helix chain 'R' and resid 4 through 46 removed outlier: 3.658A pdb=" N ILE R 8 " --> pdb=" O ASP R 4 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 81 removed outlier: 4.403A pdb=" N THR R 55 " --> pdb=" O GLY R 51 " (cutoff:3.500A) Proline residue: R 56 - end of helix Processing helix chain 'S' and resid 4 through 46 Processing helix chain 'S' and resid 48 through 81 removed outlier: 4.602A pdb=" N ARG S 52 " --> pdb=" O GLU S 48 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N THR S 55 " --> pdb=" O GLY S 51 " (cutoff:3.500A) Proline residue: S 56 - end of helix removed outlier: 3.536A pdb=" N ALA S 67 " --> pdb=" O LEU S 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 46 removed outlier: 3.583A pdb=" N ILE T 8 " --> pdb=" O ASP T 4 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 81 removed outlier: 4.039A pdb=" N THR T 55 " --> pdb=" O GLY T 51 " (cutoff:3.500A) Proline residue: T 56 - end of helix removed outlier: 3.930A pdb=" N ALA T 67 " --> pdb=" O LEU T 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 28 through 51 Processing helix chain 'a' and resid 60 through 81 Processing helix chain 'a' and resid 88 through 106 Processing helix chain 'a' and resid 107 through 109 No H-bonds generated for 'chain 'a' and resid 107 through 109' Processing helix chain 'a' and resid 126 through 129 Processing helix chain 'a' and resid 130 through 154 removed outlier: 3.585A pdb=" N VAL a 134 " --> pdb=" O ASP a 130 " (cutoff:3.500A) Processing helix chain 'a' and resid 156 through 165 Processing helix chain 'a' and resid 167 through 169 No H-bonds generated for 'chain 'a' and resid 167 through 169' Processing helix chain 'a' and resid 170 through 204 Proline residue: a 182 - end of helix removed outlier: 3.667A pdb=" N LEU a 189 " --> pdb=" O LEU a 185 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLY a 196 " --> pdb=" O ASN a 192 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA a 201 " --> pdb=" O GLY a 197 " (cutoff:3.500A) Processing helix chain 'a' and resid 207 through 245 removed outlier: 5.656A pdb=" N PHE a 213 " --> pdb=" O TYR a 209 " (cutoff:3.500A) Proline residue: a 214 - end of helix Processing helix chain 'b' and resid 29 through 49 removed outlier: 3.644A pdb=" N ALA b 33 " --> pdb=" O GLY b 29 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL b 49 " --> pdb=" O ILE b 45 " (cutoff:3.500A) Processing helix chain 'b' and resid 49 through 84 removed outlier: 3.736A pdb=" N GLN b 82 " --> pdb=" O VAL b 78 " (cutoff:3.500A) Processing helix chain 'd' and resid 2 through 22 Processing helix chain 'd' and resid 22 through 61 Processing sheet with id=AA1, first strand: chain 'a' and resid 20 through 22 Processing sheet with id=AA2, first strand: chain 'a' and resid 112 through 114 795 hydrogen bonds defined for protein. 2376 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: 4.00 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8336 1.03 - 1.22: 1 1.22 - 1.42: 3359 1.42 - 1.61: 4843 1.61 - 1.81: 55 Bond restraints: 16594 Sorted by residual: bond pdb=" CB MET O 21 " pdb=" CG MET O 21 " ideal model delta sigma weight residual 1.520 1.485 0.035 3.00e-02 1.11e+03 1.39e+00 bond pdb=" C THR a 220 " pdb=" O THR a 220 " ideal model delta sigma weight residual 1.236 1.247 -0.010 1.15e-02 7.56e+03 7.90e-01 bond pdb=" CB MET S 21 " pdb=" CG MET S 21 " ideal model delta sigma weight residual 1.520 1.499 0.021 3.00e-02 1.11e+03 4.74e-01 bond pdb=" N PHE a 213 " pdb=" CA PHE a 213 " ideal model delta sigma weight residual 1.463 1.468 -0.005 6.90e-03 2.10e+04 4.29e-01 bond pdb=" CG LEU Q 72 " pdb=" CD2 LEU Q 72 " ideal model delta sigma weight residual 1.521 1.500 0.021 3.30e-02 9.18e+02 4.07e-01 ... (remaining 16589 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 28236 1.03 - 2.07: 1776 2.07 - 3.10: 52 3.10 - 4.14: 43 4.14 - 5.17: 9 Bond angle restraints: 30116 Sorted by residual: angle pdb=" C CYS a 144 " pdb=" N TYR a 145 " pdb=" CA TYR a 145 " ideal model delta sigma weight residual 121.14 116.45 4.69 1.75e+00 3.27e-01 7.20e+00 angle pdb=" CA TYR a 145 " pdb=" CB TYR a 145 " pdb=" CG TYR a 145 " ideal model delta sigma weight residual 113.90 118.39 -4.49 1.80e+00 3.09e-01 6.24e+00 angle pdb=" N TYR a 145 " pdb=" CA TYR a 145 " pdb=" CB TYR a 145 " ideal model delta sigma weight residual 110.40 114.44 -4.04 1.63e+00 3.76e-01 6.14e+00 angle pdb=" CA TRP a 218 " pdb=" CB TRP a 218 " pdb=" CG TRP a 218 " ideal model delta sigma weight residual 113.60 110.25 3.35 1.90e+00 2.77e-01 3.11e+00 angle pdb=" C TYR a 145 " pdb=" N HIS a 146 " pdb=" CA HIS a 146 " ideal model delta sigma weight residual 120.29 117.92 2.37 1.42e+00 4.96e-01 2.79e+00 ... (remaining 30111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 6790 17.56 - 35.12: 578 35.12 - 52.68: 264 52.68 - 70.24: 122 70.24 - 87.80: 5 Dihedral angle restraints: 7759 sinusoidal: 4150 harmonic: 3609 Sorted by residual: dihedral pdb=" CB GLU b 59 " pdb=" CG GLU b 59 " pdb=" CD GLU b 59 " pdb=" OE1 GLU b 59 " ideal model delta sinusoidal sigma weight residual 0.00 87.80 -87.80 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CG ARG a 188 " pdb=" CD ARG a 188 " pdb=" NE ARG a 188 " pdb=" CZ ARG a 188 " ideal model delta sinusoidal sigma weight residual 180.00 -136.53 -43.47 2 1.50e+01 4.44e-03 1.01e+01 dihedral pdb=" CB GLU T 65 " pdb=" CG GLU T 65 " pdb=" CD GLU T 65 " pdb=" OE1 GLU T 65 " ideal model delta sinusoidal sigma weight residual 0.00 -84.72 84.72 1 3.00e+01 1.11e-03 9.69e+00 ... (remaining 7756 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 826 0.027 - 0.053: 254 0.053 - 0.080: 176 0.080 - 0.107: 59 0.107 - 0.134: 7 Chirality restraints: 1322 Sorted by residual: chirality pdb=" CA TYR a 145 " pdb=" N TYR a 145 " pdb=" C TYR a 145 " pdb=" CB TYR a 145 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CA PRO L 47 " pdb=" N PRO L 47 " pdb=" C PRO L 47 " pdb=" CB PRO L 47 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.75e-01 chirality pdb=" CA VAL a 58 " pdb=" N VAL a 58 " pdb=" C VAL a 58 " pdb=" CB VAL a 58 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.43e-01 ... (remaining 1319 not shown) Planarity restraints: 2495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY a 191 " -0.007 2.00e-02 2.50e+03 1.41e-02 1.99e+00 pdb=" C GLY a 191 " 0.024 2.00e-02 2.50e+03 pdb=" O GLY a 191 " -0.009 2.00e-02 2.50e+03 pdb=" N ASN a 192 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG a 188 " -0.007 2.00e-02 2.50e+03 1.41e-02 1.99e+00 pdb=" C ARG a 188 " 0.024 2.00e-02 2.50e+03 pdb=" O ARG a 188 " -0.009 2.00e-02 2.50e+03 pdb=" N LEU a 189 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE P 70 " 0.007 2.00e-02 2.50e+03 1.36e-02 1.84e+00 pdb=" C ILE P 70 " -0.023 2.00e-02 2.50e+03 pdb=" O ILE P 70 " 0.009 2.00e-02 2.50e+03 pdb=" N ASN P 71 " 0.008 2.00e-02 2.50e+03 ... (remaining 2492 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 968 2.21 - 2.80: 34814 2.80 - 3.40: 49880 3.40 - 4.00: 65112 4.00 - 4.60: 101376 Nonbonded interactions: 252150 Sorted by model distance: nonbonded pdb=" OD1 ASN a 132 " pdb=" H ASN b 28 " model vdw 1.608 2.450 nonbonded pdb=" OE1 GLN R 46 " pdb="HH22 ARG R 52 " model vdw 1.630 2.450 nonbonded pdb=" OD1 ASN b 28 " pdb=" H GLY b 29 " model vdw 1.655 2.450 nonbonded pdb=" O PHE T 78 " pdb=" HG1 THR T 82 " model vdw 1.670 2.450 nonbonded pdb="HE22 GLN S 86 " pdb=" OD2 ASP T 4 " model vdw 1.694 2.450 ... (remaining 252145 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 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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: 12.050 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: 0.100 Extract box with map and model: 0.280 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 17.150 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 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 0.035 8257 Z= 0.145 Angle : 0.471 5.169 11218 Z= 0.266 Chirality : 0.038 0.134 1322 Planarity : 0.004 0.038 1440 Dihedral : 13.384 87.801 2789 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % 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: 2.11 (0.27), residues: 1094 helix: 1.49 (0.18), residues: 907 sheet: None (None), residues: 0 loop : 1.38 (0.53), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG M 45 TYR 0.011 0.001 TYR a 145 PHE 0.014 0.001 PHE a 142 TRP 0.012 0.001 TRP a 218 HIS 0.002 0.001 HIS a 146 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 8257) covalent geometry : angle 0.47065 (11218) hydrogen bonds : bond 0.13575 ( 795) hydrogen bonds : angle 6.96768 ( 2376) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: M 45 ARG cc_start: 0.7554 (mpt90) cc_final: 0.7066 (mmm160) REVERT: M 46 GLN cc_start: 0.7649 (mp10) cc_final: 0.6838 (mp10) REVERT: d 2 SER cc_start: 0.8219 (p) cc_final: 0.7940 (t) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 1.5260 time to fit residues: 192.7981 Evaluate side-chains 80 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.1980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 50 GLN Q 71 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.082123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.068830 restraints weight = 42503.398| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 1.73 r_work: 0.2788 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8257 Z= 0.189 Angle : 0.525 5.544 11218 Z= 0.288 Chirality : 0.039 0.136 1322 Planarity : 0.004 0.033 1440 Dihedral : 3.689 14.005 1149 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.17 % Allowed : 8.16 % Favored : 90.67 % 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: 3.46 (0.25), residues: 1094 helix: 2.37 (0.16), residues: 944 sheet: None (None), residues: 0 loop : 1.98 (0.61), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 45 TYR 0.030 0.001 TYR a 145 PHE 0.015 0.002 PHE a 142 TRP 0.013 0.001 TRP a 218 HIS 0.004 0.001 HIS a 16 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 8257) covalent geometry : angle 0.52504 (11218) hydrogen bonds : bond 0.05280 ( 795) hydrogen bonds : angle 4.25756 ( 2376) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.437 Fit side-chains REVERT: M 46 GLN cc_start: 0.7945 (mp10) cc_final: 0.7419 (mp10) REVERT: S 21 MET cc_start: 0.8844 (mmp) cc_final: 0.8559 (mmp) REVERT: a 72 GLN cc_start: 0.7679 (OUTLIER) cc_final: 0.7082 (tp40) REVERT: a 177 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7900 (mt-10) REVERT: d 2 SER cc_start: 0.8447 (p) cc_final: 0.8123 (t) outliers start: 9 outliers final: 1 residues processed: 92 average time/residue: 1.3614 time to fit residues: 133.1445 Evaluate side-chains 80 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 78 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 72 GLN Chi-restraints excluded: chain b residue 76 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 59 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 80 optimal weight: 0.0570 chunk 46 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 71 ASN S 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.081418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.068077 restraints weight = 43022.645| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 1.76 r_work: 0.2770 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8257 Z= 0.184 Angle : 0.510 5.422 11218 Z= 0.277 Chirality : 0.039 0.132 1322 Planarity : 0.004 0.038 1440 Dihedral : 3.731 14.074 1149 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.68 % Allowed : 8.81 % Favored : 89.51 % 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: 3.83 (0.26), residues: 1094 helix: 2.64 (0.17), residues: 945 sheet: None (None), residues: 0 loop : 1.92 (0.60), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 52 TYR 0.028 0.001 TYR a 145 PHE 0.015 0.002 PHE a 142 TRP 0.014 0.001 TRP a 218 HIS 0.003 0.001 HIS a 146 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 8257) covalent geometry : angle 0.50973 (11218) hydrogen bonds : bond 0.05000 ( 795) hydrogen bonds : angle 3.98039 ( 2376) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: M 46 GLN cc_start: 0.8068 (mp10) cc_final: 0.7522 (mp10) REVERT: P 54 PHE cc_start: 0.8220 (OUTLIER) cc_final: 0.7864 (m-10) REVERT: S 21 MET cc_start: 0.8818 (mmp) cc_final: 0.8551 (mmp) REVERT: a 72 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.7101 (tp40) REVERT: d 2 SER cc_start: 0.8525 (p) cc_final: 0.8175 (t) outliers start: 13 outliers final: 1 residues processed: 93 average time/residue: 1.4460 time to fit residues: 142.3350 Evaluate side-chains 82 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 79 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 45 ARG Chi-restraints excluded: chain P residue 54 PHE Chi-restraints excluded: chain a residue 72 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 99 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 69 optimal weight: 0.1980 chunk 8 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 71 ASN a 192 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.081723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.068583 restraints weight = 43139.116| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 1.78 r_work: 0.2770 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8257 Z= 0.185 Angle : 0.511 5.448 11218 Z= 0.277 Chirality : 0.038 0.132 1322 Planarity : 0.004 0.041 1440 Dihedral : 3.773 14.206 1149 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.55 % Allowed : 9.33 % Favored : 89.12 % 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: 3.95 (0.26), residues: 1094 helix: 2.73 (0.17), residues: 945 sheet: None (None), residues: 0 loop : 1.87 (0.61), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 45 TYR 0.023 0.001 TYR a 145 PHE 0.015 0.002 PHE a 142 TRP 0.014 0.001 TRP a 218 HIS 0.003 0.001 HIS a 146 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 8257) covalent geometry : angle 0.51067 (11218) hydrogen bonds : bond 0.04898 ( 795) hydrogen bonds : angle 3.89284 ( 2376) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 46 GLN cc_start: 0.8073 (mp10) cc_final: 0.7522 (mp10) REVERT: M 65 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7945 (mt-10) REVERT: P 54 PHE cc_start: 0.8204 (OUTLIER) cc_final: 0.7878 (m-10) REVERT: T 75 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8718 (tmm) REVERT: a 72 GLN cc_start: 0.7706 (OUTLIER) cc_final: 0.7094 (tp40) REVERT: a 177 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.8033 (mt-10) REVERT: d 2 SER cc_start: 0.8491 (p) cc_final: 0.8148 (t) outliers start: 12 outliers final: 3 residues processed: 92 average time/residue: 1.5731 time to fit residues: 152.3822 Evaluate side-chains 85 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 45 ARG Chi-restraints excluded: chain P residue 54 PHE Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain T residue 75 MET Chi-restraints excluded: chain a residue 72 GLN Chi-restraints excluded: chain a residue 125 LYS Chi-restraints excluded: chain a residue 177 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 27 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 40 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 71 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.080720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.067426 restraints weight = 43452.570| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 1.79 r_work: 0.2747 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8257 Z= 0.215 Angle : 0.526 5.460 11218 Z= 0.288 Chirality : 0.039 0.136 1322 Planarity : 0.004 0.044 1440 Dihedral : 3.873 14.386 1149 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.07 % Allowed : 9.33 % Favored : 88.60 % 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: 3.82 (0.26), residues: 1094 helix: 2.81 (0.17), residues: 909 sheet: None (None), residues: 0 loop : 1.09 (0.52), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 45 TYR 0.023 0.001 TYR a 145 PHE 0.016 0.002 PHE a 142 TRP 0.014 0.001 TRP a 218 HIS 0.003 0.001 HIS a 146 Details of bonding type rmsd covalent geometry : bond 0.00477 ( 8257) covalent geometry : angle 0.52647 (11218) hydrogen bonds : bond 0.05045 ( 795) hydrogen bonds : angle 3.90729 ( 2376) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.449 Fit side-chains revert: symmetry clash REVERT: M 46 GLN cc_start: 0.8073 (mp10) cc_final: 0.7621 (mp10) REVERT: M 65 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7974 (mt-10) REVERT: P 54 PHE cc_start: 0.8222 (OUTLIER) cc_final: 0.7888 (m-10) REVERT: R 65 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8320 (mp0) REVERT: T 75 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8733 (tmm) REVERT: a 72 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.7083 (tp40) REVERT: a 177 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.8034 (mt-10) REVERT: d 2 SER cc_start: 0.8511 (p) cc_final: 0.8171 (t) outliers start: 16 outliers final: 3 residues processed: 87 average time/residue: 1.5295 time to fit residues: 140.5611 Evaluate side-chains 83 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 45 ARG Chi-restraints excluded: chain P residue 54 PHE Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain T residue 75 MET Chi-restraints excluded: chain a residue 72 GLN Chi-restraints excluded: chain a residue 125 LYS Chi-restraints excluded: chain a residue 177 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 55 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 89 optimal weight: 0.0980 chunk 53 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 61 optimal weight: 0.0970 chunk 47 optimal weight: 0.4980 chunk 16 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 71 ASN a 192 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.081738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.068490 restraints weight = 42308.533| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 1.74 r_work: 0.2776 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8257 Z= 0.148 Angle : 0.500 6.807 11218 Z= 0.268 Chirality : 0.038 0.128 1322 Planarity : 0.004 0.042 1440 Dihedral : 3.784 14.324 1149 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.20 % Allowed : 9.07 % Favored : 88.73 % 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: 4.11 (0.26), residues: 1094 helix: 2.85 (0.17), residues: 945 sheet: None (None), residues: 0 loop : 1.87 (0.61), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 45 TYR 0.021 0.001 TYR a 145 PHE 0.013 0.001 PHE a 142 TRP 0.014 0.001 TRP a 218 HIS 0.002 0.001 HIS a 146 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 8257) covalent geometry : angle 0.49953 (11218) hydrogen bonds : bond 0.04662 ( 795) hydrogen bonds : angle 3.79233 ( 2376) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: M 46 GLN cc_start: 0.8060 (mp10) cc_final: 0.7607 (mp10) REVERT: M 65 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7984 (mt-10) REVERT: P 54 PHE cc_start: 0.8216 (OUTLIER) cc_final: 0.7902 (m-10) REVERT: R 45 ARG cc_start: 0.8300 (mtp-110) cc_final: 0.7199 (mtm-85) REVERT: R 65 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8400 (mp0) REVERT: T 75 MET cc_start: 0.8978 (OUTLIER) cc_final: 0.8755 (tmm) REVERT: a 72 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.7097 (tp40) REVERT: a 177 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.8033 (mt-10) REVERT: d 2 SER cc_start: 0.8509 (p) cc_final: 0.8167 (t) outliers start: 17 outliers final: 4 residues processed: 88 average time/residue: 1.4111 time to fit residues: 131.5923 Evaluate side-chains 82 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 45 ARG Chi-restraints excluded: chain P residue 54 PHE Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain T residue 75 MET Chi-restraints excluded: chain a residue 54 THR Chi-restraints excluded: chain a residue 72 GLN Chi-restraints excluded: chain a residue 125 LYS Chi-restraints excluded: chain a residue 177 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 93 optimal weight: 0.9980 chunk 97 optimal weight: 0.3980 chunk 91 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 chunk 80 optimal weight: 0.0970 chunk 15 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 71 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.082145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.069194 restraints weight = 42858.410| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 1.77 r_work: 0.2788 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8257 Z= 0.161 Angle : 0.506 6.425 11218 Z= 0.272 Chirality : 0.038 0.130 1322 Planarity : 0.004 0.042 1440 Dihedral : 3.751 14.304 1149 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.68 % Allowed : 9.84 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.14 (0.26), residues: 1094 helix: 2.87 (0.17), residues: 945 sheet: None (None), residues: 0 loop : 1.86 (0.61), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 45 TYR 0.021 0.001 TYR a 145 PHE 0.014 0.001 PHE a 142 TRP 0.013 0.001 TRP a 218 HIS 0.002 0.001 HIS a 146 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 8257) covalent geometry : angle 0.50648 (11218) hydrogen bonds : bond 0.04668 ( 795) hydrogen bonds : angle 3.76844 ( 2376) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: M 46 GLN cc_start: 0.8065 (mp10) cc_final: 0.7613 (mp10) REVERT: M 65 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7953 (mt-10) REVERT: P 54 PHE cc_start: 0.8199 (OUTLIER) cc_final: 0.7881 (m-10) REVERT: R 65 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8418 (mp0) REVERT: T 75 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8708 (tmm) REVERT: a 72 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.7084 (tp40) REVERT: a 177 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7947 (mt-10) REVERT: d 2 SER cc_start: 0.8472 (p) cc_final: 0.8159 (t) outliers start: 13 outliers final: 3 residues processed: 86 average time/residue: 1.6153 time to fit residues: 146.5897 Evaluate side-chains 80 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 45 ARG Chi-restraints excluded: chain P residue 54 PHE Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain T residue 75 MET Chi-restraints excluded: chain a residue 54 THR Chi-restraints excluded: chain a residue 72 GLN Chi-restraints excluded: chain a residue 177 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 24 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 103 optimal weight: 0.0270 chunk 1 optimal weight: 0.4980 chunk 60 optimal weight: 0.8980 chunk 77 optimal weight: 0.0980 chunk 58 optimal weight: 0.9980 chunk 73 optimal weight: 0.1980 chunk 105 optimal weight: 1.9990 overall best weight: 0.3438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 192 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.083361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.070360 restraints weight = 42991.971| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 1.77 r_work: 0.2798 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8257 Z= 0.132 Angle : 0.499 7.995 11218 Z= 0.264 Chirality : 0.038 0.126 1322 Planarity : 0.004 0.050 1440 Dihedral : 3.677 14.280 1149 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.94 % Allowed : 9.84 % Favored : 88.21 % 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: 4.37 (0.26), residues: 1094 helix: 3.02 (0.17), residues: 945 sheet: None (None), residues: 0 loop : 1.95 (0.62), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 45 TYR 0.020 0.001 TYR a 145 PHE 0.013 0.001 PHE a 142 TRP 0.013 0.001 TRP a 218 HIS 0.002 0.001 HIS a 146 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 8257) covalent geometry : angle 0.49913 (11218) hydrogen bonds : bond 0.04411 ( 795) hydrogen bonds : angle 3.69002 ( 2376) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: M 46 GLN cc_start: 0.8014 (mp10) cc_final: 0.7563 (mp10) REVERT: M 65 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7950 (mt-10) REVERT: P 54 PHE cc_start: 0.8193 (OUTLIER) cc_final: 0.7872 (m-10) REVERT: R 45 ARG cc_start: 0.8328 (mtp-110) cc_final: 0.7204 (mtm-85) REVERT: R 65 GLU cc_start: 0.8744 (mm-30) cc_final: 0.8457 (mp0) REVERT: T 75 MET cc_start: 0.8955 (OUTLIER) cc_final: 0.8745 (tmm) REVERT: a 72 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.7114 (tp40) REVERT: a 177 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7992 (mt-10) REVERT: d 2 SER cc_start: 0.8472 (p) cc_final: 0.8154 (t) outliers start: 15 outliers final: 4 residues processed: 87 average time/residue: 1.4739 time to fit residues: 135.8724 Evaluate side-chains 83 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 48 GLU Chi-restraints excluded: chain N residue 45 ARG Chi-restraints excluded: chain P residue 54 PHE Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain T residue 75 MET Chi-restraints excluded: chain a residue 54 THR Chi-restraints excluded: chain a residue 72 GLN Chi-restraints excluded: chain a residue 177 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 10 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.081135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.068157 restraints weight = 43400.718| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 1.78 r_work: 0.2754 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8257 Z= 0.210 Angle : 0.536 8.671 11218 Z= 0.290 Chirality : 0.038 0.134 1322 Planarity : 0.004 0.041 1440 Dihedral : 3.778 14.138 1149 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.55 % Allowed : 10.62 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.04 (0.26), residues: 1094 helix: 2.96 (0.17), residues: 909 sheet: None (None), residues: 0 loop : 1.13 (0.52), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 45 TYR 0.020 0.001 TYR a 145 PHE 0.016 0.002 PHE a 142 TRP 0.013 0.001 TRP a 218 HIS 0.003 0.001 HIS a 16 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 8257) covalent geometry : angle 0.53597 (11218) hydrogen bonds : bond 0.04868 ( 795) hydrogen bonds : angle 3.80715 ( 2376) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.469 Fit side-chains revert: symmetry clash REVERT: M 46 GLN cc_start: 0.8115 (mp10) cc_final: 0.7664 (mp10) REVERT: M 65 GLU cc_start: 0.8260 (mm-30) cc_final: 0.8007 (mt-10) REVERT: P 54 PHE cc_start: 0.8247 (OUTLIER) cc_final: 0.7913 (m-10) REVERT: R 45 ARG cc_start: 0.8345 (mtp-110) cc_final: 0.7173 (mtm-85) REVERT: R 65 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8488 (mp0) REVERT: T 75 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.8769 (tmm) REVERT: a 72 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.7084 (tp40) REVERT: a 177 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7973 (mt-10) REVERT: d 2 SER cc_start: 0.8520 (p) cc_final: 0.8190 (t) outliers start: 12 outliers final: 3 residues processed: 85 average time/residue: 1.4765 time to fit residues: 132.9579 Evaluate side-chains 83 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 45 ARG Chi-restraints excluded: chain P residue 54 PHE Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain T residue 75 MET Chi-restraints excluded: chain a residue 54 THR Chi-restraints excluded: chain a residue 72 GLN Chi-restraints excluded: chain a residue 177 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 74 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 0.4980 chunk 81 optimal weight: 0.5980 chunk 96 optimal weight: 0.3980 chunk 51 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 84 optimal weight: 0.2980 chunk 72 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 192 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.082297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.069369 restraints weight = 42873.323| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 1.76 r_work: 0.2780 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8257 Z= 0.154 Angle : 0.517 7.907 11218 Z= 0.276 Chirality : 0.038 0.127 1322 Planarity : 0.004 0.042 1440 Dihedral : 3.731 14.219 1149 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.17 % Allowed : 11.14 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.18 (0.26), residues: 1094 helix: 2.89 (0.17), residues: 945 sheet: None (None), residues: 0 loop : 1.86 (0.61), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 45 TYR 0.020 0.001 TYR a 145 PHE 0.013 0.001 PHE a 142 TRP 0.013 0.001 TRP a 218 HIS 0.002 0.001 HIS a 146 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 8257) covalent geometry : angle 0.51672 (11218) hydrogen bonds : bond 0.04616 ( 795) hydrogen bonds : angle 3.74431 ( 2376) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.449 Fit side-chains revert: symmetry clash REVERT: M 46 GLN cc_start: 0.8074 (mp10) cc_final: 0.7620 (mp10) REVERT: M 65 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7974 (mt-10) REVERT: P 54 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.7879 (m-10) REVERT: R 45 ARG cc_start: 0.8295 (mtp-110) cc_final: 0.7121 (mtm-85) REVERT: R 65 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8437 (mp0) REVERT: T 75 MET cc_start: 0.8970 (OUTLIER) cc_final: 0.8761 (tmm) REVERT: a 72 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.7078 (tp40) REVERT: a 177 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7976 (mt-10) REVERT: d 2 SER cc_start: 0.8484 (p) cc_final: 0.8158 (t) outliers start: 9 outliers final: 3 residues processed: 83 average time/residue: 1.4601 time to fit residues: 128.4982 Evaluate side-chains 82 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 45 ARG Chi-restraints excluded: chain P residue 54 PHE Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain T residue 75 MET Chi-restraints excluded: chain a residue 54 THR Chi-restraints excluded: chain a residue 72 GLN Chi-restraints excluded: chain a residue 177 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 1 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 89 optimal weight: 0.2980 chunk 31 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 80 optimal weight: 0.0670 chunk 68 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.081814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.068895 restraints weight = 42927.207| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 1.76 r_work: 0.2770 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8257 Z= 0.175 Angle : 0.526 9.017 11218 Z= 0.282 Chirality : 0.038 0.129 1322 Planarity : 0.004 0.042 1440 Dihedral : 3.741 14.105 1149 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.04 % Allowed : 11.53 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.11 (0.26), residues: 1094 helix: 2.85 (0.17), residues: 945 sheet: None (None), residues: 0 loop : 1.82 (0.60), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 45 TYR 0.020 0.001 TYR a 145 PHE 0.015 0.002 PHE a 142 TRP 0.013 0.001 TRP a 218 HIS 0.002 0.001 HIS a 146 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 8257) covalent geometry : angle 0.52628 (11218) hydrogen bonds : bond 0.04708 ( 795) hydrogen bonds : angle 3.76277 ( 2376) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5120.56 seconds wall clock time: 87 minutes 20.78 seconds (5240.78 seconds total)