Starting phenix.real_space_refine on Wed Sep 17 22:49:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dpe_47104/09_2025/9dpe_47104_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dpe_47104/09_2025/9dpe_47104.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dpe_47104/09_2025/9dpe_47104_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dpe_47104/09_2025/9dpe_47104_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dpe_47104/09_2025/9dpe_47104.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dpe_47104/09_2025/9dpe_47104.map" } resolution = 3.86 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.000 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 27 5.16 5 C 3766 2.51 5 N 1022 2.21 5 O 1199 1.98 5 H 5786 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11800 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 3343 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} Chain: "H" Number of atoms: 3382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3382 Classifications: {'peptide': 230} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 218} Chain: "L" Number of atoms: 3228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3228 Classifications: {'peptide': 215} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 204} Chain: "N" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1791 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 2.40, per 1000 atoms: 0.20 Number of scatterers: 11800 At special positions: 0 Unit cell: (108.63, 89.46, 146.97, 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 27 16.00 O 1199 8.00 N 1022 7.00 C 3766 6.00 H 5786 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 97 " distance=2.04 Simple disulfide: pdb=" SG CYS A 137 " - pdb=" SG CYS A 191 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 149 " - pdb=" SG CYS H 205 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS N 31 " - pdb=" SG CYS N 105 " 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 Links applied NAG-ASN " NAG A 301 " - " ASN A 86 " " NAG A 302 " - " ASN A 18 " " NAG A 303 " - " ASN A 188 " " NAG A 304 " - " ASN A 92 " Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 382.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1430 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 18 sheets defined 7.3% alpha, 48.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 61 through 65 Processing helix chain 'A' and resid 88 through 92 removed outlier: 3.534A pdb=" N ASN A 92 " --> pdb=" O ALA A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 213 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 137 through 142 Processing helix chain 'H' and resid 165 through 167 No H-bonds generated for 'chain 'H' and resid 165 through 167' Processing helix chain 'H' and resid 196 through 200 Processing helix chain 'L' and resid 121 through 126 Processing helix chain 'L' and resid 183 through 189 removed outlier: 3.732A pdb=" N HIS L 189 " --> pdb=" O ASP L 185 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 41 removed outlier: 4.072A pdb=" N ARG N 40 " --> pdb=" O THR N 37 " (cutoff:3.500A) Processing helix chain 'N' and resid 96 through 100 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 14 removed outlier: 6.630A pdb=" N ILE A 11 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ALA A 115 " --> pdb=" O ILE A 11 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ALA A 13 " --> pdb=" O ALA A 115 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 122 through 129 removed outlier: 3.654A pdb=" N GLU A 136 " --> pdb=" O SER A 124 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ARG A 134 " --> pdb=" O ARG A 126 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N HIS A 128 " --> pdb=" O GLY A 132 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLY A 132 " --> pdb=" O HIS A 128 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N PHE A 173 " --> pdb=" O GLY A 141 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 147 through 151 Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.278A pdb=" N SER H 32 " --> pdb=" O TYR H 52 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N TYR H 52 " --> pdb=" O SER H 32 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N SER H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.819A pdb=" N ARG H 98 " --> pdb=" O TYR H 111 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N TYR H 111 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 129 through 133 removed outlier: 5.979A pdb=" N TYR H 185 " --> pdb=" O ASP H 153 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 129 through 133 removed outlier: 5.979A pdb=" N TYR H 185 " --> pdb=" O ASP H 153 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 159 through 163 removed outlier: 4.601A pdb=" N TYR H 203 " --> pdb=" O VAL H 220 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.800A pdb=" N VAL L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N TYR L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.927A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 114 through 118 removed outlier: 5.254A pdb=" N SER L 131 " --> pdb=" O LEU L 181 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N LEU L 181 " --> pdb=" O SER L 131 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL L 133 " --> pdb=" O LEU L 179 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LEU L 179 " --> pdb=" O VAL L 133 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N LEU L 135 " --> pdb=" O SER L 177 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N SER L 177 " --> pdb=" O LEU L 135 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ASN L 137 " --> pdb=" O LEU L 175 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LEU L 175 " --> pdb=" O ASN L 137 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 153 through 154 Processing sheet with id=AB7, first strand: chain 'N' and resid 12 through 16 Processing sheet with id=AB8, first strand: chain 'N' and resid 19 through 21 removed outlier: 6.228A pdb=" N GLY N 19 " --> pdb=" O THR N 127 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA N 42 " --> pdb=" O ASP N 108 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N MET N 43 " --> pdb=" O VAL N 59 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N VAL N 59 " --> pdb=" O MET N 43 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N TRP N 45 " --> pdb=" O VAL N 57 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 19 through 21 removed outlier: 6.228A pdb=" N GLY N 19 " --> pdb=" O THR N 127 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TYR N 119 " --> pdb=" O ILE N 107 " (cutoff:3.500A) 277 hydrogen bonds defined for protein. 654 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: 2.67 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5784 1.03 - 1.23: 18 1.23 - 1.43: 2634 1.43 - 1.62: 3458 1.62 - 1.82: 38 Bond restraints: 11932 Sorted by residual: bond pdb=" N ILE L 2 " pdb=" CA ILE L 2 " ideal model delta sigma weight residual 1.474 1.457 0.017 1.57e-02 4.06e+03 1.22e+00 bond pdb=" C ILE A 208 " pdb=" O ILE A 208 " ideal model delta sigma weight residual 1.232 1.240 -0.008 1.01e-02 9.80e+03 6.28e-01 bond pdb=" CA VAL A 186 " pdb=" CB VAL A 186 " ideal model delta sigma weight residual 1.530 1.538 -0.008 1.05e-02 9.07e+03 5.82e-01 bond pdb=" N GLY N 75 " pdb=" CA GLY N 75 " ideal model delta sigma weight residual 1.463 1.449 0.013 2.01e-02 2.48e+03 4.43e-01 bond pdb=" N ILE A 208 " pdb=" CA ILE A 208 " ideal model delta sigma weight residual 1.456 1.461 -0.005 8.60e-03 1.35e+04 3.89e-01 ... (remaining 11927 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.76: 19250 0.76 - 1.53: 1964 1.53 - 2.29: 176 2.29 - 3.05: 26 3.05 - 3.82: 15 Bond angle restraints: 21431 Sorted by residual: angle pdb=" N GLY A 93 " pdb=" CA GLY A 93 " pdb=" C GLY A 93 " ideal model delta sigma weight residual 111.56 115.38 -3.82 1.01e+00 9.80e-01 1.43e+01 angle pdb=" N ALA L 51 " pdb=" CA ALA L 51 " pdb=" CB ALA L 51 " ideal model delta sigma weight residual 113.65 110.41 3.24 1.47e+00 4.63e-01 4.86e+00 angle pdb=" CA ILE L 2 " pdb=" C ILE L 2 " pdb=" O ILE L 2 " ideal model delta sigma weight residual 122.63 120.74 1.89 8.70e-01 1.32e+00 4.72e+00 angle pdb=" C ILE L 2 " pdb=" CA ILE L 2 " pdb=" CB ILE L 2 " ideal model delta sigma weight residual 113.22 111.23 1.99 1.12e+00 7.97e-01 3.16e+00 angle pdb=" N ILE L 2 " pdb=" CA ILE L 2 " pdb=" C ILE L 2 " ideal model delta sigma weight residual 106.21 108.11 -1.90 1.07e+00 8.73e-01 3.16e+00 ... (remaining 21426 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.58: 5396 14.58 - 29.15: 237 29.15 - 43.73: 85 43.73 - 58.30: 50 58.30 - 72.88: 13 Dihedral angle restraints: 5781 sinusoidal: 3143 harmonic: 2638 Sorted by residual: dihedral pdb=" CA PRO L 113 " pdb=" C PRO L 113 " pdb=" N SER L 114 " pdb=" CA SER L 114 " ideal model delta harmonic sigma weight residual 180.00 162.91 17.09 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA PHE A 173 " pdb=" C PHE A 173 " pdb=" N MET A 174 " pdb=" CA MET A 174 " ideal model delta harmonic sigma weight residual 180.00 164.24 15.76 0 5.00e+00 4.00e-02 9.94e+00 dihedral pdb=" CA ARG L 142 " pdb=" C ARG L 142 " pdb=" N GLU L 143 " pdb=" CA GLU L 143 " ideal model delta harmonic sigma weight residual -180.00 -164.84 -15.16 0 5.00e+00 4.00e-02 9.19e+00 ... (remaining 5778 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 569 0.028 - 0.055: 242 0.055 - 0.083: 37 0.083 - 0.110: 57 0.110 - 0.138: 30 Chirality restraints: 935 Sorted by residual: chirality pdb=" CA ILE A 84 " pdb=" N ILE A 84 " pdb=" C ILE A 84 " pdb=" CB ILE A 84 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA ILE A 193 " pdb=" N ILE A 193 " pdb=" C ILE A 193 " pdb=" CB ILE A 193 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.55e-01 chirality pdb=" CA ILE L 75 " pdb=" N ILE L 75 " pdb=" C ILE L 75 " pdb=" CB ILE L 75 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.13e-01 ... (remaining 932 not shown) Planarity restraints: 1811 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 157 " 0.026 5.00e-02 4.00e+02 3.85e-02 2.38e+00 pdb=" N PRO H 158 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO H 158 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO H 158 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL L 58 " -0.019 5.00e-02 4.00e+02 2.91e-02 1.36e+00 pdb=" N PRO L 59 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO L 59 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO L 59 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 213 " -0.017 5.00e-02 4.00e+02 2.58e-02 1.07e+00 pdb=" N PRO A 214 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 214 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 214 " -0.014 5.00e-02 4.00e+02 ... (remaining 1808 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 1025 2.22 - 2.82: 25354 2.82 - 3.41: 30238 3.41 - 4.01: 42544 4.01 - 4.60: 64149 Nonbonded interactions: 163310 Sorted by model distance: nonbonded pdb=" O GLU A 58 " pdb=" HG SER H 55 " model vdw 1.630 2.450 nonbonded pdb=" O SER H 137 " pdb=" HG1 THR H 140 " model vdw 1.659 2.450 nonbonded pdb=" O PRO H 194 " pdb=" HG SER H 197 " model vdw 1.661 2.450 nonbonded pdb=" OE1 GLU A 58 " pdb=" H GLU A 58 " model vdw 1.665 2.450 nonbonded pdb=" O GLN L 124 " pdb=" HG SER L 127 " model vdw 1.666 2.450 ... (remaining 163305 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 5.410 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: 0.090 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.320 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 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 : 0.002 0.017 6157 Z= 0.098 Angle : 0.451 3.819 8364 Z= 0.260 Chirality : 0.042 0.138 935 Planarity : 0.003 0.039 1068 Dihedral : 7.388 57.426 2280 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.15 % Allowed : 0.76 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.31), residues: 771 helix: -1.27 (1.13), residues: 20 sheet: 1.04 (0.27), residues: 352 loop : 0.88 (0.34), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 98 TYR 0.006 0.001 TYR A 98 PHE 0.006 0.001 PHE A 70 TRP 0.004 0.001 TRP H 106 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00181 ( 6146) covalent geometry : angle 0.44830 ( 8338) SS BOND : bond 0.00266 ( 7) SS BOND : angle 0.59043 ( 14) hydrogen bonds : bond 0.11334 ( 246) hydrogen bonds : angle 6.00114 ( 654) link_NAG-ASN : bond 0.00134 ( 4) link_NAG-ASN : angle 1.31797 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 PHE cc_start: 0.9093 (m-80) cc_final: 0.8766 (m-80) REVERT: A 184 LYS cc_start: 0.9580 (ptmt) cc_final: 0.9167 (ttmt) REVERT: H 45 LEU cc_start: 0.9418 (mt) cc_final: 0.8965 (mm) REVERT: H 83 MET cc_start: 0.8858 (mtm) cc_final: 0.8571 (mpp) REVERT: L 122 ASP cc_start: 0.9666 (m-30) cc_final: 0.9416 (p0) REVERT: L 170 ASP cc_start: 0.8736 (p0) cc_final: 0.8449 (p0) REVERT: L 196 VAL cc_start: 0.9529 (t) cc_final: 0.9162 (m) REVERT: L 213 GLU cc_start: 0.8326 (tt0) cc_final: 0.7799 (tm-30) outliers start: 1 outliers final: 1 residues processed: 99 average time/residue: 0.2948 time to fit residues: 34.5109 Evaluate side-chains 67 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 66 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 213 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.040095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.030847 restraints weight = 113364.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.032785 restraints weight = 46303.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.034157 restraints weight = 25224.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.035074 restraints weight = 16278.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.035711 restraints weight = 11712.195| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6157 Z= 0.162 Angle : 0.492 5.127 8364 Z= 0.263 Chirality : 0.042 0.142 935 Planarity : 0.004 0.050 1068 Dihedral : 4.765 45.016 937 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.76 % Allowed : 4.98 % Favored : 94.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.31), residues: 771 helix: -1.42 (1.04), residues: 20 sheet: 0.66 (0.26), residues: 360 loop : 0.72 (0.34), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 103 TYR 0.009 0.001 TYR A 98 PHE 0.008 0.001 PHE A 212 TRP 0.005 0.001 TRP A 150 HIS 0.002 0.001 HIS H 229 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 6146) covalent geometry : angle 0.48901 ( 8338) SS BOND : bond 0.00298 ( 7) SS BOND : angle 1.04552 ( 14) hydrogen bonds : bond 0.02815 ( 246) hydrogen bonds : angle 5.41092 ( 654) link_NAG-ASN : bond 0.00162 ( 4) link_NAG-ASN : angle 1.06810 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 PHE cc_start: 0.9102 (m-80) cc_final: 0.8858 (m-80) REVERT: A 184 LYS cc_start: 0.9597 (ptmt) cc_final: 0.9141 (ttmt) REVERT: A 202 LYS cc_start: 0.8859 (mmtp) cc_final: 0.8540 (mttt) REVERT: H 83 MET cc_start: 0.8858 (mtm) cc_final: 0.8563 (mpp) REVERT: L 122 ASP cc_start: 0.9663 (m-30) cc_final: 0.9441 (p0) REVERT: L 213 GLU cc_start: 0.8445 (tt0) cc_final: 0.7879 (tm-30) REVERT: N 43 MET cc_start: 0.8518 (mmm) cc_final: 0.8288 (mpp) outliers start: 5 outliers final: 3 residues processed: 71 average time/residue: 0.3149 time to fit residues: 26.4067 Evaluate side-chains 61 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASN Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 149 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 26 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.039178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.029886 restraints weight = 115658.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.031778 restraints weight = 48406.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.033114 restraints weight = 26880.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.034023 restraints weight = 17488.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.034591 restraints weight = 12665.720| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6157 Z= 0.216 Angle : 0.523 5.234 8364 Z= 0.280 Chirality : 0.041 0.135 935 Planarity : 0.004 0.040 1068 Dihedral : 5.148 47.337 937 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.51 % Allowed : 5.59 % Favored : 92.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.30), residues: 771 helix: -1.44 (0.99), residues: 20 sheet: 0.36 (0.26), residues: 367 loop : 0.39 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 103 TYR 0.011 0.001 TYR L 140 PHE 0.007 0.001 PHE A 207 TRP 0.007 0.001 TRP A 142 HIS 0.003 0.001 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 6146) covalent geometry : angle 0.52114 ( 8338) SS BOND : bond 0.00360 ( 7) SS BOND : angle 0.93866 ( 14) hydrogen bonds : bond 0.03002 ( 246) hydrogen bonds : angle 5.20174 ( 654) link_NAG-ASN : bond 0.00255 ( 4) link_NAG-ASN : angle 1.02132 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 PHE cc_start: 0.9124 (m-80) cc_final: 0.8854 (m-80) REVERT: A 184 LYS cc_start: 0.9568 (ptmt) cc_final: 0.9350 (ptmm) REVERT: H 83 MET cc_start: 0.8917 (mtm) cc_final: 0.8588 (mpp) REVERT: L 122 ASP cc_start: 0.9671 (m-30) cc_final: 0.9453 (p0) REVERT: L 213 GLU cc_start: 0.8598 (tt0) cc_final: 0.7990 (tm-30) outliers start: 10 outliers final: 7 residues processed: 63 average time/residue: 0.3233 time to fit residues: 24.1225 Evaluate side-chains 63 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASN Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 204 ILE Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 167 ASP Chi-restraints excluded: chain N residue 44 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 55 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 20 optimal weight: 0.0000 overall best weight: 1.5590 ------------------------------------------------------------------------------- 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 = 0.3169 r_free = 0.3169 target = 0.038928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.029765 restraints weight = 114511.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.031622 restraints weight = 47738.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.032932 restraints weight = 26449.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.033828 restraints weight = 17172.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.034428 restraints weight = 12399.352| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6157 Z= 0.193 Angle : 0.506 5.264 8364 Z= 0.269 Chirality : 0.041 0.131 935 Planarity : 0.004 0.036 1068 Dihedral : 5.073 45.454 937 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.91 % Allowed : 6.50 % Favored : 92.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.30), residues: 771 helix: -1.29 (1.05), residues: 20 sheet: 0.26 (0.26), residues: 364 loop : 0.20 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 24 TYR 0.010 0.001 TYR L 140 PHE 0.006 0.001 PHE N 68 TRP 0.006 0.001 TRP H 36 HIS 0.003 0.001 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 6146) covalent geometry : angle 0.50367 ( 8338) SS BOND : bond 0.00300 ( 7) SS BOND : angle 0.96333 ( 14) hydrogen bonds : bond 0.02711 ( 246) hydrogen bonds : angle 5.13779 ( 654) link_NAG-ASN : bond 0.00198 ( 4) link_NAG-ASN : angle 0.94749 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 PHE cc_start: 0.9109 (m-80) cc_final: 0.8852 (m-80) REVERT: H 83 MET cc_start: 0.8925 (mtm) cc_final: 0.8579 (mpp) REVERT: L 122 ASP cc_start: 0.9672 (m-30) cc_final: 0.9456 (p0) REVERT: L 170 ASP cc_start: 0.8978 (p0) cc_final: 0.8550 (p0) REVERT: L 213 GLU cc_start: 0.8662 (tt0) cc_final: 0.8049 (tm-30) outliers start: 6 outliers final: 6 residues processed: 59 average time/residue: 0.3415 time to fit residues: 23.7807 Evaluate side-chains 57 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASN Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 154 TYR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain L residue 135 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 60 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3180 r_free = 0.3180 target = 0.039192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.029947 restraints weight = 113605.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.031834 restraints weight = 47334.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.033182 restraints weight = 26220.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.034100 restraints weight = 16907.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.034673 restraints weight = 12140.238| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6157 Z= 0.115 Angle : 0.475 5.741 8364 Z= 0.249 Chirality : 0.042 0.134 935 Planarity : 0.004 0.037 1068 Dihedral : 4.748 40.709 937 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.06 % Allowed : 6.19 % Favored : 92.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.31), residues: 771 helix: -1.22 (1.32), residues: 14 sheet: 0.30 (0.26), residues: 365 loop : 0.34 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 40 TYR 0.007 0.001 TYR N 113 PHE 0.006 0.001 PHE L 98 TRP 0.004 0.001 TRP H 47 HIS 0.002 0.001 HIS H 229 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 6146) covalent geometry : angle 0.47395 ( 8338) SS BOND : bond 0.00257 ( 7) SS BOND : angle 0.70871 ( 14) hydrogen bonds : bond 0.02431 ( 246) hydrogen bonds : angle 4.86262 ( 654) link_NAG-ASN : bond 0.00100 ( 4) link_NAG-ASN : angle 0.84152 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.8405 (mtp) cc_final: 0.8195 (mtp) REVERT: A 99 PHE cc_start: 0.9091 (m-80) cc_final: 0.8857 (m-80) REVERT: H 83 MET cc_start: 0.8897 (mtm) cc_final: 0.8548 (mpp) REVERT: L 4 MET cc_start: 0.9015 (mmm) cc_final: 0.8808 (mtm) REVERT: L 105 GLU cc_start: 0.8663 (mp0) cc_final: 0.8443 (mp0) REVERT: L 122 ASP cc_start: 0.9683 (m-30) cc_final: 0.9474 (p0) REVERT: L 213 GLU cc_start: 0.8641 (tt0) cc_final: 0.8003 (tm-30) outliers start: 7 outliers final: 7 residues processed: 56 average time/residue: 0.2900 time to fit residues: 19.5657 Evaluate side-chains 52 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASN Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 154 TYR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain N residue 13 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 11 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 76 optimal weight: 0.4980 chunk 58 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 47 optimal weight: 0.0870 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.039257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.030028 restraints weight = 113135.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.031913 restraints weight = 47318.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.033254 restraints weight = 26209.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.034173 restraints weight = 16913.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.034749 restraints weight = 12126.355| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6157 Z= 0.107 Angle : 0.489 6.378 8364 Z= 0.252 Chirality : 0.042 0.135 935 Planarity : 0.004 0.036 1068 Dihedral : 4.563 38.207 937 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.36 % Allowed : 7.25 % Favored : 91.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.31), residues: 771 helix: -0.89 (1.36), residues: 14 sheet: 0.29 (0.26), residues: 366 loop : 0.44 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 151 TYR 0.007 0.001 TYR A 98 PHE 0.006 0.001 PHE L 98 TRP 0.003 0.001 TRP H 163 HIS 0.003 0.001 HIS H 209 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 6146) covalent geometry : angle 0.48763 ( 8338) SS BOND : bond 0.00337 ( 7) SS BOND : angle 0.60894 ( 14) hydrogen bonds : bond 0.02366 ( 246) hydrogen bonds : angle 4.74680 ( 654) link_NAG-ASN : bond 0.00102 ( 4) link_NAG-ASN : angle 0.86163 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 83 MET cc_start: 0.8889 (mtm) cc_final: 0.8534 (mpp) REVERT: L 105 GLU cc_start: 0.8623 (mp0) cc_final: 0.8389 (mp0) REVERT: L 122 ASP cc_start: 0.9689 (m-30) cc_final: 0.9476 (p0) REVERT: L 213 GLU cc_start: 0.8584 (tt0) cc_final: 0.7933 (tm-30) outliers start: 9 outliers final: 9 residues processed: 51 average time/residue: 0.2637 time to fit residues: 16.5909 Evaluate side-chains 54 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASN Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 154 TYR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain H residue 213 ASN Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain N residue 13 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 41 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN L 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.037874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.028895 restraints weight = 121038.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.030653 restraints weight = 51149.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.031902 restraints weight = 28765.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.032767 restraints weight = 18823.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.033358 restraints weight = 13719.666| |-----------------------------------------------------------------------------| r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 6157 Z= 0.361 Angle : 0.641 6.821 8364 Z= 0.341 Chirality : 0.041 0.144 935 Planarity : 0.005 0.048 1068 Dihedral : 5.809 49.125 937 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.51 % Allowed : 7.70 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.30), residues: 771 helix: -1.78 (1.22), residues: 14 sheet: -0.18 (0.26), residues: 367 loop : -0.21 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 126 TYR 0.024 0.002 TYR L 140 PHE 0.012 0.002 PHE A 207 TRP 0.017 0.002 TRP A 142 HIS 0.006 0.002 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00720 ( 6146) covalent geometry : angle 0.63930 ( 8338) SS BOND : bond 0.00416 ( 7) SS BOND : angle 0.98818 ( 14) hydrogen bonds : bond 0.03509 ( 246) hydrogen bonds : angle 5.51790 ( 654) link_NAG-ASN : bond 0.00533 ( 4) link_NAG-ASN : angle 1.15843 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.8440 (mtp) cc_final: 0.8218 (mpp) REVERT: H 83 MET cc_start: 0.8949 (mtm) cc_final: 0.8552 (mpp) REVERT: L 213 GLU cc_start: 0.8613 (tt0) cc_final: 0.7945 (tm-30) outliers start: 10 outliers final: 8 residues processed: 47 average time/residue: 0.2625 time to fit residues: 15.3500 Evaluate side-chains 48 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASN Chi-restraints excluded: chain A residue 85 HIS Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 154 TYR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 204 ILE Chi-restraints excluded: chain L residue 135 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 10 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.038637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.029425 restraints weight = 114827.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.031301 restraints weight = 48077.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.032615 restraints weight = 26698.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.033512 restraints weight = 17326.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.034129 restraints weight = 12535.882| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6157 Z= 0.123 Angle : 0.514 7.208 8364 Z= 0.266 Chirality : 0.043 0.133 935 Planarity : 0.004 0.034 1068 Dihedral : 5.047 39.415 937 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.51 % Allowed : 8.31 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.30), residues: 771 helix: -1.66 (1.20), residues: 14 sheet: -0.10 (0.26), residues: 366 loop : 0.05 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 61 TYR 0.008 0.001 TYR L 173 PHE 0.007 0.001 PHE L 118 TRP 0.007 0.001 TRP H 47 HIS 0.003 0.001 HIS H 209 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 6146) covalent geometry : angle 0.51383 ( 8338) SS BOND : bond 0.00320 ( 7) SS BOND : angle 0.63559 ( 14) hydrogen bonds : bond 0.02521 ( 246) hydrogen bonds : angle 5.06568 ( 654) link_NAG-ASN : bond 0.00110 ( 4) link_NAG-ASN : angle 0.75047 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 LYS cc_start: 0.9498 (tmmt) cc_final: 0.9261 (tmmt) REVERT: H 83 MET cc_start: 0.8970 (mtm) cc_final: 0.8571 (mpp) REVERT: L 213 GLU cc_start: 0.8534 (tt0) cc_final: 0.7880 (tm-30) outliers start: 10 outliers final: 10 residues processed: 47 average time/residue: 0.2141 time to fit residues: 12.6567 Evaluate side-chains 51 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASN Chi-restraints excluded: chain A residue 85 HIS Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 154 TYR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 204 ILE Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain N residue 13 LEU Chi-restraints excluded: chain N residue 104 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 75 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 56 optimal weight: 0.2980 chunk 55 optimal weight: 1.9990 chunk 48 optimal weight: 0.0970 chunk 47 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.038536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.029393 restraints weight = 116120.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.031243 restraints weight = 49090.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.032550 restraints weight = 27351.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.033446 restraints weight = 17750.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.034054 restraints weight = 12845.168| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6157 Z= 0.161 Angle : 0.514 7.771 8364 Z= 0.268 Chirality : 0.042 0.133 935 Planarity : 0.004 0.036 1068 Dihedral : 4.921 37.647 937 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.66 % Allowed : 8.01 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.30), residues: 771 helix: -1.63 (1.19), residues: 14 sheet: -0.12 (0.26), residues: 366 loop : 0.06 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 61 TYR 0.009 0.001 TYR L 140 PHE 0.008 0.001 PHE L 98 TRP 0.005 0.001 TRP A 142 HIS 0.002 0.001 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 6146) covalent geometry : angle 0.51259 ( 8338) SS BOND : bond 0.00357 ( 7) SS BOND : angle 0.67846 ( 14) hydrogen bonds : bond 0.02533 ( 246) hydrogen bonds : angle 5.05172 ( 654) link_NAG-ASN : bond 0.00143 ( 4) link_NAG-ASN : angle 0.88407 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 LYS cc_start: 0.9519 (tmmt) cc_final: 0.9318 (tmmt) REVERT: H 83 MET cc_start: 0.8969 (mtm) cc_final: 0.8578 (mpp) REVERT: L 213 GLU cc_start: 0.8532 (tt0) cc_final: 0.7815 (tm-30) outliers start: 11 outliers final: 11 residues processed: 46 average time/residue: 0.2483 time to fit residues: 14.1756 Evaluate side-chains 50 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASN Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 85 HIS Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 154 TYR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 213 ASN Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain N residue 13 LEU Chi-restraints excluded: chain N residue 104 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 56 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 7 optimal weight: 0.0170 chunk 75 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.038293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.029169 restraints weight = 116640.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.031015 restraints weight = 48887.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.032314 restraints weight = 27149.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.033218 restraints weight = 17588.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.033832 restraints weight = 12651.091| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6157 Z= 0.174 Angle : 0.528 7.945 8364 Z= 0.275 Chirality : 0.042 0.131 935 Planarity : 0.004 0.050 1068 Dihedral : 4.927 35.922 937 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.51 % Allowed : 8.46 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.31), residues: 771 helix: -1.41 (1.21), residues: 14 sheet: -0.14 (0.26), residues: 366 loop : 0.06 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 77 TYR 0.009 0.001 TYR A 98 PHE 0.009 0.001 PHE L 118 TRP 0.006 0.001 TRP A 142 HIS 0.002 0.001 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 6146) covalent geometry : angle 0.52722 ( 8338) SS BOND : bond 0.00350 ( 7) SS BOND : angle 0.66621 ( 14) hydrogen bonds : bond 0.02577 ( 246) hydrogen bonds : angle 5.08383 ( 654) link_NAG-ASN : bond 0.00146 ( 4) link_NAG-ASN : angle 0.88232 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 83 MET cc_start: 0.8983 (mtm) cc_final: 0.8582 (mpp) REVERT: L 213 GLU cc_start: 0.8442 (tt0) cc_final: 0.7631 (tm-30) outliers start: 10 outliers final: 10 residues processed: 44 average time/residue: 0.2302 time to fit residues: 12.8455 Evaluate side-chains 49 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASN Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 85 HIS Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 154 TYR Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain N residue 13 LEU Chi-restraints excluded: chain N residue 104 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 28 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 11 optimal weight: 0.0980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.038211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.029096 restraints weight = 116854.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.030939 restraints weight = 49525.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.032218 restraints weight = 27595.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.033121 restraints weight = 18010.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.033725 restraints weight = 13000.073| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6157 Z= 0.200 Angle : 0.539 8.062 8364 Z= 0.282 Chirality : 0.041 0.131 935 Planarity : 0.004 0.037 1068 Dihedral : 5.016 35.256 937 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.81 % Allowed : 8.01 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.31), residues: 771 helix: -1.30 (1.23), residues: 14 sheet: -0.15 (0.26), residues: 363 loop : -0.03 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 77 TYR 0.010 0.001 TYR L 140 PHE 0.046 0.002 PHE L 83 TRP 0.007 0.001 TRP A 142 HIS 0.003 0.001 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 6146) covalent geometry : angle 0.53764 ( 8338) SS BOND : bond 0.00351 ( 7) SS BOND : angle 0.69436 ( 14) hydrogen bonds : bond 0.02655 ( 246) hydrogen bonds : angle 5.13803 ( 654) link_NAG-ASN : bond 0.00180 ( 4) link_NAG-ASN : angle 0.91403 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2512.34 seconds wall clock time: 43 minutes 28.06 seconds (2608.06 seconds total)