Starting phenix.real_space_refine on Thu Jul 2 05:33:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zyi_15024/07_2026/7zyi_15024.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zyi_15024/07_2026/7zyi_15024.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7zyi_15024/07_2026/7zyi_15024.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zyi_15024/07_2026/7zyi_15024.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7zyi_15024/07_2026/7zyi_15024.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zyi_15024/07_2026/7zyi_15024.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zyi_15024/07_2026/7zyi_15024.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zyi_15024/07_2026/7zyi_15024.map" } resolution = 2.88 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 46 5.16 5 Na 2 4.78 5 C 4286 2.51 5 N 1075 2.21 5 O 1232 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6641 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2248 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 14, 'TRANS': 278} Chain: "H" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1714 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 11, 'TRANS': 215} Chain: "L" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1626 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 200} Chain: "K" Number of atoms: 930 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 120, 922 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Conformer: "B" Number of residues, atoms: 120, 922 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} bond proxies already assigned to first conformer: 931 Chain: "A" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {' NA': 2, 'CHO': 2, 'CLR': 2} Classifications: {'undetermined': 6, 'water': 1} Link IDs: {None: 6} Time building chain proxies: 1.50, per 1000 atoms: 0.23 Number of scatterers: 6641 At special positions: 0 Unit cell: (118.8, 116.82, 89.1, 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 46 16.00 Na 2 11.00 O 1232 8.00 N 1075 7.00 C 4286 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.46 Conformation dependent library (CDL) restraints added in 404.0 milliseconds 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1572 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 15 sheets defined 35.0% alpha, 31.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 21 through 43 Processing helix chain 'A' and resid 44 through 46 No H-bonds generated for 'chain 'A' and resid 44 through 46' Processing helix chain 'A' and resid 47 through 57 Processing helix chain 'A' and resid 59 through 70 Processing helix chain 'A' and resid 71 through 83 Processing helix chain 'A' and resid 86 through 97 Processing helix chain 'A' and resid 103 through 112 removed outlier: 3.743A pdb=" N VAL A 107 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 142 removed outlier: 3.528A pdb=" N SER A 119 " --> pdb=" O ASP A 115 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU A 131 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLY A 132 " --> pdb=" O PHE A 128 " (cutoff:3.500A) Proline residue: A 135 - end of helix Processing helix chain 'A' and resid 150 through 154 removed outlier: 3.742A pdb=" N VAL A 154 " --> pdb=" O LYS A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 180 Proline residue: A 169 - end of helix Processing helix chain 'A' and resid 183 through 213 removed outlier: 3.571A pdb=" N LEU A 196 " --> pdb=" O MET A 192 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA A 201 " --> pdb=" O LEU A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 244 removed outlier: 3.577A pdb=" N ILE A 223 " --> pdb=" O THR A 219 " (cutoff:3.500A) Proline residue: A 230 - end of helix removed outlier: 3.666A pdb=" N PHE A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 260 Processing helix chain 'A' and resid 262 through 274 removed outlier: 4.308A pdb=" N CYS A 266 " --> pdb=" O ASN A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 283 Processing helix chain 'A' and resid 284 through 310 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.907A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 156 through 158 No H-bonds generated for 'chain 'H' and resid 156 through 158' Processing helix chain 'H' and resid 187 through 192 removed outlier: 4.106A pdb=" N GLN H 192 " --> pdb=" O LEU H 189 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.160A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 128 Processing helix chain 'L' and resid 183 through 189 Processing helix chain 'K' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 5.874A pdb=" N SER H 33 " --> pdb=" O TYR H 95 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.555A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 120 through 124 removed outlier: 6.319A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 120 through 124 removed outlier: 6.319A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 136 through 137 Processing sheet with id=AA7, first strand: chain 'H' and resid 151 through 154 removed outlier: 3.599A pdb=" N VAL H 198 " --> pdb=" O VAL H 207 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL H 207 " --> pdb=" O VAL H 198 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS H 200 " --> pdb=" O THR H 205 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THR H 205 " --> pdb=" O HIS H 200 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.896A pdb=" N VAL L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N TYR L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.891A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.636A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 153 through 154 removed outlier: 3.711A pdb=" N TYR L 192 " --> pdb=" O PHE L 209 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 3 through 7 removed outlier: 3.902A pdb=" N GLN K 3 " --> pdb=" O SER K 25 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER K 25 " --> pdb=" O GLN K 3 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN K 5 " --> pdb=" O ALA K 23 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA K 23 " --> pdb=" O GLN K 5 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL K 78 " --> pdb=" O CYS K 22 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.659A pdb=" N THR K 110 " --> pdb=" O GLY K 10 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA K 33 " --> pdb=" O ASP K 95 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N MET K 34 " --> pdb=" O VAL K 50 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N VAL K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL K 48 " --> pdb=" O TRP K 36 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.659A pdb=" N THR K 110 " --> pdb=" O GLY K 10 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE K 94 " --> pdb=" O TYR K 102 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N TYR K 102 " --> pdb=" O ILE K 94 " (cutoff:3.500A) 370 hydrogen bonds defined for protein. 980 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: 1.06 Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1028 1.31 - 1.43: 1856 1.43 - 1.56: 3825 1.56 - 1.69: 19 1.69 - 1.81: 71 Bond restraints: 6799 Sorted by residual: bond pdb=" C12 CHO A 702 " pdb=" C13 CHO A 702 " ideal model delta sigma weight residual 1.529 1.198 0.331 2.00e-02 2.50e+03 2.73e+02 bond pdb=" C12 CHO A 703 " pdb=" C13 CHO A 703 " ideal model delta sigma weight residual 1.529 1.202 0.327 2.00e-02 2.50e+03 2.67e+02 bond pdb=" C13 CHO A 702 " pdb=" C17 CHO A 702 " ideal model delta sigma weight residual 1.549 1.234 0.315 2.00e-02 2.50e+03 2.49e+02 bond pdb=" C13 CHO A 703 " pdb=" C17 CHO A 703 " ideal model delta sigma weight residual 1.549 1.242 0.307 2.00e-02 2.50e+03 2.36e+02 bond pdb=" C11 CHO A 702 " pdb=" C12 CHO A 702 " ideal model delta sigma weight residual 1.529 1.812 -0.283 2.00e-02 2.50e+03 2.00e+02 ... (remaining 6794 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 9113 2.71 - 5.42: 105 5.42 - 8.13: 28 8.13 - 10.84: 3 10.84 - 13.55: 2 Bond angle restraints: 9251 Sorted by residual: angle pdb=" CA PRO A 58 " pdb=" N PRO A 58 " pdb=" CD PRO A 58 " ideal model delta sigma weight residual 112.00 103.01 8.99 1.40e+00 5.10e-01 4.12e+01 angle pdb=" N MET A 229 " pdb=" CA MET A 229 " pdb=" CB MET A 229 " ideal model delta sigma weight residual 110.42 104.69 5.73 1.18e+00 7.18e-01 2.36e+01 angle pdb=" CA GLU H 46 " pdb=" CB GLU H 46 " pdb=" CG GLU H 46 " ideal model delta sigma weight residual 114.10 123.54 -9.44 2.00e+00 2.50e-01 2.23e+01 angle pdb=" CB MET A 229 " pdb=" CG MET A 229 " pdb=" SD MET A 229 " ideal model delta sigma weight residual 112.70 126.25 -13.55 3.00e+00 1.11e-01 2.04e+01 angle pdb=" CA LYS A 151 " pdb=" C LYS A 151 " pdb=" O LYS A 151 " ideal model delta sigma weight residual 120.90 116.14 4.76 1.07e+00 8.73e-01 1.98e+01 ... (remaining 9246 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.30: 3664 21.30 - 42.60: 277 42.60 - 63.91: 57 63.91 - 85.21: 7 85.21 - 106.51: 3 Dihedral angle restraints: 4008 sinusoidal: 1542 harmonic: 2466 Sorted by residual: dihedral pdb=" CA TYR A 183 " pdb=" C TYR A 183 " pdb=" N MET A 184 " pdb=" CA MET A 184 " ideal model delta harmonic sigma weight residual -180.00 -158.87 -21.13 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" C10 CHO A 702 " pdb=" C1 CHO A 702 " pdb=" C2 CHO A 702 " pdb=" C3 CHO A 702 " ideal model delta sinusoidal sigma weight residual 57.70 -48.81 106.51 1 3.00e+01 1.11e-03 1.37e+01 dihedral pdb=" C10 CHO A 703 " pdb=" C1 CHO A 703 " pdb=" C2 CHO A 703 " pdb=" C3 CHO A 703 " ideal model delta sinusoidal sigma weight residual 57.70 -44.03 101.73 1 3.00e+01 1.11e-03 1.28e+01 ... (remaining 4005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.331: 1065 0.331 - 0.662: 3 0.662 - 0.992: 0 0.992 - 1.323: 0 1.323 - 1.654: 2 Chirality restraints: 1070 Sorted by residual: chirality pdb=" C13 CHO A 702 " pdb=" C12 CHO A 702 " pdb=" C14 CHO A 702 " pdb=" C17 CHO A 702 " both_signs ideal model delta sigma weight residual False -2.94 -1.29 -1.65 2.00e-01 2.50e+01 6.84e+01 chirality pdb=" C13 CHO A 703 " pdb=" C12 CHO A 703 " pdb=" C14 CHO A 703 " pdb=" C17 CHO A 703 " both_signs ideal model delta sigma weight residual False -2.94 -1.30 -1.64 2.00e-01 2.50e+01 6.71e+01 chirality pdb=" C9 CHO A 703 " pdb=" C10 CHO A 703 " pdb=" C11 CHO A 703 " pdb=" C8 CHO A 703 " both_signs ideal model delta sigma weight residual False -2.52 -2.05 -0.47 2.00e-01 2.50e+01 5.48e+00 ... (remaining 1067 not shown) Planarity restraints: 1133 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS L 107 " -0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C LYS L 107 " 0.060 2.00e-02 2.50e+03 pdb=" O LYS L 107 " -0.022 2.00e-02 2.50e+03 pdb=" N ARG L 108 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 57 " 0.059 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO A 58 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 58 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 58 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 150 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.13e+00 pdb=" C LEU A 150 " -0.043 2.00e-02 2.50e+03 pdb=" O LEU A 150 " 0.016 2.00e-02 2.50e+03 pdb=" N LYS A 151 " 0.015 2.00e-02 2.50e+03 ... (remaining 1130 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 140 2.70 - 3.25: 6091 3.25 - 3.80: 10069 3.80 - 4.35: 12979 4.35 - 4.90: 22646 Nonbonded interactions: 51925 Sorted by model distance: nonbonded pdb=" OD2 ASP K 97 " pdb=" OG SER K 100A" model vdw 2.152 3.040 nonbonded pdb=" OG SER L 182 " pdb=" OD2 ASP L 185 " model vdw 2.210 3.040 nonbonded pdb=" O TYR L 186 " pdb=" OH TYR L 192 " model vdw 2.285 3.040 nonbonded pdb=" OG SER K 17 " pdb=" OD1 ASN K 82A" model vdw 2.311 3.040 nonbonded pdb=" NH1 ARG L 66 " pdb=" O GLY L 68 " model vdw 2.324 3.120 ... (remaining 51920 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.48 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: 3.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.910 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 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 : 0.013 0.331 6802 Z= 0.653 Angle : 0.753 13.548 9257 Z= 0.364 Chirality : 0.087 1.654 1070 Planarity : 0.005 0.084 1133 Dihedral : 15.699 106.510 2427 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.69 % Allowed : 14.42 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.17 (0.29), residues: 846 helix: 1.90 (0.33), residues: 260 sheet: 1.43 (0.35), residues: 211 loop : -0.41 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 108 TYR 0.024 0.001 TYR L 140 PHE 0.006 0.001 PHE A 37 TRP 0.005 0.001 TRP L 93 HIS 0.024 0.003 HIS H 200 Details of bonding type rmsd/Z covalent geometry : bond 0.01309 / 0.65 ( 6799) covalent geometry : angle 0.75360 / 0.36 ( 9251) SS BOND : bond 0.00202 / 0.11 ( 3) SS BOND : angle 0.18228 / 0.10 ( 6) hydrogen bonds : bond 0.19631 / 13.58 ( 343) hydrogen bonds : angle 7.46331 / 5.12 ( 980) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 108 ARG cc_start: 0.7510 (ttp80) cc_final: 0.7020 (ptm-80) REVERT: L 142 ARG cc_start: 0.7657 (ttt180) cc_final: 0.7071 (ttt-90) outliers start: 5 outliers final: 5 residues processed: 94 average time/residue: 0.4728 time to fit residues: 46.8896 Evaluate side-chains 91 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 97 LYS Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 172 THR Chi-restraints excluded: chain K residue 70 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 8.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.1980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 10.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 HIS A 103 ASN A 293 GLN H 100EGLN H 105 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.190546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.135449 restraints weight = 15640.103| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 3.85 r_work: 0.3070 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 6802 Z= 0.125 Angle : 0.581 7.732 9257 Z= 0.286 Chirality : 0.042 0.270 1070 Planarity : 0.004 0.033 1133 Dihedral : 7.867 102.547 966 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.61 % Allowed : 14.15 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.30 (0.29), residues: 846 helix: 2.23 (0.32), residues: 261 sheet: 1.34 (0.33), residues: 238 loop : -0.57 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 66 TYR 0.013 0.001 TYR A 238 PHE 0.008 0.001 PHE A 128 TRP 0.006 0.001 TRP L 93 HIS 0.001 0.001 HIS A 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 6799) covalent geometry : angle 0.58085 / 0.29 ( 9251) SS BOND : bond 0.00508 / 0.26 ( 3) SS BOND : angle 0.61818 / 0.30 ( 6) hydrogen bonds : bond 0.04205 / 2.81 ( 343) hydrogen bonds : angle 5.24791 / 3.63 ( 980) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: L 11 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8135 (tt) REVERT: L 108 ARG cc_start: 0.7655 (ttp80) cc_final: 0.6987 (ptm-80) REVERT: K 34 MET cc_start: 0.7352 (ttt) cc_final: 0.6582 (mmm) outliers start: 18 outliers final: 9 residues processed: 100 average time/residue: 0.5437 time to fit residues: 57.1609 Evaluate side-chains 96 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain H residue 97 LYS Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 170 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 69 optimal weight: 9.9990 chunk 4 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 71 optimal weight: 10.0000 chunk 26 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 99 GLN H 100EGLN H 105 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.190914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.135023 restraints weight = 15410.753| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 3.87 r_work: 0.3069 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6802 Z= 0.114 Angle : 0.550 8.103 9257 Z= 0.269 Chirality : 0.041 0.246 1070 Planarity : 0.004 0.032 1133 Dihedral : 7.642 100.660 960 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.30 % Allowed : 15.38 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.41 (0.29), residues: 846 helix: 2.46 (0.32), residues: 261 sheet: 1.38 (0.33), residues: 239 loop : -0.62 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 66 TYR 0.010 0.001 TYR A 238 PHE 0.008 0.001 PHE A 37 TRP 0.006 0.001 TRP L 93 HIS 0.001 0.000 HIS L 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 6799) covalent geometry : angle 0.54968 / 0.27 ( 9251) SS BOND : bond 0.00490 / 0.25 ( 3) SS BOND : angle 0.49622 / 0.26 ( 6) hydrogen bonds : bond 0.03755 / 2.51 ( 343) hydrogen bonds : angle 4.89012 / 3.39 ( 980) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.277 Fit side-chains REVERT: L 11 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8173 (tt) REVERT: L 105 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7187 (pt0) REVERT: L 108 ARG cc_start: 0.7649 (ttp80) cc_final: 0.6970 (ptm-80) REVERT: L 142 ARG cc_start: 0.7343 (tmt90) cc_final: 0.6999 (ttt-90) REVERT: K 34 MET cc_start: 0.7353 (ttt) cc_final: 0.6638 (mmm) outliers start: 23 outliers final: 14 residues processed: 100 average time/residue: 0.4876 time to fit residues: 51.7825 Evaluate side-chains 103 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain H residue 97 LYS Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 170 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 29 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 5 optimal weight: 0.0670 chunk 22 optimal weight: 0.0170 chunk 66 optimal weight: 8.9990 chunk 80 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 74 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 117 ASN A 293 GLN H 100EGLN H 105 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.190976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.132992 restraints weight = 21242.239| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 4.88 r_work: 0.3062 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3040 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3040 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6802 Z= 0.110 Angle : 0.539 7.802 9257 Z= 0.263 Chirality : 0.041 0.235 1070 Planarity : 0.004 0.033 1133 Dihedral : 7.570 100.834 960 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.85 % Allowed : 16.48 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.49 (0.29), residues: 846 helix: 2.55 (0.32), residues: 261 sheet: 1.63 (0.34), residues: 220 loop : -0.63 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 52A TYR 0.009 0.001 TYR A 238 PHE 0.007 0.001 PHE A 37 TRP 0.007 0.001 TRP H 100H HIS 0.001 0.000 HIS H 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 6799) covalent geometry : angle 0.53949 / 0.26 ( 9251) SS BOND : bond 0.00518 / 0.26 ( 3) SS BOND : angle 0.41950 / 0.21 ( 6) hydrogen bonds : bond 0.03466 / 2.32 ( 343) hydrogen bonds : angle 4.66634 / 3.25 ( 980) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 88 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: A 39 MET cc_start: 0.8581 (mmm) cc_final: 0.8357 (mmm) REVERT: A 215 MET cc_start: 0.8150 (mmm) cc_final: 0.7650 (mmp) REVERT: H 46 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8364 (tm-30) REVERT: L 11 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8177 (tt) REVERT: L 105 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7219 (pt0) REVERT: L 108 ARG cc_start: 0.7558 (ttp80) cc_final: 0.6833 (ptm-80) REVERT: L 142 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.6801 (ttt-90) REVERT: K 34 MET cc_start: 0.7290 (ttt) cc_final: 0.6598 (mmm) outliers start: 27 outliers final: 11 residues processed: 101 average time/residue: 0.4610 time to fit residues: 49.3328 Evaluate side-chains 102 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 97 LYS Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 142 ARG Chi-restraints excluded: chain L residue 170 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 72 optimal weight: 6.9990 chunk 51 optimal weight: 0.0670 chunk 48 optimal weight: 5.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 99 GLN H 100EGLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.192162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.137587 restraints weight = 23960.938| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 5.44 r_work: 0.3065 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3052 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3052 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6802 Z= 0.100 Angle : 0.516 7.119 9257 Z= 0.253 Chirality : 0.041 0.228 1070 Planarity : 0.004 0.032 1133 Dihedral : 7.437 100.493 960 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.57 % Allowed : 16.35 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.57 (0.29), residues: 846 helix: 2.71 (0.32), residues: 260 sheet: 1.62 (0.34), residues: 220 loop : -0.60 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 52A TYR 0.009 0.001 TYR A 238 PHE 0.007 0.001 PHE A 37 TRP 0.006 0.001 TRP L 93 HIS 0.001 0.000 HIS H 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 ( 6799) covalent geometry : angle 0.51601 / 0.25 ( 9251) SS BOND : bond 0.00397 / 0.20 ( 3) SS BOND : angle 0.39256 / 0.19 ( 6) hydrogen bonds : bond 0.03218 / 2.15 ( 343) hydrogen bonds : angle 4.47541 / 3.13 ( 980) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.211 Fit side-chains revert: symmetry clash REVERT: A 39 MET cc_start: 0.8601 (mmm) cc_final: 0.8322 (mmm) REVERT: A 215 MET cc_start: 0.8133 (mmm) cc_final: 0.7615 (mmp) REVERT: H 105 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7401 (pp30) REVERT: L 11 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8144 (tt) REVERT: L 108 ARG cc_start: 0.7384 (ttp80) cc_final: 0.6627 (ptm-80) REVERT: L 142 ARG cc_start: 0.7242 (OUTLIER) cc_final: 0.6915 (ttt-90) REVERT: K 34 MET cc_start: 0.7252 (ttt) cc_final: 0.6509 (mmm) outliers start: 25 outliers final: 7 residues processed: 105 average time/residue: 0.4644 time to fit residues: 51.7451 Evaluate side-chains 97 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 142 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 29 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 46 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 83 optimal weight: 30.0000 chunk 56 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 98 GLN ** H 100EGLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.187079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.131303 restraints weight = 15702.343| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 4.03 r_work: 0.3015 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 6802 Z= 0.229 Angle : 0.666 8.539 9257 Z= 0.329 Chirality : 0.045 0.237 1070 Planarity : 0.005 0.042 1133 Dihedral : 7.823 109.157 956 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.53 % Allowed : 17.03 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.14 (0.29), residues: 846 helix: 2.11 (0.32), residues: 260 sheet: 1.50 (0.34), residues: 222 loop : -0.76 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 66 TYR 0.015 0.002 TYR A 186 PHE 0.031 0.002 PHE K 67 TRP 0.009 0.001 TRP H 103 HIS 0.003 0.001 HIS H 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.23 ( 6799) covalent geometry : angle 0.66525 / 0.33 ( 9251) SS BOND : bond 0.00925 / 0.49 ( 3) SS BOND : angle 1.11829 / 0.67 ( 6) hydrogen bonds : bond 0.04761 / 3.16 ( 343) hydrogen bonds : angle 4.80899 / 3.35 ( 980) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 85 time to evaluate : 0.191 Fit side-chains revert: symmetry clash REVERT: A 39 MET cc_start: 0.8703 (mmm) cc_final: 0.8270 (mmm) REVERT: A 279 ILE cc_start: 0.8162 (tp) cc_final: 0.7921 (mm) REVERT: L 82 ASP cc_start: 0.9089 (m-30) cc_final: 0.8778 (m-30) REVERT: L 105 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7203 (pt0) REVERT: L 108 ARG cc_start: 0.7532 (ttp80) cc_final: 0.6826 (ptm-80) REVERT: L 142 ARG cc_start: 0.7366 (OUTLIER) cc_final: 0.7010 (ttt-90) REVERT: K 34 MET cc_start: 0.7254 (ttt) cc_final: 0.6500 (mmm) outliers start: 32 outliers final: 17 residues processed: 101 average time/residue: 0.4568 time to fit residues: 48.9462 Evaluate side-chains 103 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain H residue 97 LYS Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 142 ARG Chi-restraints excluded: chain L residue 170 ASP Chi-restraints excluded: chain K residue 63 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 23 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 5 optimal weight: 0.3980 chunk 77 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 69 optimal weight: 8.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 98 GLN ** H 100EGLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.190784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.137036 restraints weight = 23849.467| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 5.94 r_work: 0.3013 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6802 Z= 0.112 Angle : 0.544 7.308 9257 Z= 0.266 Chirality : 0.041 0.233 1070 Planarity : 0.004 0.034 1133 Dihedral : 7.431 102.304 956 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.88 % Allowed : 18.68 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.37 (0.29), residues: 846 helix: 2.54 (0.32), residues: 260 sheet: 1.51 (0.34), residues: 220 loop : -0.72 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 52A TYR 0.012 0.001 TYR A 238 PHE 0.018 0.001 PHE K 67 TRP 0.009 0.001 TRP H 100H HIS 0.001 0.000 HIS L 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 6799) covalent geometry : angle 0.54387 / 0.27 ( 9251) SS BOND : bond 0.00397 / 0.20 ( 3) SS BOND : angle 0.58974 / 0.33 ( 6) hydrogen bonds : bond 0.03486 / 2.30 ( 343) hydrogen bonds : angle 4.47139 / 3.14 ( 980) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: A 39 MET cc_start: 0.8643 (mmm) cc_final: 0.8146 (mmm) REVERT: A 215 MET cc_start: 0.8114 (mmm) cc_final: 0.7645 (mmp) REVERT: L 11 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8176 (tt) REVERT: L 82 ASP cc_start: 0.9055 (m-30) cc_final: 0.8744 (m-30) REVERT: L 105 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7234 (pt0) REVERT: L 108 ARG cc_start: 0.7434 (ttp80) cc_final: 0.6712 (ptm-80) REVERT: L 142 ARG cc_start: 0.7316 (OUTLIER) cc_final: 0.6870 (ttt-90) REVERT: K 34 MET cc_start: 0.7275 (ttt) cc_final: 0.6528 (mmm) outliers start: 20 outliers final: 12 residues processed: 101 average time/residue: 0.4753 time to fit residues: 50.7373 Evaluate side-chains 104 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 97 LYS Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 142 ARG Chi-restraints excluded: chain L residue 170 ASP Chi-restraints excluded: chain K residue 63 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 38 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 65 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 chunk 69 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 35 optimal weight: 0.0270 overall best weight: 2.1644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.187523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.132899 restraints weight = 24388.471| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 5.79 r_work: 0.2970 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2967 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6802 Z= 0.188 Angle : 0.623 8.510 9257 Z= 0.306 Chirality : 0.043 0.228 1070 Planarity : 0.005 0.035 1133 Dihedral : 7.660 108.546 956 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.98 % Allowed : 17.86 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.10 (0.29), residues: 846 helix: 2.29 (0.32), residues: 260 sheet: 1.37 (0.35), residues: 216 loop : -0.86 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 66 TYR 0.013 0.002 TYR A 186 PHE 0.018 0.002 PHE K 67 TRP 0.009 0.001 TRP H 100H HIS 0.002 0.001 HIS H 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.19 ( 6799) covalent geometry : angle 0.62324 / 0.31 ( 9251) SS BOND : bond 0.00589 / 0.30 ( 3) SS BOND : angle 0.68052 / 0.38 ( 6) hydrogen bonds : bond 0.04339 / 2.86 ( 343) hydrogen bonds : angle 4.60844 / 3.22 ( 980) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 85 time to evaluate : 0.188 Fit side-chains revert: symmetry clash REVERT: A 39 MET cc_start: 0.8657 (mmm) cc_final: 0.8282 (mmm) REVERT: A 261 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.7816 (mp10) REVERT: L 82 ASP cc_start: 0.9109 (m-30) cc_final: 0.8781 (m-30) REVERT: L 105 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7310 (pt0) REVERT: L 108 ARG cc_start: 0.7545 (ttp80) cc_final: 0.6827 (ptm-80) REVERT: L 142 ARG cc_start: 0.7375 (OUTLIER) cc_final: 0.6993 (ttt-90) REVERT: K 34 MET cc_start: 0.7239 (ttt) cc_final: 0.6451 (mmm) outliers start: 28 outliers final: 18 residues processed: 100 average time/residue: 0.4312 time to fit residues: 45.9877 Evaluate side-chains 103 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 97 LYS Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 142 ARG Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 170 ASP Chi-restraints excluded: chain K residue 63 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 12 optimal weight: 0.7980 chunk 65 optimal weight: 0.3980 chunk 56 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 51 optimal weight: 0.0370 chunk 31 optimal weight: 0.8980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.191717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.129894 restraints weight = 16585.620| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 3.54 r_work: 0.3095 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3090 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3090 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6802 Z= 0.099 Angle : 0.523 7.187 9257 Z= 0.256 Chirality : 0.041 0.229 1070 Planarity : 0.004 0.035 1133 Dihedral : 7.265 100.108 956 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.75 % Allowed : 19.09 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.36 (0.29), residues: 846 helix: 2.62 (0.32), residues: 261 sheet: 1.44 (0.35), residues: 214 loop : -0.74 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 185 TYR 0.013 0.001 TYR A 238 PHE 0.011 0.001 PHE K 67 TRP 0.008 0.001 TRP L 93 HIS 0.001 0.000 HIS L 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 ( 6799) covalent geometry : angle 0.52279 / 0.26 ( 9251) SS BOND : bond 0.00355 / 0.18 ( 3) SS BOND : angle 0.54336 / 0.29 ( 6) hydrogen bonds : bond 0.03121 / 2.05 ( 343) hydrogen bonds : angle 4.26948 / 3.01 ( 980) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.151 Fit side-chains revert: symmetry clash REVERT: A 39 MET cc_start: 0.8533 (mmm) cc_final: 0.8006 (mmm) REVERT: A 184 MET cc_start: 0.5348 (OUTLIER) cc_final: 0.4977 (tmm) REVERT: A 215 MET cc_start: 0.8092 (mmm) cc_final: 0.7692 (mmp) REVERT: H 100 MET cc_start: 0.6431 (mtm) cc_final: 0.6215 (mtt) REVERT: L 11 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8184 (tt) REVERT: L 82 ASP cc_start: 0.9011 (m-30) cc_final: 0.8707 (m-30) REVERT: L 105 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7091 (pt0) REVERT: L 142 ARG cc_start: 0.7261 (OUTLIER) cc_final: 0.6985 (ttt-90) REVERT: K 34 MET cc_start: 0.7304 (ttt) cc_final: 0.6490 (mmm) outliers start: 19 outliers final: 11 residues processed: 101 average time/residue: 0.4233 time to fit residues: 45.3030 Evaluate side-chains 103 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 97 LYS Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 142 ARG Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain K residue 63 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 14 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 47 optimal weight: 7.9990 chunk 68 optimal weight: 8.9990 chunk 43 optimal weight: 20.0000 chunk 5 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.191617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.148343 restraints weight = 14113.067| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 6.20 r_work: 0.3014 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6802 Z= 0.110 Angle : 0.528 7.079 9257 Z= 0.259 Chirality : 0.041 0.219 1070 Planarity : 0.004 0.033 1133 Dihedral : 7.246 103.632 956 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.47 % Allowed : 19.23 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.39 (0.29), residues: 846 helix: 2.65 (0.32), residues: 262 sheet: 1.45 (0.35), residues: 214 loop : -0.72 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 52A TYR 0.010 0.001 TYR A 238 PHE 0.011 0.001 PHE K 67 TRP 0.007 0.001 TRP H 47 HIS 0.001 0.000 HIS H 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 6799) covalent geometry : angle 0.52774 / 0.26 ( 9251) SS BOND : bond 0.00385 / 0.20 ( 3) SS BOND : angle 0.52517 / 0.28 ( 6) hydrogen bonds : bond 0.03299 / 2.18 ( 343) hydrogen bonds : angle 4.21742 / 2.97 ( 980) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: A 39 MET cc_start: 0.8615 (mmm) cc_final: 0.8117 (mmm) REVERT: A 215 MET cc_start: 0.8153 (mmm) cc_final: 0.7623 (mmp) REVERT: L 11 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8176 (tt) REVERT: L 82 ASP cc_start: 0.9066 (m-30) cc_final: 0.8757 (m-30) REVERT: L 105 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7301 (pt0) REVERT: L 142 ARG cc_start: 0.7302 (OUTLIER) cc_final: 0.6972 (ttt-90) REVERT: K 34 MET cc_start: 0.7287 (ttt) cc_final: 0.6474 (mmm) outliers start: 17 outliers final: 10 residues processed: 97 average time/residue: 0.4619 time to fit residues: 47.4979 Evaluate side-chains 101 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 97 LYS Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 142 ARG Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain K residue 63 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 46 optimal weight: 0.0670 chunk 50 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 44 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 74 optimal weight: 20.0000 chunk 17 optimal weight: 0.9980 chunk 83 optimal weight: 8.9990 overall best weight: 0.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.192047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.135360 restraints weight = 21251.054| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 5.19 r_work: 0.3057 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6802 Z= 0.108 Angle : 0.537 9.374 9257 Z= 0.261 Chirality : 0.041 0.219 1070 Planarity : 0.004 0.034 1133 Dihedral : 7.185 102.679 956 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.34 % Allowed : 19.51 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.44 (0.29), residues: 846 helix: 2.69 (0.32), residues: 262 sheet: 1.46 (0.35), residues: 214 loop : -0.69 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 52A TYR 0.011 0.001 TYR A 238 PHE 0.010 0.001 PHE K 67 TRP 0.007 0.001 TRP H 47 HIS 0.001 0.000 HIS L 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 6799) covalent geometry : angle 0.53656 / 0.26 ( 9251) SS BOND : bond 0.00383 / 0.20 ( 3) SS BOND : angle 0.51771 / 0.28 ( 6) hydrogen bonds : bond 0.03216 / 2.12 ( 343) hydrogen bonds : angle 4.17326 / 2.94 ( 980) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2646.71 seconds wall clock time: 45 minutes 50.83 seconds (2750.83 seconds total)