Starting phenix.real_space_refine on Fri Jul 25 02:41:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zyi_15024/07_2025/7zyi_15024.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zyi_15024/07_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_15024/07_2025/7zyi_15024.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zyi_15024/07_2025/7zyi_15024.map" model { file = "/net/cci-nas-00/data/ceres_data/7zyi_15024/07_2025/7zyi_15024.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zyi_15024/07_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-5711/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: 7.76, per 1000 atoms: 1.17 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: 1.96 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: 0.89 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: 2.02 Time building geometry restraints manager: 2.05 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: 133.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.610 Find NCS groups from input model: 0.080 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:12.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 170.650 ------------------------------------------------------------------------------- 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 6802 Z= 0.653 Angle : 0.753 13.548 9257 Z= 0.364 Chirality : 0.087 1.654 1070 Planarity : 0.005 0.084 1133 Dihedral : 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 Details of bonding type rmsd hydrogen bonds : bond 0.19631 ( 343) hydrogen bonds : angle 7.46331 ( 980) SS BOND : bond 0.00202 ( 3) SS BOND : angle 0.18228 ( 6) covalent geometry : bond 0.01309 ( 6799) covalent geometry : angle 0.75360 ( 9251) *********************** 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 : 0.965 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: 1.7741 time to fit residues: 176.1243 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 : 0.787 ------------------------------------------------------------------------------- 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: 6.9990 chunk 76 optimal weight: 20.0000 overall best weight: 2.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 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 = 0.4063 r_free = 0.4063 target = 0.186687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.123781 restraints weight = 18604.147| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 3.95 r_work: 0.2991 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2985 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2985 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 6802 Z= 0.227 Angle : 0.700 7.909 9257 Z= 0.347 Chirality : 0.048 0.271 1070 Planarity : 0.005 0.037 1133 Dihedral : 10.073 81.897 1206 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.98 % Allowed : 14.97 % Favored : 81.04 % 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: 0.93 (0.29), residues: 846 helix: 1.72 (0.32), residues: 261 sheet: 1.43 (0.34), residues: 219 loop : -0.73 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 103 HIS 0.003 0.001 HIS H 164 PHE 0.017 0.002 PHE A 128 TYR 0.015 0.002 TYR A 183 ARG 0.006 0.001 ARG L 66 Details of bonding type rmsd hydrogen bonds : bond 0.05208 ( 343) hydrogen bonds : angle 5.40855 ( 980) SS BOND : bond 0.00696 ( 3) SS BOND : angle 0.72663 ( 6) covalent geometry : bond 0.00546 ( 6799) covalent geometry : angle 0.69958 ( 9251) *********************** 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 116 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 88 time to evaluate : 0.872 Fit side-chains revert: symmetry clash REVERT: A 39 MET cc_start: 0.8688 (mmm) cc_final: 0.8288 (mmm) REVERT: L 82 ASP cc_start: 0.9070 (m-30) cc_final: 0.8777 (m-30) REVERT: L 105 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7233 (pt0) REVERT: L 108 ARG cc_start: 0.7677 (ttp80) cc_final: 0.7052 (ptm-80) REVERT: L 142 ARG cc_start: 0.7651 (ttt180) cc_final: 0.7159 (ttt-90) REVERT: K 34 MET cc_start: 0.7404 (ttt) cc_final: 0.6506 (mmm) outliers start: 28 outliers final: 14 residues processed: 104 average time/residue: 1.1003 time to fit residues: 121.3041 Evaluate side-chains 99 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 121 VAL 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 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 105 GLN 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 170 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 1 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 60 optimal weight: 0.4980 chunk 40 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 39 optimal weight: 0.4980 chunk 44 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 80 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN H 99 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 = 0.4100 r_free = 0.4100 target = 0.190526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.131523 restraints weight = 19464.544| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 4.39 r_work: 0.3054 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3041 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3041 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 6802 Z= 0.111 Angle : 0.541 7.534 9257 Z= 0.269 Chirality : 0.043 0.246 1070 Planarity : 0.004 0.034 1133 Dihedral : 7.666 55.334 1201 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.57 % Allowed : 15.66 % Favored : 80.77 % 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: 2.29 (0.32), residues: 261 sheet: 1.49 (0.35), residues: 214 loop : -0.68 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 93 HIS 0.001 0.000 HIS H 35 PHE 0.007 0.001 PHE A 37 TYR 0.012 0.001 TYR A 238 ARG 0.003 0.000 ARG L 66 Details of bonding type rmsd hydrogen bonds : bond 0.03747 ( 343) hydrogen bonds : angle 4.86491 ( 980) SS BOND : bond 0.00451 ( 3) SS BOND : angle 0.48548 ( 6) covalent geometry : bond 0.00242 ( 6799) covalent geometry : angle 0.54099 ( 9251) *********************** 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 115 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 1.166 Fit side-chains revert: symmetry clash REVERT: A 39 MET cc_start: 0.8686 (mmm) cc_final: 0.8296 (mmm) REVERT: A 215 MET cc_start: 0.8103 (mmm) cc_final: 0.7656 (mmp) REVERT: H 46 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8368 (tm-30) REVERT: H 105 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.7506 (pp30) REVERT: L 11 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8153 (tt) REVERT: L 82 ASP cc_start: 0.9008 (m-30) cc_final: 0.8695 (m-30) REVERT: L 108 ARG cc_start: 0.7549 (ttp80) cc_final: 0.6841 (ptm-80) REVERT: K 34 MET cc_start: 0.7346 (ttt) cc_final: 0.6603 (mmm) outliers start: 25 outliers final: 7 residues processed: 104 average time/residue: 1.9244 time to fit residues: 213.1586 Evaluate side-chains 94 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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: 2.9990 chunk 69 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 19 optimal weight: 0.0040 chunk 61 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 overall best weight: 0.9994 ------------------------------------------------------------------------------- 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 105 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.190236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.132774 restraints weight = 25727.637| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 5.81 r_work: 0.3006 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 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 = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6802 Z= 0.118 Angle : 0.547 7.830 9257 Z= 0.270 Chirality : 0.042 0.241 1070 Planarity : 0.004 0.033 1133 Dihedral : 6.972 51.593 1196 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.61 % Allowed : 17.99 % Favored : 79.40 % 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: 2.45 (0.32), residues: 260 sheet: 1.46 (0.35), residues: 214 loop : -0.65 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 100H HIS 0.001 0.000 HIS A 54 PHE 0.008 0.001 PHE A 37 TYR 0.010 0.001 TYR A 238 ARG 0.002 0.000 ARG L 66 Details of bonding type rmsd hydrogen bonds : bond 0.03643 ( 343) hydrogen bonds : angle 4.66350 ( 980) SS BOND : bond 0.00434 ( 3) SS BOND : angle 0.48605 ( 6) covalent geometry : bond 0.00268 ( 6799) covalent geometry : angle 0.54725 ( 9251) *********************** 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 107 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.757 Fit side-chains revert: symmetry clash REVERT: A 39 MET cc_start: 0.8740 (mmm) cc_final: 0.8286 (mmm) REVERT: A 215 MET cc_start: 0.8151 (mmm) cc_final: 0.7654 (mmp) REVERT: H 46 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8381 (tm-30) REVERT: L 11 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8181 (tt) REVERT: L 42 LYS cc_start: 0.8558 (mppt) cc_final: 0.7934 (mmtt) REVERT: L 82 ASP cc_start: 0.9034 (m-30) cc_final: 0.8730 (m-30) REVERT: L 105 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7247 (pt0) REVERT: L 108 ARG cc_start: 0.7637 (ttp80) cc_final: 0.6954 (ptm-80) REVERT: L 142 ARG cc_start: 0.7403 (tmt90) cc_final: 0.7046 (ttt-90) REVERT: K 34 MET cc_start: 0.7363 (ttt) cc_final: 0.6687 (mmm) outliers start: 18 outliers final: 9 residues processed: 97 average time/residue: 1.2254 time to fit residues: 125.4741 Evaluate side-chains 99 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain H residue 97 LYS 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 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: 2.9990 chunk 55 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 49 optimal weight: 30.0000 chunk 56 optimal weight: 0.0370 chunk 74 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 overall best weight: 1.4064 ------------------------------------------------------------------------------- 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 = 0.4086 r_free = 0.4086 target = 0.189280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.129376 restraints weight = 18505.249| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 4.09 r_work: 0.3027 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6802 Z= 0.138 Angle : 0.550 7.289 9257 Z= 0.274 Chirality : 0.042 0.241 1070 Planarity : 0.004 0.034 1133 Dihedral : 6.811 50.169 1196 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.85 % Allowed : 16.90 % Favored : 79.26 % 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: 1.31 (0.29), residues: 846 helix: 2.42 (0.32), residues: 261 sheet: 1.45 (0.35), residues: 214 loop : -0.66 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 93 HIS 0.002 0.001 HIS A 54 PHE 0.010 0.001 PHE A 128 TYR 0.010 0.001 TYR A 238 ARG 0.003 0.000 ARG L 66 Details of bonding type rmsd hydrogen bonds : bond 0.03824 ( 343) hydrogen bonds : angle 4.58978 ( 980) SS BOND : bond 0.00478 ( 3) SS BOND : angle 0.49270 ( 6) covalent geometry : bond 0.00323 ( 6799) covalent geometry : angle 0.54999 ( 9251) *********************** 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 117 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 0.781 Fit side-chains revert: symmetry clash REVERT: A 39 MET cc_start: 0.8710 (mmm) cc_final: 0.8194 (mmm) REVERT: H 46 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8278 (tm-30) REVERT: L 82 ASP cc_start: 0.9023 (m-30) cc_final: 0.8734 (m-30) REVERT: L 105 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7191 (pt0) REVERT: L 108 ARG cc_start: 0.7574 (ttp80) cc_final: 0.6884 (ptm-80) REVERT: L 142 ARG cc_start: 0.7314 (tmt90) cc_final: 0.6947 (ttt-90) REVERT: K 34 MET cc_start: 0.7318 (ttt) cc_final: 0.6602 (mmm) outliers start: 27 outliers final: 14 residues processed: 105 average time/residue: 1.0853 time to fit residues: 120.7453 Evaluate side-chains 102 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.696 ------------------------------------------------------------------------------- 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 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 H residue 46 GLU 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 135 LEU 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: 20.0000 chunk 30 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 81 optimal weight: 20.0000 chunk 65 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.4087 r_free = 0.4087 target = 0.189395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.131727 restraints weight = 12457.058| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 3.18 r_work: 0.3120 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6802 Z= 0.132 Angle : 0.546 8.509 9257 Z= 0.272 Chirality : 0.042 0.239 1070 Planarity : 0.004 0.034 1133 Dihedral : 6.634 51.120 1196 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.81 % Allowed : 16.35 % 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: 1.31 (0.29), residues: 846 helix: 2.45 (0.32), residues: 261 sheet: 1.45 (0.35), residues: 214 loop : -0.68 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 103 HIS 0.001 0.001 HIS A 54 PHE 0.009 0.001 PHE A 37 TYR 0.010 0.001 TYR A 238 ARG 0.002 0.000 ARG L 66 Details of bonding type rmsd hydrogen bonds : bond 0.03717 ( 343) hydrogen bonds : angle 4.47814 ( 980) SS BOND : bond 0.00532 ( 3) SS BOND : angle 0.47309 ( 6) covalent geometry : bond 0.00308 ( 6799) covalent geometry : angle 0.54651 ( 9251) *********************** 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 123 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 89 time to evaluate : 0.714 Fit side-chains revert: symmetry clash REVERT: A 39 MET cc_start: 0.8754 (mmm) cc_final: 0.8171 (mmm) REVERT: H 46 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8386 (tm-30) REVERT: H 105 GLN cc_start: 0.7655 (OUTLIER) cc_final: 0.7204 (pp30) REVERT: L 82 ASP cc_start: 0.9022 (m-30) cc_final: 0.8731 (m-30) REVERT: L 105 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7327 (pt0) REVERT: L 108 ARG cc_start: 0.7666 (ttp80) cc_final: 0.7017 (ptm-80) REVERT: L 142 ARG cc_start: 0.7365 (OUTLIER) cc_final: 0.6877 (ttt-90) REVERT: K 34 MET cc_start: 0.7272 (ttt) cc_final: 0.6523 (mmm) outliers start: 34 outliers final: 16 residues processed: 108 average time/residue: 1.0529 time to fit residues: 120.6208 Evaluate side-chains 108 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.691 ------------------------------------------------------------------------------- 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 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 290 MET Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 97 LYS 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 33 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 69 optimal weight: 9.9990 chunk 12 optimal weight: 0.4980 chunk 40 optimal weight: 0.9990 chunk 73 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 = 0.4093 r_free = 0.4093 target = 0.189981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.132659 restraints weight = 19623.218| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 4.66 r_work: 0.3043 rms_B_bonded: 3.66 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 = 0.15 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 = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6802 Z= 0.129 Angle : 0.544 7.218 9257 Z= 0.271 Chirality : 0.042 0.238 1070 Planarity : 0.004 0.034 1133 Dihedral : 6.516 51.610 1196 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.26 % Allowed : 17.45 % 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: 2.50 (0.32), residues: 261 sheet: 1.41 (0.35), residues: 214 loop : -0.68 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 103 HIS 0.001 0.001 HIS A 54 PHE 0.026 0.001 PHE K 67 TYR 0.010 0.001 TYR A 238 ARG 0.002 0.000 ARG L 66 Details of bonding type rmsd hydrogen bonds : bond 0.03626 ( 343) hydrogen bonds : angle 4.42161 ( 980) SS BOND : bond 0.00491 ( 3) SS BOND : angle 0.75114 ( 6) covalent geometry : bond 0.00299 ( 6799) covalent geometry : angle 0.54409 ( 9251) *********************** 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 120 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 90 time to evaluate : 0.738 Fit side-chains revert: symmetry clash REVERT: A 39 MET cc_start: 0.8573 (mmm) cc_final: 0.8122 (mmm) REVERT: A 279 ILE cc_start: 0.7936 (OUTLIER) cc_final: 0.7725 (tp) REVERT: H 46 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8246 (tm-30) REVERT: H 100 MET cc_start: 0.6292 (mtm) cc_final: 0.6084 (mtt) REVERT: L 11 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8136 (tt) REVERT: L 82 ASP cc_start: 0.9031 (m-30) cc_final: 0.8715 (m-30) REVERT: L 105 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7149 (pt0) REVERT: L 108 ARG cc_start: 0.7441 (ttp80) cc_final: 0.6791 (ptm-80) REVERT: L 142 ARG cc_start: 0.7322 (OUTLIER) cc_final: 0.6939 (ttt-90) REVERT: K 34 MET cc_start: 0.7227 (ttt) cc_final: 0.6411 (mmm) outliers start: 30 outliers final: 16 residues processed: 105 average time/residue: 0.9951 time to fit residues: 111.2365 Evaluate side-chains 111 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.818 ------------------------------------------------------------------------------- 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 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 46 GLU 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 L residue 172 THR 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: 1.9990 chunk 41 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 80 optimal weight: 7.9990 chunk 15 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.4085 r_free = 0.4085 target = 0.189202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.132624 restraints weight = 26386.060| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 6.53 r_work: 0.2980 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2966 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2966 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6802 Z= 0.148 Angle : 0.563 7.251 9257 Z= 0.281 Chirality : 0.042 0.238 1070 Planarity : 0.004 0.034 1133 Dihedral : 6.630 53.063 1196 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.12 % Allowed : 17.72 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.22 (0.29), residues: 846 helix: 2.40 (0.32), residues: 262 sheet: 1.35 (0.35), residues: 214 loop : -0.73 (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 A 54 PHE 0.018 0.001 PHE K 67 TYR 0.010 0.001 TYR A 238 ARG 0.003 0.000 ARG L 66 Details of bonding type rmsd hydrogen bonds : bond 0.03895 ( 343) hydrogen bonds : angle 4.43897 ( 980) SS BOND : bond 0.00477 ( 3) SS BOND : angle 0.65677 ( 6) covalent geometry : bond 0.00350 ( 6799) covalent geometry : angle 0.56286 ( 9251) *********************** 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 118 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 89 time to evaluate : 0.693 Fit side-chains revert: symmetry clash REVERT: H 46 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8301 (tm-30) REVERT: H 100 MET cc_start: 0.6261 (mtm) cc_final: 0.6029 (mtt) REVERT: L 82 ASP cc_start: 0.9066 (m-30) cc_final: 0.8747 (m-30) REVERT: L 105 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7287 (pt0) REVERT: L 108 ARG cc_start: 0.7577 (ttp80) cc_final: 0.6954 (ptm-80) REVERT: L 142 ARG cc_start: 0.7351 (OUTLIER) cc_final: 0.6970 (ttt-90) REVERT: K 34 MET cc_start: 0.7215 (ttt) cc_final: 0.6402 (mmm) outliers start: 29 outliers final: 18 residues processed: 105 average time/residue: 1.0354 time to fit residues: 115.3859 Evaluate side-chains 111 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.750 ------------------------------------------------------------------------------- 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 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 290 MET Chi-restraints excluded: chain H residue 46 GLU 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 L residue 172 THR 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: 0.3980 chunk 21 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 45 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 76 optimal weight: 20.0000 chunk 26 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.190538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.134171 restraints weight = 20688.853| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 4.90 r_work: 0.3051 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6802 Z= 0.112 Angle : 0.540 8.387 9257 Z= 0.265 Chirality : 0.041 0.236 1070 Planarity : 0.004 0.034 1133 Dihedral : 6.271 51.837 1196 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.16 % Allowed : 18.96 % Favored : 77.88 % 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: 2.49 (0.33), residues: 262 sheet: 1.34 (0.35), residues: 214 loop : -0.75 (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 A 54 PHE 0.015 0.001 PHE K 67 TYR 0.011 0.001 TYR A 238 ARG 0.002 0.000 ARG L 66 Details of bonding type rmsd hydrogen bonds : bond 0.03354 ( 343) hydrogen bonds : angle 4.30353 ( 980) SS BOND : bond 0.00400 ( 3) SS BOND : angle 0.57645 ( 6) covalent geometry : bond 0.00256 ( 6799) covalent geometry : angle 0.53983 ( 9251) *********************** 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 113 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.687 Fit side-chains revert: symmetry clash REVERT: A 39 MET cc_start: 0.8518 (mmm) cc_final: 0.7939 (tpp) REVERT: A 184 MET cc_start: 0.5335 (OUTLIER) cc_final: 0.5111 (tmt) REVERT: A 215 MET cc_start: 0.8141 (mmm) cc_final: 0.7633 (mmp) REVERT: H 46 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8249 (tm-30) REVERT: L 11 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8124 (tt) REVERT: L 82 ASP cc_start: 0.9020 (m-30) cc_final: 0.8708 (m-30) REVERT: L 108 ARG cc_start: 0.7371 (ttp80) cc_final: 0.6716 (ptm-80) REVERT: L 142 ARG cc_start: 0.7279 (OUTLIER) cc_final: 0.6964 (ttt-90) REVERT: K 34 MET cc_start: 0.7138 (ttt) cc_final: 0.6265 (mmm) outliers start: 22 outliers final: 14 residues processed: 103 average time/residue: 1.0539 time to fit residues: 115.0283 Evaluate side-chains 108 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 184 MET Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 229 MET 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 46 GLU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 97 LYS Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 142 ARG Chi-restraints excluded: chain L residue 170 ASP Chi-restraints excluded: chain L residue 172 THR 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: 1.9990 chunk 65 optimal weight: 0.2980 chunk 6 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.4089 r_free = 0.4089 target = 0.189636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.133173 restraints weight = 26557.722| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 6.05 r_work: 0.3020 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- 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 = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6802 Z= 0.118 Angle : 0.530 7.156 9257 Z= 0.264 Chirality : 0.041 0.233 1070 Planarity : 0.004 0.034 1133 Dihedral : 6.204 53.275 1196 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.61 % Allowed : 19.37 % Favored : 78.02 % 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: 1.26 (0.29), residues: 846 helix: 2.52 (0.33), residues: 262 sheet: 1.34 (0.36), residues: 214 loop : -0.75 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 103 HIS 0.001 0.000 HIS A 54 PHE 0.013 0.001 PHE K 67 TYR 0.010 0.001 TYR A 238 ARG 0.002 0.000 ARG L 66 Details of bonding type rmsd hydrogen bonds : bond 0.03429 ( 343) hydrogen bonds : angle 4.27830 ( 980) SS BOND : bond 0.00404 ( 3) SS BOND : angle 0.55786 ( 6) covalent geometry : bond 0.00275 ( 6799) covalent geometry : angle 0.53041 ( 9251) ********************** 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 107 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.746 Fit side-chains revert: symmetry clash REVERT: A 39 MET cc_start: 0.8504 (mmm) cc_final: 0.7937 (tpp) REVERT: A 184 MET cc_start: 0.5474 (OUTLIER) cc_final: 0.5197 (tmm) REVERT: H 46 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8325 (tm-30) REVERT: L 11 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8137 (tt) REVERT: L 82 ASP cc_start: 0.9043 (m-30) cc_final: 0.8746 (m-30) REVERT: L 108 ARG cc_start: 0.7448 (ttp80) cc_final: 0.6808 (ptm-80) REVERT: L 142 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.6904 (ttt-90) REVERT: K 34 MET cc_start: 0.7129 (ttt) cc_final: 0.6289 (mmm) outliers start: 18 outliers final: 14 residues processed: 98 average time/residue: 1.0683 time to fit residues: 111.1056 Evaluate side-chains 107 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 184 MET Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 229 MET 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 46 GLU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 97 LYS Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 142 ARG Chi-restraints excluded: chain L residue 170 ASP Chi-restraints excluded: chain L residue 172 THR 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: 10.0000 chunk 41 optimal weight: 7.9990 chunk 15 optimal weight: 0.4980 chunk 66 optimal weight: 5.9990 chunk 12 optimal weight: 0.0670 chunk 50 optimal weight: 3.9990 chunk 8 optimal weight: 0.1980 chunk 76 optimal weight: 0.7980 chunk 80 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 = 0.4120 r_free = 0.4120 target = 0.192753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.134067 restraints weight = 18645.037| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 4.05 r_work: 0.3098 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3092 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3092 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6802 Z= 0.096 Angle : 0.512 10.019 9257 Z= 0.251 Chirality : 0.041 0.233 1070 Planarity : 0.004 0.034 1133 Dihedral : 5.813 51.976 1196 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.06 % Allowed : 19.92 % Favored : 78.02 % 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: 2.62 (0.33), residues: 262 sheet: 1.35 (0.35), residues: 214 loop : -0.69 (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 0.010 0.001 PHE K 67 TYR 0.010 0.001 TYR A 238 ARG 0.001 0.000 ARG K 52A Details of bonding type rmsd hydrogen bonds : bond 0.02994 ( 343) hydrogen bonds : angle 4.14115 ( 980) SS BOND : bond 0.00322 ( 3) SS BOND : angle 0.47688 ( 6) covalent geometry : bond 0.00212 ( 6799) covalent geometry : angle 0.51241 ( 9251) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7580.66 seconds wall clock time: 134 minutes 19.31 seconds (8059.31 seconds total)