Starting phenix.real_space_refine on Wed Mar 12 01:08:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zyi_15024/03_2025/7zyi_15024.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zyi_15024/03_2025/7zyi_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7zyi_15024/03_2025/7zyi_15024.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zyi_15024/03_2025/7zyi_15024.map" model { file = "/net/cci-nas-00/data/ceres_data/7zyi_15024/03_2025/7zyi_15024.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zyi_15024/03_2025/7zyi_15024.cif" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.21, per 1000 atoms: 0.78 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: 1.52 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.85 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: 1.88 Time building geometry restraints manager: 1.81 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 - 25.81: 3935 25.81 - 51.63: 255 51.63 - 77.44: 39 77.44 - 103.25: 7 103.25 - 129.07: 12 Dihedral angle restraints: 4248 sinusoidal: 1782 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=" C5 CHO A 703 " pdb=" C6 CHO A 703 " pdb=" C7 CHO A 703 " pdb=" O7 CHO A 703 " ideal model delta sinusoidal sigma weight residual 287.57 158.50 129.07 1 3.00e+01 1.11e-03 1.74e+01 dihedral pdb=" C5 CHO A 702 " pdb=" C6 CHO A 702 " pdb=" C7 CHO A 702 " pdb=" O7 CHO A 702 " ideal model delta sinusoidal sigma weight residual 287.57 163.57 124.00 1 3.00e+01 1.11e-03 1.66e+01 ... (remaining 4245 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: 4.420 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: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.540 Find NCS groups from input model: 0.060 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:11.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 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 6799 Z= 0.804 Angle : 0.754 13.548 9251 Z= 0.364 Chirality : 0.087 1.654 1070 Planarity : 0.005 0.084 1133 Dihedral : 18.278 129.069 2667 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.005 0.001 TRP L 93 HIS 0.024 0.003 HIS H 200 PHE 0.006 0.001 PHE A 37 TYR 0.024 0.001 TYR L 140 ARG 0.005 0.000 ARG L 108 *********************** 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 : 0.706 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: 1.1412 time to fit residues: 113.1776 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 : 0.735 ------------------------------------------------------------------------------- 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 70 optimal weight: 20.0000 chunk 63 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 25 optimal weight: 0.0570 chunk 40 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 76 optimal weight: 20.0000 overall best weight: 1.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 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 = 0.4086 r_free = 0.4086 target = 0.188804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.128885 restraints weight = 18694.159| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 4.14 r_work: 0.3043 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 6799 Z= 0.259 Angle : 0.641 7.690 9251 Z= 0.314 Chirality : 0.046 0.278 1070 Planarity : 0.004 0.033 1133 Dihedral : 10.016 85.443 1206 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.02 % Allowed : 14.84 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.29), residues: 846 helix: 2.04 (0.32), residues: 261 sheet: 1.50 (0.34), residues: 219 loop : -0.63 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 103 HIS 0.002 0.001 HIS A 54 PHE 0.012 0.002 PHE A 128 TYR 0.012 0.001 TYR A 238 ARG 0.004 0.001 ARG L 66 *********************** 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 108 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.786 Fit side-chains revert: symmetry clash REVERT: L 82 ASP cc_start: 0.9022 (m-30) cc_final: 0.8712 (m-30) REVERT: L 108 ARG cc_start: 0.7633 (ttp80) cc_final: 0.6997 (ptm-80) REVERT: K 34 MET cc_start: 0.7309 (ttt) cc_final: 0.6549 (mmm) outliers start: 21 outliers final: 12 residues processed: 98 average time/residue: 1.1741 time to fit residues: 121.4837 Evaluate side-chains 96 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.678 ------------------------------------------------------------------------------- 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 235 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 279 ILE 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 22 THR 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 1 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 39 optimal weight: 0.0060 chunk 44 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 99 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 = 0.4101 r_free = 0.4101 target = 0.190211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.130322 restraints weight = 19506.191| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 4.35 r_work: 0.3062 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3054 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 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 = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3054 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 6799 Z= 0.157 Angle : 0.552 8.021 9251 Z= 0.272 Chirality : 0.043 0.252 1070 Planarity : 0.004 0.033 1133 Dihedral : 7.788 56.508 1201 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.88 % Allowed : 16.76 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.29), residues: 846 helix: 2.39 (0.32), residues: 261 sheet: 1.54 (0.34), residues: 220 loop : -0.65 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 100H HIS 0.001 0.000 HIS H 35 PHE 0.008 0.001 PHE A 37 TYR 0.011 0.001 TYR A 238 ARG 0.002 0.000 ARG K 52A *********************** 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 111 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.670 Fit side-chains REVERT: A 39 MET cc_start: 0.8662 (mmm) cc_final: 0.8267 (mmm) REVERT: L 11 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8160 (tt) REVERT: L 105 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7194 (pt0) REVERT: L 108 ARG cc_start: 0.7596 (ttp80) cc_final: 0.6899 (ptm-80) REVERT: L 142 ARG cc_start: 0.7311 (tmt90) cc_final: 0.6985 (ttt-90) REVERT: K 34 MET cc_start: 0.7339 (ttt) cc_final: 0.6604 (mmm) outliers start: 20 outliers final: 9 residues processed: 101 average time/residue: 1.1570 time to fit residues: 124.4791 Evaluate side-chains 97 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 290 MET 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 170 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 31 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 57 optimal weight: 0.0770 chunk 6 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 overall best weight: 1.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN A 293 GLN H 99 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 = 0.4080 r_free = 0.4080 target = 0.188412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.134141 restraints weight = 25730.778| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 6.26 r_work: 0.2975 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2961 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 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 = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2961 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6799 Z= 0.276 Angle : 0.601 7.497 9251 Z= 0.301 Chirality : 0.044 0.249 1070 Planarity : 0.004 0.033 1133 Dihedral : 7.528 52.175 1200 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.67 % Allowed : 16.48 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.29), residues: 846 helix: 2.23 (0.32), residues: 261 sheet: 1.50 (0.34), residues: 220 loop : -0.76 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 100H HIS 0.003 0.001 HIS A 54 PHE 0.013 0.002 PHE A 128 TYR 0.012 0.001 TYR A 186 ARG 0.004 0.000 ARG L 66 *********************** 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 121 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 88 time to evaluate : 0.681 Fit side-chains REVERT: A 39 MET cc_start: 0.8770 (mmm) cc_final: 0.8314 (mmm) REVERT: H 105 GLN cc_start: 0.7738 (OUTLIER) cc_final: 0.7497 (pp30) REVERT: L 82 ASP cc_start: 0.9090 (m-30) cc_final: 0.8777 (m-30) REVERT: L 105 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7329 (pt0) REVERT: L 108 ARG cc_start: 0.7636 (ttp80) cc_final: 0.6929 (ptm-80) REVERT: L 142 ARG cc_start: 0.7351 (OUTLIER) cc_final: 0.6981 (ttt-90) REVERT: K 34 MET cc_start: 0.7254 (ttt) cc_final: 0.6590 (mmm) outliers start: 33 outliers final: 16 residues processed: 107 average time/residue: 1.0454 time to fit residues: 118.6887 Evaluate side-chains 104 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL 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 171 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 H residue 97 LYS Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain H residue 105 GLN 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 9.9990 chunk 39 optimal weight: 0.0370 chunk 55 optimal weight: 0.2980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.0770 chunk 54 optimal weight: 2.9990 chunk 48 optimal weight: 0.0870 chunk 49 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 74 optimal weight: 0.0020 chunk 62 optimal weight: 3.9990 overall best weight: 0.1002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 HIS H 105 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.192020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.136750 restraints weight = 18525.582| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 4.32 r_work: 0.3104 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3098 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3098 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6799 Z= 0.120 Angle : 0.493 7.195 9251 Z= 0.248 Chirality : 0.041 0.240 1070 Planarity : 0.004 0.033 1133 Dihedral : 6.522 52.460 1200 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.88 % Allowed : 18.54 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.29), residues: 846 helix: 2.69 (0.33), residues: 261 sheet: 1.59 (0.34), residues: 220 loop : -0.68 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 100H HIS 0.001 0.000 HIS L 189 PHE 0.005 0.001 PHE A 37 TYR 0.011 0.001 TYR A 238 ARG 0.002 0.000 ARG K 52A *********************** 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 113 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.779 Fit side-chains revert: symmetry clash REVERT: A 39 MET cc_start: 0.8610 (mmm) cc_final: 0.8117 (mmm) REVERT: A 215 MET cc_start: 0.8045 (mmm) cc_final: 0.7632 (mmp) REVERT: H 105 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.7471 (pp30) REVERT: L 11 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8148 (tt) REVERT: L 42 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.7884 (mmtt) REVERT: L 108 ARG cc_start: 0.7318 (ttp80) cc_final: 0.6608 (ptm-80) REVERT: L 142 ARG cc_start: 0.7216 (tmt90) cc_final: 0.6924 (ttt-90) REVERT: K 34 MET cc_start: 0.7264 (ttt) cc_final: 0.6508 (mmm) outliers start: 20 outliers final: 6 residues processed: 102 average time/residue: 1.0949 time to fit residues: 118.2305 Evaluate side-chains 98 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 135 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 5.9990 chunk 30 optimal weight: 0.5980 chunk 42 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 17 optimal weight: 0.0050 chunk 25 optimal weight: 0.5980 chunk 81 optimal weight: 20.0000 chunk 65 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN H 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.189301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.131161 restraints weight = 12508.187| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 3.01 r_work: 0.3098 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2968 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6799 Z= 0.221 Angle : 0.548 8.464 9251 Z= 0.273 Chirality : 0.042 0.243 1070 Planarity : 0.004 0.033 1133 Dihedral : 6.566 51.418 1196 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.53 % Allowed : 16.62 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.29), residues: 846 helix: 2.60 (0.32), residues: 261 sheet: 1.50 (0.35), residues: 214 loop : -0.70 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 100H HIS 0.002 0.000 HIS H 164 PHE 0.027 0.001 PHE K 67 TYR 0.012 0.001 TYR A 238 ARG 0.003 0.000 ARG L 66 *********************** 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 124 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 92 time to evaluate : 0.651 Fit side-chains revert: symmetry clash REVERT: A 39 MET cc_start: 0.8758 (mmm) cc_final: 0.8259 (mmm) REVERT: H 46 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7893 (tm-30) REVERT: L 82 ASP cc_start: 0.9093 (m-30) cc_final: 0.8795 (m-30) REVERT: L 105 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7373 (pt0) REVERT: L 108 ARG cc_start: 0.7576 (ttp80) cc_final: 0.6911 (ptm-80) REVERT: L 142 ARG cc_start: 0.7320 (OUTLIER) cc_final: 0.7016 (ttt-90) REVERT: K 34 MET cc_start: 0.7325 (ttt) cc_final: 0.6571 (mmm) outliers start: 32 outliers final: 11 residues processed: 108 average time/residue: 1.1198 time to fit residues: 128.2921 Evaluate side-chains 106 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.693 ------------------------------------------------------------------------------- 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 46 GLU 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 135 LEU 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 37 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 33 optimal weight: 0.0870 chunk 4 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 69 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 73 optimal weight: 20.0000 chunk 13 optimal weight: 1.9990 overall best weight: 1.1164 ------------------------------------------------------------------------------- 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 = 0.4095 r_free = 0.4095 target = 0.189866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.133743 restraints weight = 19559.345| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 4.83 r_work: 0.3048 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3035 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 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 = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3035 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6799 Z= 0.184 Angle : 0.520 7.163 9251 Z= 0.261 Chirality : 0.041 0.233 1070 Planarity : 0.004 0.033 1133 Dihedral : 6.356 52.007 1196 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.30 % Allowed : 17.99 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.29), residues: 846 helix: 2.61 (0.32), residues: 262 sheet: 1.46 (0.35), residues: 214 loop : -0.70 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 103 HIS 0.001 0.000 HIS H 164 PHE 0.018 0.001 PHE K 67 TYR 0.013 0.001 TYR A 238 ARG 0.002 0.000 ARG L 66 *********************** 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 113 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.715 Fit side-chains revert: symmetry clash REVERT: A 39 MET cc_start: 0.8678 (mmm) cc_final: 0.8087 (mmm) REVERT: A 261 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.7651 (mp10) REVERT: H 105 GLN cc_start: 0.7531 (OUTLIER) cc_final: 0.7098 (pp30) REVERT: L 11 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8162 (tt) REVERT: L 82 ASP cc_start: 0.9046 (m-30) cc_final: 0.8739 (m-30) REVERT: L 105 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7182 (pt0) REVERT: L 108 ARG cc_start: 0.7377 (ttp80) cc_final: 0.6681 (ptm-80) REVERT: L 142 ARG cc_start: 0.7275 (OUTLIER) cc_final: 0.6972 (ttt-90) REVERT: K 34 MET cc_start: 0.7240 (ttt) cc_final: 0.6443 (mmm) outliers start: 23 outliers final: 10 residues processed: 99 average time/residue: 1.0550 time to fit residues: 110.7207 Evaluate side-chains 105 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 CYS 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 46 GLU Chi-restraints excluded: chain H residue 105 GLN 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 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 67 optimal weight: 6.9990 chunk 41 optimal weight: 8.9990 chunk 81 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 23 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 53 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 15 optimal weight: 0.0670 overall best weight: 1.6920 ------------------------------------------------------------------------------- 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 = 0.4083 r_free = 0.4083 target = 0.188819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.134622 restraints weight = 26386.560| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 6.35 r_work: 0.2981 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2977 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2977 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6799 Z= 0.249 Angle : 0.564 7.262 9251 Z= 0.284 Chirality : 0.042 0.233 1070 Planarity : 0.004 0.034 1133 Dihedral : 6.653 54.665 1196 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.43 % Allowed : 17.58 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.29), residues: 846 helix: 2.48 (0.32), residues: 262 sheet: 1.39 (0.35), residues: 214 loop : -0.79 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 103 HIS 0.002 0.001 HIS H 35 PHE 0.016 0.002 PHE K 67 TYR 0.013 0.001 TYR A 238 ARG 0.003 0.000 ARG L 66 *********************** 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 109 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.639 Fit side-chains revert: symmetry clash REVERT: A 39 MET cc_start: 0.8638 (mmm) cc_final: 0.8333 (mmm) REVERT: L 82 ASP cc_start: 0.9100 (m-30) cc_final: 0.8779 (m-30) REVERT: L 105 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7293 (pt0) REVERT: L 108 ARG cc_start: 0.7552 (ttp80) cc_final: 0.6869 (ptm-80) REVERT: L 142 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.7023 (ttt-90) REVERT: K 34 MET cc_start: 0.7268 (ttt) cc_final: 0.6468 (mmm) outliers start: 24 outliers final: 16 residues processed: 95 average time/residue: 0.9791 time to fit residues: 99.0066 Evaluate side-chains 101 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 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 46 GLU Chi-restraints excluded: chain H residue 87 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 17 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 45 optimal weight: 0.0970 chunk 20 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 76 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 = 0.4108 r_free = 0.4108 target = 0.191369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.134711 restraints weight = 20644.396| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 5.00 r_work: 0.3070 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6799 Z= 0.149 Angle : 0.516 9.464 9251 Z= 0.256 Chirality : 0.041 0.233 1070 Planarity : 0.004 0.034 1133 Dihedral : 6.157 51.915 1196 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.75 % Allowed : 18.41 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.29), residues: 846 helix: 2.68 (0.32), residues: 262 sheet: 1.43 (0.35), residues: 214 loop : -0.76 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 93 HIS 0.001 0.000 HIS H 35 PHE 0.012 0.001 PHE K 67 TYR 0.014 0.001 TYR A 238 ARG 0.002 0.000 ARG K 52A *********************** 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 107 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.656 Fit side-chains revert: symmetry clash REVERT: A 39 MET cc_start: 0.8571 (mmm) cc_final: 0.8306 (mmm) REVERT: A 215 MET cc_start: 0.8117 (mmm) cc_final: 0.7641 (mmp) REVERT: A 261 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.7594 (mp10) REVERT: L 11 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8169 (tt) REVERT: L 82 ASP cc_start: 0.9019 (m-30) cc_final: 0.8724 (m-30) REVERT: L 105 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7157 (pt0) REVERT: L 108 ARG cc_start: 0.7390 (ttp80) cc_final: 0.6713 (ptm-80) REVERT: L 142 ARG cc_start: 0.7289 (OUTLIER) cc_final: 0.7004 (ttt-90) REVERT: K 34 MET cc_start: 0.7257 (ttt) cc_final: 0.6456 (mmm) outliers start: 19 outliers final: 10 residues processed: 99 average time/residue: 1.0098 time to fit residues: 106.3531 Evaluate side-chains 101 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL 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 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 110 THR 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 K residue 63 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 79 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 50 optimal weight: 0.0040 chunk 5 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 overall best weight: 0.9196 ------------------------------------------------------------------------------- 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 = 0.4097 r_free = 0.4097 target = 0.190176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.135629 restraints weight = 26442.326| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 6.21 r_work: 0.3017 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6799 Z= 0.172 Angle : 0.515 7.118 9251 Z= 0.259 Chirality : 0.041 0.229 1070 Planarity : 0.004 0.034 1133 Dihedral : 6.107 53.936 1196 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.47 % Allowed : 18.82 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.29), residues: 846 helix: 2.70 (0.33), residues: 262 sheet: 1.40 (0.35), residues: 214 loop : -0.74 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.001 0.000 HIS H 164 PHE 0.011 0.001 PHE K 67 TYR 0.012 0.001 TYR A 238 ARG 0.002 0.000 ARG K 52A ********************** 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 : 0.743 Fit side-chains revert: symmetry clash REVERT: A 39 MET cc_start: 0.8624 (mmm) cc_final: 0.8339 (mmm) REVERT: A 134 MET cc_start: 0.8380 (ttp) cc_final: 0.8106 (ttm) REVERT: A 184 MET cc_start: 0.5469 (OUTLIER) cc_final: 0.5015 (tmm) REVERT: A 215 MET cc_start: 0.8175 (mmm) cc_final: 0.7629 (mmp) REVERT: A 261 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.7647 (mp10) REVERT: L 11 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8183 (tt) REVERT: L 82 ASP cc_start: 0.9060 (m-30) cc_final: 0.8763 (m-30) REVERT: L 105 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7274 (pt0) REVERT: L 108 ARG cc_start: 0.7421 (ttp80) cc_final: 0.6750 (ptm-80) REVERT: L 142 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.6990 (ttt-90) REVERT: K 34 MET cc_start: 0.7238 (ttt) cc_final: 0.6443 (mmm) outliers start: 17 outliers final: 10 residues processed: 99 average time/residue: 1.0866 time to fit residues: 114.0163 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 : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 96 CYS 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 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 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 K residue 63 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 33 optimal weight: 0.8980 chunk 81 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 76 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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 = 0.4094 r_free = 0.4094 target = 0.190015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.133128 restraints weight = 18554.781| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 4.10 r_work: 0.3064 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6799 Z= 0.205 Angle : 0.552 9.843 9251 Z= 0.273 Chirality : 0.041 0.231 1070 Planarity : 0.004 0.035 1133 Dihedral : 6.244 55.195 1196 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.47 % Allowed : 18.82 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.29), residues: 846 helix: 2.64 (0.33), residues: 262 sheet: 1.38 (0.36), residues: 214 loop : -0.77 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 103 HIS 0.001 0.000 HIS H 164 PHE 0.012 0.001 PHE K 67 TYR 0.013 0.001 TYR A 238 ARG 0.002 0.000 ARG K 52A Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6158.53 seconds wall clock time: 105 minutes 49.73 seconds (6349.73 seconds total)