Starting phenix.real_space_refine on Wed Feb 12 01:27:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zyi_15024/02_2025/7zyi_15024.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zyi_15024/02_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_15024/02_2025/7zyi_15024.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zyi_15024/02_2025/7zyi_15024.map" model { file = "/net/cci-nas-00/data/ceres_data/7zyi_15024/02_2025/7zyi_15024.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zyi_15024/02_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-5592/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: 6.08, per 1000 atoms: 0.92 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: 1.90 Conformation dependent library (CDL) restraints added in 1.2 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: 0.94 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: 1.98 Time building geometry restraints manager: 2.00 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: 5.310 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: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.180 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:12.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.710 ------------------------------------------------------------------------------- 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 : 0.688 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: 1.1719 time to fit residues: 116.3560 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 : 0.720 ------------------------------------------------------------------------------- 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: 0.3042 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- 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: 0.8175 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 : 0.664 Fit side-chains revert: symmetry clash REVERT: L 82 ASP cc_start: 0.9022 (m-30) cc_final: 0.8711 (m-30) REVERT: L 108 ARG cc_start: 0.7637 (ttp80) cc_final: 0.7002 (ptm-80) REVERT: K 34 MET cc_start: 0.7322 (ttt) cc_final: 0.6564 (mmm) outliers start: 21 outliers final: 12 residues processed: 98 average time/residue: 1.2428 time to fit residues: 128.5335 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 : 0.716 ------------------------------------------------------------------------------- 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: 1.9990 chunk 23 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 39 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.4093 r_free = 0.4093 target = 0.189369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.128192 restraints weight = 19469.949| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 4.27 r_work: 0.3043 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3039 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3039 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6799 Z= 0.194 Angle : 0.567 8.074 9251 Z= 0.281 Chirality : 0.043 0.249 1070 Planarity : 0.004 0.033 1133 Dihedral : 7.840 55.476 1201 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.43 % Allowed : 16.35 % Favored : 80.22 % 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: 1.32 (0.29), residues: 846 helix: 2.34 (0.32), residues: 260 sheet: 1.54 (0.34), residues: 220 loop : -0.67 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 100H HIS 0.001 0.001 HIS A 54 PHE 0.009 0.001 PHE A 37 TYR 0.011 0.001 TYR A 238 ARG 0.003 0.000 ARG L 66 *********************** 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: 24 poor density : 90 time to evaluate : 0.709 Fit side-chains REVERT: A 39 MET cc_start: 0.8674 (mmm) cc_final: 0.8368 (mmm) REVERT: H 46 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8380 (tm-30) REVERT: L 11 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8159 (tt) REVERT: L 82 ASP cc_start: 0.9021 (m-30) cc_final: 0.8717 (m-30) REVERT: L 105 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7177 (pt0) REVERT: L 108 ARG cc_start: 0.7585 (ttp80) cc_final: 0.6881 (ptm-80) REVERT: L 142 ARG cc_start: 0.7298 (tmt90) cc_final: 0.6964 (ttt-90) REVERT: K 34 MET cc_start: 0.7324 (ttt) cc_final: 0.6591 (mmm) outliers start: 24 outliers final: 11 residues processed: 103 average time/residue: 1.0437 time to fit residues: 114.1268 Evaluate side-chains 100 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 235 LEU Chi-restraints excluded: chain A residue 265 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: 3.9990 chunk 48 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 chunk 6 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN H 99 GLN H 105 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.189724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.130059 restraints weight = 25703.775| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 5.91 r_work: 0.2989 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2983 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2983 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6799 Z= 0.225 Angle : 0.573 7.395 9251 Z= 0.286 Chirality : 0.043 0.245 1070 Planarity : 0.004 0.033 1133 Dihedral : 7.274 51.451 1200 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.40 % Allowed : 15.93 % 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 (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: 1.28 (0.29), residues: 846 helix: 2.37 (0.32), residues: 260 sheet: 1.49 (0.34), residues: 220 loop : -0.72 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 93 HIS 0.002 0.001 HIS A 54 PHE 0.011 0.001 PHE A 128 TYR 0.010 0.001 TYR A 238 ARG 0.003 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: 31 poor density : 90 time to evaluate : 0.688 Fit side-chains revert: symmetry clash REVERT: A 39 MET cc_start: 0.8748 (mmm) cc_final: 0.8277 (mmm) REVERT: H 97 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.7079 (mptp) REVERT: L 82 ASP cc_start: 0.9041 (m-30) cc_final: 0.8717 (m-30) REVERT: L 105 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7256 (pt0) REVERT: L 108 ARG cc_start: 0.7634 (ttp80) cc_final: 0.6915 (ptm-80) REVERT: L 142 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.6849 (ttt-90) REVERT: K 34 MET cc_start: 0.7309 (ttt) cc_final: 0.6612 (mmm) outliers start: 31 outliers final: 15 residues processed: 107 average time/residue: 1.0895 time to fit residues: 123.5165 Evaluate side-chains 104 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.778 ------------------------------------------------------------------------------- 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 265 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 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: 8.9990 chunk 39 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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 = 0.189037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.129115 restraints weight = 18589.610| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 4.40 r_work: 0.3014 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3012 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6799 Z= 0.250 Angle : 0.587 9.361 9251 Z= 0.292 Chirality : 0.043 0.243 1070 Planarity : 0.004 0.034 1133 Dihedral : 7.148 50.931 1200 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.53 % Allowed : 16.48 % 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: 1.25 (0.29), residues: 846 helix: 2.35 (0.32), residues: 261 sheet: 1.49 (0.34), residues: 220 loop : -0.77 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 103 HIS 0.002 0.001 HIS A 54 PHE 0.011 0.001 PHE A 128 TYR 0.011 0.001 TYR A 186 ARG 0.003 0.000 ARG L 66 *********************** 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: 32 poor density : 87 time to evaluate : 0.669 Fit side-chains revert: symmetry clash REVERT: A 39 MET cc_start: 0.8710 (mmm) cc_final: 0.8200 (mmm) REVERT: H 97 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.7221 (mptp) REVERT: L 82 ASP cc_start: 0.9040 (m-30) cc_final: 0.8734 (m-30) REVERT: L 105 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7209 (pt0) REVERT: L 108 ARG cc_start: 0.7587 (ttp80) cc_final: 0.6886 (ptm-80) REVERT: L 142 ARG cc_start: 0.7348 (OUTLIER) cc_final: 0.6991 (ttt-90) REVERT: K 34 MET cc_start: 0.7278 (ttt) cc_final: 0.6544 (mmm) outliers start: 32 outliers final: 17 residues processed: 105 average time/residue: 1.0300 time to fit residues: 114.9055 Evaluate side-chains 104 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL 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 265 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 0.1980 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 81 optimal weight: 20.0000 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 0.0050 overall best weight: 0.9798 ------------------------------------------------------------------------------- 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 = 0.189902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.147438 restraints weight = 12466.200| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 6.00 r_work: 0.3011 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3001 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 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 = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6799 Z= 0.176 Angle : 0.538 7.266 9251 Z= 0.268 Chirality : 0.041 0.240 1070 Planarity : 0.004 0.033 1133 Dihedral : 6.779 50.306 1200 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.98 % Allowed : 17.72 % 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 (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: 2.57 (0.33), residues: 260 sheet: 1.45 (0.35), residues: 214 loop : -0.74 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.001 0.000 HIS A 54 PHE 0.029 0.001 PHE K 67 TYR 0.011 0.001 TYR A 238 ARG 0.002 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 119 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 91 time to evaluate : 0.684 Fit side-chains revert: symmetry clash REVERT: A 39 MET cc_start: 0.8655 (mmm) cc_final: 0.8082 (mmm) REVERT: L 82 ASP cc_start: 0.9042 (m-30) cc_final: 0.8710 (m-30) REVERT: L 105 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7219 (pt0) REVERT: L 108 ARG cc_start: 0.7492 (ttp80) cc_final: 0.6845 (ptm-80) REVERT: L 142 ARG cc_start: 0.7328 (OUTLIER) cc_final: 0.6840 (ttt-90) REVERT: K 34 MET cc_start: 0.7226 (ttt) cc_final: 0.6459 (mmm) outliers start: 28 outliers final: 12 residues processed: 107 average time/residue: 1.0060 time to fit residues: 114.4514 Evaluate side-chains 104 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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 124 THR 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 0.3980 chunk 50 optimal weight: 7.9990 chunk 33 optimal weight: 0.0030 chunk 4 optimal weight: 0.0370 chunk 67 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 73 optimal weight: 9.9990 chunk 13 optimal weight: 0.5980 overall best weight: 0.4070 ------------------------------------------------------------------------------- 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 = 0.4126 r_free = 0.4126 target = 0.193207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.137181 restraints weight = 19576.007| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 4.82 r_work: 0.3107 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3096 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 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 = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3096 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2031 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= 0.128 Angle : 0.508 9.375 9251 Z= 0.250 Chirality : 0.040 0.234 1070 Planarity : 0.004 0.033 1133 Dihedral : 5.949 50.804 1196 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.75 % Allowed : 18.27 % 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: 1.48 (0.29), residues: 846 helix: 2.72 (0.33), residues: 262 sheet: 1.49 (0.35), residues: 214 loop : -0.67 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 93 HIS 0.001 0.000 HIS H 35 PHE 0.014 0.001 PHE K 67 TYR 0.009 0.001 TYR A 238 ARG 0.002 0.000 ARG A 185 *********************** 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 117 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.722 Fit side-chains revert: symmetry clash REVERT: A 39 MET cc_start: 0.8549 (mmm) cc_final: 0.8041 (mmm) REVERT: A 215 MET cc_start: 0.8095 (mmm) cc_final: 0.7616 (mmp) REVERT: L 11 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8195 (tt) REVERT: L 42 LYS cc_start: 0.8468 (mppt) cc_final: 0.7838 (mmtt) REVERT: L 103 LYS cc_start: 0.8943 (ttmt) cc_final: 0.8645 (tttp) REVERT: L 142 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.6914 (ttt-90) REVERT: K 34 MET cc_start: 0.7318 (ttt) cc_final: 0.6535 (mmm) outliers start: 19 outliers final: 9 residues processed: 108 average time/residue: 1.1336 time to fit residues: 129.6951 Evaluate side-chains 103 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.676 ------------------------------------------------------------------------------- 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 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 110 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 142 ARG 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: 3.9990 chunk 41 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 80 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.189933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.136203 restraints weight = 26437.741| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 6.56 r_work: 0.2990 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- 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 = 0.00 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 = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2977 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6799 Z= 0.241 Angle : 0.553 7.193 9251 Z= 0.277 Chirality : 0.042 0.245 1070 Planarity : 0.004 0.034 1133 Dihedral : 6.397 53.574 1196 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.43 % Allowed : 18.13 % 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 (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: 1.34 (0.29), residues: 846 helix: 2.58 (0.33), residues: 262 sheet: 1.45 (0.35), residues: 214 loop : -0.76 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.002 0.001 HIS A 54 PHE 0.015 0.001 PHE K 67 TYR 0.011 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 114 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.831 Fit side-chains revert: symmetry clash REVERT: A 39 MET cc_start: 0.8632 (mmm) cc_final: 0.8084 (mmm) REVERT: H 97 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.7067 (mptp) REVERT: L 82 ASP cc_start: 0.9079 (m-30) cc_final: 0.8779 (m-30) REVERT: L 105 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7286 (pt0) REVERT: L 108 ARG cc_start: 0.7493 (ttp80) cc_final: 0.6849 (ptm-80) REVERT: L 142 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.6939 (ttt-90) REVERT: K 34 MET cc_start: 0.7245 (ttt) cc_final: 0.6438 (mmm) outliers start: 24 outliers final: 13 residues processed: 104 average time/residue: 1.1052 time to fit residues: 122.7803 Evaluate side-chains 104 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.759 ------------------------------------------------------------------------------- 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 235 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 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: 4.9990 chunk 21 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 45 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 13 optimal weight: 0.0030 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 HIS 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 = 0.191914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.136675 restraints weight = 20666.470| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 5.28 r_work: 0.3078 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3049 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 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 = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3049 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6799 Z= 0.146 Angle : 0.514 9.576 9251 Z= 0.252 Chirality : 0.041 0.232 1070 Planarity : 0.004 0.034 1133 Dihedral : 6.020 51.807 1196 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.34 % Allowed : 19.09 % 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: 1.41 (0.29), residues: 846 helix: 2.66 (0.33), residues: 263 sheet: 1.48 (0.35), residues: 214 loop : -0.74 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.001 0.000 HIS A 54 PHE 0.012 0.001 PHE K 67 TYR 0.013 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 109 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.613 Fit side-chains revert: symmetry clash REVERT: A 39 MET cc_start: 0.8561 (mmm) cc_final: 0.8008 (mmm) REVERT: A 215 MET cc_start: 0.8144 (mmm) cc_final: 0.7638 (mmp) REVERT: H 97 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.7030 (mptp) REVERT: L 11 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8161 (tt) REVERT: L 82 ASP cc_start: 0.9020 (m-30) cc_final: 0.8731 (m-30) REVERT: L 105 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7186 (pt0) REVERT: L 108 ARG cc_start: 0.7346 (ttp80) cc_final: 0.6664 (ptm-80) REVERT: L 142 ARG cc_start: 0.7267 (OUTLIER) cc_final: 0.6965 (ttt-90) REVERT: K 34 MET cc_start: 0.7279 (ttt) cc_final: 0.6456 (mmm) outliers start: 16 outliers final: 10 residues processed: 102 average time/residue: 1.1068 time to fit residues: 119.7512 Evaluate side-chains 105 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.799 ------------------------------------------------------------------------------- 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 171 THR 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 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: 0.8980 chunk 65 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.4102 r_free = 0.4102 target = 0.190785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.137057 restraints weight = 26590.956| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 6.61 r_work: 0.3004 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2244 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= 0.187 Angle : 0.526 7.143 9251 Z= 0.263 Chirality : 0.041 0.228 1070 Planarity : 0.004 0.034 1133 Dihedral : 6.139 54.640 1196 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.88 % Allowed : 18.41 % 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: 2.69 (0.33), residues: 262 sheet: 1.45 (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 H 47 HIS 0.001 0.000 HIS H 164 PHE 0.012 0.001 PHE K 67 TYR 0.012 0.001 TYR A 238 ARG 0.002 0.000 ARG L 66 ********************** 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 111 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.720 Fit side-chains revert: symmetry clash REVERT: A 39 MET cc_start: 0.8577 (mmm) cc_final: 0.8197 (mmm) REVERT: H 97 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.6959 (mptp) REVERT: L 11 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8144 (tt) REVERT: L 82 ASP cc_start: 0.9076 (m-30) cc_final: 0.8770 (m-30) REVERT: L 105 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7264 (pt0) REVERT: L 108 ARG cc_start: 0.7368 (ttp80) cc_final: 0.6689 (ptm-80) REVERT: L 142 ARG cc_start: 0.7278 (OUTLIER) cc_final: 0.6954 (ttt-90) REVERT: K 34 MET cc_start: 0.7224 (ttt) cc_final: 0.6416 (mmm) outliers start: 20 outliers final: 13 residues processed: 101 average time/residue: 1.1003 time to fit residues: 117.8457 Evaluate side-chains 109 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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 171 THR Chi-restraints excluded: chain A residue 197 LEU 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 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 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: 0.0030 chunk 81 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 chunk 66 optimal weight: 10.0000 chunk 12 optimal weight: 0.0040 chunk 50 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 overall best weight: 0.4804 ------------------------------------------------------------------------------- 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 = 0.4122 r_free = 0.4122 target = 0.192586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.134633 restraints weight = 18578.031| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 4.13 r_work: 0.3101 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3093 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3093 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2296 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= 0.132 Angle : 0.494 7.021 9251 Z= 0.245 Chirality : 0.040 0.231 1070 Planarity : 0.004 0.033 1133 Dihedral : 5.753 52.362 1196 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.20 % Allowed : 19.23 % 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: 1.49 (0.29), residues: 846 helix: 2.76 (0.33), residues: 263 sheet: 1.51 (0.35), residues: 214 loop : -0.71 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 93 HIS 0.001 0.000 HIS L 189 PHE 0.009 0.001 PHE K 67 TYR 0.012 0.001 TYR A 238 ARG 0.001 0.000 ARG K 52A Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5895.88 seconds wall clock time: 105 minutes 10.36 seconds (6310.36 seconds total)