Starting phenix.real_space_refine on Tue Jun 10 19:38:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dpe_47104/06_2025/9dpe_47104_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dpe_47104/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9dpe_47104/06_2025/9dpe_47104.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dpe_47104/06_2025/9dpe_47104.map" model { file = "/net/cci-nas-00/data/ceres_data/9dpe_47104/06_2025/9dpe_47104_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dpe_47104/06_2025/9dpe_47104_trim.cif" } resolution = 3.86 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= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 6.83, per 1000 atoms: 0.58 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: 3.08 Conformation dependent library (CDL) restraints added in 990.9 milliseconds 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: 1.33 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: 4.35 Time building geometry restraints manager: 3.76 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: 4.220 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: 0.200 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 29.690 Find NCS groups from input model: 0.100 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: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.760 ------------------------------------------------------------------------------- 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 (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: 1.23 (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 TRP 0.004 0.001 TRP H 106 HIS 0.002 0.001 HIS H 35 PHE 0.006 0.001 PHE A 70 TYR 0.006 0.001 TYR A 98 ARG 0.002 0.000 ARG H 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00134 ( 4) link_NAG-ASN : angle 1.31797 ( 12) hydrogen bonds : bond 0.11334 ( 246) hydrogen bonds : angle 6.00114 ( 654) SS BOND : bond 0.00266 ( 7) SS BOND : angle 0.59043 ( 14) covalent geometry : bond 0.00181 ( 6146) covalent geometry : angle 0.44830 ( 8338) *********************** 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 : 0.893 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: 0.8964 (mm) REVERT: H 83 MET cc_start: 0.8858 (mtm) cc_final: 0.8497 (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: 0.6309 time to fit residues: 74.5387 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 : 0.903 ------------------------------------------------------------------------------- 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 65 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 44 optimal weight: 0.4980 chunk 69 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- 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 = 38)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.030878 restraints weight = 111860.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.032801 restraints weight = 45845.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.034162 restraints weight = 25202.262| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1585 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 : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.76 % Allowed : 5.14 % Favored : 94.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.44 % 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: 0.82 (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 TRP 0.005 0.001 TRP A 150 HIS 0.002 0.001 HIS H 229 PHE 0.008 0.001 PHE A 212 TYR 0.009 0.001 TYR A 98 ARG 0.005 0.000 ARG A 103 Details of bonding type rmsd link_NAG-ASN : bond 0.00162 ( 4) link_NAG-ASN : angle 1.06810 ( 12) hydrogen bonds : bond 0.02815 ( 246) hydrogen bonds : angle 5.41092 ( 654) SS BOND : bond 0.00298 ( 7) SS BOND : angle 1.04553 ( 14) covalent geometry : bond 0.00333 ( 6146) covalent geometry : angle 0.48901 ( 8338) *********************** 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 : 0.858 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 32 GLU cc_start: 0.9098 (tt0) cc_final: 0.8790 (pt0) REVERT: A 99 PHE cc_start: 0.9138 (m-80) cc_final: 0.8883 (m-80) REVERT: A 184 LYS cc_start: 0.9609 (ptmt) cc_final: 0.9151 (ttmt) REVERT: A 202 LYS cc_start: 0.8867 (mmtp) cc_final: 0.8542 (mttt) REVERT: L 122 ASP cc_start: 0.9696 (m-30) cc_final: 0.9476 (p0) REVERT: L 213 GLU cc_start: 0.8515 (tt0) cc_final: 0.7938 (tm-30) REVERT: N 43 MET cc_start: 0.8548 (mmm) cc_final: 0.8292 (mpp) outliers start: 5 outliers final: 3 residues processed: 71 average time/residue: 0.6488 time to fit residues: 55.1915 Evaluate side-chains 62 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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 18 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 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 = 0.3154 r_free = 0.3154 target = 0.038697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.029400 restraints weight = 117893.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.031244 restraints weight = 49771.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.032539 restraints weight = 27903.850| |-----------------------------------------------------------------------------| r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 6157 Z= 0.307 Angle : 0.596 5.184 8364 Z= 0.321 Chirality : 0.041 0.143 935 Planarity : 0.005 0.038 1068 Dihedral : 5.688 51.991 937 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.66 % Allowed : 5.89 % Favored : 92.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.44 % 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: 0.00 (0.30), residues: 771 helix: -1.87 (0.93), residues: 20 sheet: 0.22 (0.26), residues: 364 loop : 0.04 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 142 HIS 0.005 0.001 HIS A 111 PHE 0.011 0.002 PHE A 207 TYR 0.018 0.002 TYR L 140 ARG 0.004 0.001 ARG A 40 Details of bonding type rmsd link_NAG-ASN : bond 0.00447 ( 4) link_NAG-ASN : angle 1.14445 ( 12) hydrogen bonds : bond 0.03466 ( 246) hydrogen bonds : angle 5.61738 ( 654) SS BOND : bond 0.00520 ( 7) SS BOND : angle 1.03173 ( 14) covalent geometry : bond 0.00614 ( 6146) covalent geometry : angle 0.59368 ( 8338) *********************** 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 68 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 1.016 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: A 32 GLU cc_start: 0.9112 (tt0) cc_final: 0.8905 (pt0) REVERT: A 184 LYS cc_start: 0.9568 (ptmt) cc_final: 0.9339 (ptmm) REVERT: H 83 MET cc_start: 0.8246 (mpp) cc_final: 0.7917 (mpp) REVERT: L 122 ASP cc_start: 0.9689 (m-30) cc_final: 0.9479 (p0) REVERT: L 213 GLU cc_start: 0.8735 (tt0) cc_final: 0.8123 (tm-30) outliers start: 11 outliers final: 9 residues processed: 63 average time/residue: 0.6603 time to fit residues: 49.8167 Evaluate side-chains 64 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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 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 30 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.3148 r_free = 0.3148 target = 0.038432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.029380 restraints weight = 118452.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.031197 restraints weight = 49609.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.032500 restraints weight = 27612.339| |-----------------------------------------------------------------------------| r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6157 Z= 0.256 Angle : 0.547 5.106 8364 Z= 0.292 Chirality : 0.041 0.134 935 Planarity : 0.004 0.034 1068 Dihedral : 5.545 49.007 937 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.51 % Allowed : 6.19 % Favored : 92.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.44 % 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: -0.24 (0.30), residues: 771 helix: -2.28 (1.07), residues: 14 sheet: 0.02 (0.26), residues: 363 loop : -0.12 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.004 0.001 HIS A 111 PHE 0.008 0.001 PHE N 68 TYR 0.012 0.001 TYR L 140 ARG 0.002 0.000 ARG L 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00284 ( 4) link_NAG-ASN : angle 1.02210 ( 12) hydrogen bonds : bond 0.02969 ( 246) hydrogen bonds : angle 5.46700 ( 654) SS BOND : bond 0.00323 ( 7) SS BOND : angle 1.04334 ( 14) covalent geometry : bond 0.00507 ( 6146) covalent geometry : angle 0.54527 ( 8338) *********************** 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 64 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.968 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: L 213 GLU cc_start: 0.8833 (tt0) cc_final: 0.8211 (tm-30) outliers start: 10 outliers final: 10 residues processed: 60 average time/residue: 0.6276 time to fit residues: 45.4307 Evaluate side-chains 56 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.991 ------------------------------------------------------------------------------- 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 204 ILE Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 167 ASP Chi-restraints excluded: chain N residue 107 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 41 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3164 r_free = 0.3164 target = 0.038627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.029535 restraints weight = 114344.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.031370 restraints weight = 47783.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.032668 restraints weight = 26498.800| |-----------------------------------------------------------------------------| r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6157 Z= 0.130 Angle : 0.483 5.533 8364 Z= 0.255 Chirality : 0.042 0.133 935 Planarity : 0.004 0.035 1068 Dihedral : 5.030 42.837 937 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.51 % Allowed : 7.55 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.44 % 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: -0.10 (0.30), residues: 771 helix: -2.00 (1.21), residues: 14 sheet: 0.03 (0.26), residues: 365 loop : 0.08 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 47 HIS 0.002 0.001 HIS H 229 PHE 0.006 0.001 PHE L 98 TYR 0.008 0.001 TYR N 113 ARG 0.002 0.000 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00108 ( 4) link_NAG-ASN : angle 0.84855 ( 12) hydrogen bonds : bond 0.02560 ( 246) hydrogen bonds : angle 5.11201 ( 654) SS BOND : bond 0.00334 ( 7) SS BOND : angle 0.63243 ( 14) covalent geometry : bond 0.00270 ( 6146) covalent geometry : angle 0.48180 ( 8338) *********************** 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 58 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.974 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: A 99 PHE cc_start: 0.9196 (m-80) cc_final: 0.8876 (m-80) REVERT: A 184 LYS cc_start: 0.9567 (ptmt) cc_final: 0.9365 (mmtt) REVERT: L 118 PHE cc_start: 0.8303 (m-80) cc_final: 0.8084 (m-80) REVERT: L 213 GLU cc_start: 0.8764 (tt0) cc_final: 0.8086 (tm-30) outliers start: 10 outliers final: 10 residues processed: 54 average time/residue: 0.5626 time to fit residues: 37.6168 Evaluate side-chains 55 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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 H residue 206 ASN 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 71 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 chunk 42 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 64 optimal weight: 0.0980 chunk 67 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.3170 r_free = 0.3170 target = 0.038723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.029479 restraints weight = 115206.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.031351 restraints weight = 48476.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.032664 restraints weight = 26898.678| |-----------------------------------------------------------------------------| r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3271 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= 0.124 Angle : 0.493 6.872 8364 Z= 0.256 Chirality : 0.042 0.132 935 Planarity : 0.004 0.036 1068 Dihedral : 4.827 40.072 937 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.66 % Allowed : 7.85 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.44 % 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: -0.10 (0.30), residues: 771 helix: -1.61 (1.06), residues: 20 sheet: -0.01 (0.26), residues: 366 loop : 0.14 (0.33), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 163 HIS 0.002 0.001 HIS H 229 PHE 0.010 0.001 PHE L 98 TYR 0.007 0.001 TYR A 98 ARG 0.003 0.000 ARG N 40 Details of bonding type rmsd link_NAG-ASN : bond 0.00116 ( 4) link_NAG-ASN : angle 0.86457 ( 12) hydrogen bonds : bond 0.02466 ( 246) hydrogen bonds : angle 4.98094 ( 654) SS BOND : bond 0.00321 ( 7) SS BOND : angle 0.64335 ( 14) covalent geometry : bond 0.00265 ( 6146) covalent geometry : angle 0.49218 ( 8338) *********************** 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: 11 poor density : 45 time to evaluate : 0.912 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: A 99 PHE cc_start: 0.9188 (m-80) cc_final: 0.8880 (m-80) REVERT: L 118 PHE cc_start: 0.8309 (m-80) cc_final: 0.8104 (m-80) REVERT: L 170 ASP cc_start: 0.9128 (p0) cc_final: 0.8797 (p0) REVERT: L 213 GLU cc_start: 0.8718 (tt0) cc_final: 0.8052 (tm-30) outliers start: 11 outliers final: 11 residues processed: 52 average time/residue: 0.5490 time to fit residues: 35.6060 Evaluate side-chains 53 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 1.548 ------------------------------------------------------------------------------- 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 138 LYS Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 206 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 37 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 71 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3171 r_free = 0.3171 target = 0.038754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.029569 restraints weight = 115222.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.031439 restraints weight = 47975.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.032755 restraints weight = 26556.693| |-----------------------------------------------------------------------------| r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6157 Z= 0.117 Angle : 0.493 6.038 8364 Z= 0.255 Chirality : 0.042 0.132 935 Planarity : 0.004 0.036 1068 Dihedral : 4.726 38.391 937 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.11 % Allowed : 7.85 % 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 (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: 0.06 (0.30), residues: 771 helix: -1.85 (1.25), residues: 14 sheet: 0.04 (0.26), residues: 366 loop : 0.29 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 163 HIS 0.002 0.001 HIS H 209 PHE 0.005 0.001 PHE L 98 TYR 0.007 0.001 TYR A 98 ARG 0.002 0.000 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00094 ( 4) link_NAG-ASN : angle 0.82630 ( 12) hydrogen bonds : bond 0.02402 ( 246) hydrogen bonds : angle 4.89054 ( 654) SS BOND : bond 0.00325 ( 7) SS BOND : angle 0.64225 ( 14) covalent geometry : bond 0.00253 ( 6146) covalent geometry : angle 0.49192 ( 8338) *********************** 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 56 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.981 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: A 99 PHE cc_start: 0.9174 (m-80) cc_final: 0.8866 (m-80) REVERT: L 213 GLU cc_start: 0.8668 (tt0) cc_final: 0.7944 (tm-30) outliers start: 14 outliers final: 13 residues processed: 51 average time/residue: 0.4950 time to fit residues: 32.1196 Evaluate side-chains 55 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 177 THR 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 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 Chi-restraints excluded: chain N residue 104 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 65 optimal weight: 9.9990 chunk 19 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 43 optimal weight: 0.0670 chunk 54 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 overall best weight: 0.6718 ------------------------------------------------------------------------------- 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 = 0.3171 r_free = 0.3171 target = 0.038695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.029508 restraints weight = 114413.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.031389 restraints weight = 47876.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.032696 restraints weight = 26569.417| |-----------------------------------------------------------------------------| r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6157 Z= 0.108 Angle : 0.488 7.380 8364 Z= 0.252 Chirality : 0.042 0.132 935 Planarity : 0.004 0.036 1068 Dihedral : 4.616 36.683 937 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.11 % Allowed : 7.70 % 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 (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: 0.18 (0.30), residues: 771 helix: -1.76 (1.27), residues: 14 sheet: 0.11 (0.26), residues: 366 loop : 0.38 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 163 HIS 0.002 0.001 HIS H 209 PHE 0.007 0.001 PHE L 118 TYR 0.007 0.001 TYR A 98 ARG 0.002 0.000 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00093 ( 4) link_NAG-ASN : angle 0.83730 ( 12) hydrogen bonds : bond 0.02356 ( 246) hydrogen bonds : angle 4.78962 ( 654) SS BOND : bond 0.00328 ( 7) SS BOND : angle 0.56463 ( 14) covalent geometry : bond 0.00239 ( 6146) covalent geometry : angle 0.48733 ( 8338) *********************** 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 57 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.957 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: A 99 PHE cc_start: 0.9168 (m-80) cc_final: 0.8855 (m-80) REVERT: A 202 LYS cc_start: 0.9021 (mmtp) cc_final: 0.8739 (mttt) REVERT: L 213 GLU cc_start: 0.8666 (tt0) cc_final: 0.7920 (tm-30) outliers start: 14 outliers final: 12 residues processed: 51 average time/residue: 0.5143 time to fit residues: 33.3120 Evaluate side-chains 54 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.888 ------------------------------------------------------------------------------- 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 130 ASP 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 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 Chi-restraints excluded: chain N residue 104 TYR Chi-restraints excluded: chain N residue 107 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 76 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3170 r_free = 0.3170 target = 0.038632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.029380 restraints weight = 115254.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.031255 restraints weight = 48013.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.032571 restraints weight = 26708.400| |-----------------------------------------------------------------------------| r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6157 Z= 0.131 Angle : 0.494 6.987 8364 Z= 0.255 Chirality : 0.042 0.131 935 Planarity : 0.004 0.036 1068 Dihedral : 4.647 37.064 937 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.11 % Allowed : 8.01 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.44 % 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: 0.12 (0.31), residues: 771 helix: -1.65 (1.32), residues: 14 sheet: 0.06 (0.26), residues: 366 loop : 0.36 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 142 HIS 0.002 0.001 HIS A 111 PHE 0.013 0.001 PHE H 109 TYR 0.008 0.001 TYR A 98 ARG 0.002 0.000 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00099 ( 4) link_NAG-ASN : angle 0.85103 ( 12) hydrogen bonds : bond 0.02386 ( 246) hydrogen bonds : angle 4.83843 ( 654) SS BOND : bond 0.00318 ( 7) SS BOND : angle 0.62874 ( 14) covalent geometry : bond 0.00280 ( 6146) covalent geometry : angle 0.49340 ( 8338) *********************** 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 55 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.887 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: A 99 PHE cc_start: 0.9158 (m-80) cc_final: 0.8849 (m-80) REVERT: L 213 GLU cc_start: 0.8607 (tt0) cc_final: 0.7832 (tm-30) outliers start: 14 outliers final: 12 residues processed: 51 average time/residue: 0.5127 time to fit residues: 33.0097 Evaluate side-chains 53 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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 H residue 46 GLU Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 204 ILE 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 Chi-restraints excluded: chain N residue 107 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 15 optimal weight: 0.3980 chunk 49 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 = 0.3148 r_free = 0.3148 target = 0.038101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.029025 restraints weight = 118158.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.030859 restraints weight = 49861.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.032140 restraints weight = 27864.877| |-----------------------------------------------------------------------------| r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6157 Z= 0.226 Angle : 0.543 7.483 8364 Z= 0.284 Chirality : 0.041 0.134 935 Planarity : 0.004 0.038 1068 Dihedral : 5.116 40.118 937 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.11 % Allowed : 7.85 % 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 (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: -0.18 (0.30), residues: 771 helix: -1.85 (1.27), residues: 14 sheet: -0.12 (0.26), residues: 364 loop : 0.12 (0.33), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 142 HIS 0.004 0.001 HIS A 111 PHE 0.010 0.001 PHE A 207 TYR 0.014 0.001 TYR L 140 ARG 0.003 0.000 ARG L 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00268 ( 4) link_NAG-ASN : angle 0.96419 ( 12) hydrogen bonds : bond 0.02823 ( 246) hydrogen bonds : angle 5.17181 ( 654) SS BOND : bond 0.00398 ( 7) SS BOND : angle 0.80869 ( 14) covalent geometry : bond 0.00457 ( 6146) covalent geometry : angle 0.54128 ( 8338) ********************** 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 56 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 1.055 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: L 213 GLU cc_start: 0.8573 (tt0) cc_final: 0.7753 (tm-30) outliers start: 14 outliers final: 12 residues processed: 50 average time/residue: 0.5445 time to fit residues: 34.9081 Evaluate side-chains 53 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain N residue 107 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 32 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 15 optimal weight: 0.0980 chunk 48 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.038508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.029356 restraints weight = 114988.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.031232 restraints weight = 48337.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.032551 restraints weight = 26782.031| |-----------------------------------------------------------------------------| r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6157 Z= 0.110 Angle : 0.497 7.741 8364 Z= 0.258 Chirality : 0.043 0.134 935 Planarity : 0.004 0.039 1068 Dihedral : 4.691 33.555 937 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.66 % Allowed : 8.46 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 19.44 % 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: 0.02 (0.31), residues: 771 helix: -1.72 (1.28), residues: 14 sheet: -0.03 (0.26), residues: 365 loop : 0.31 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 112 HIS 0.002 0.001 HIS H 209 PHE 0.036 0.001 PHE L 83 TYR 0.007 0.001 TYR L 173 ARG 0.003 0.000 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00104 ( 4) link_NAG-ASN : angle 0.78192 ( 12) hydrogen bonds : bond 0.02377 ( 246) hydrogen bonds : angle 4.90985 ( 654) SS BOND : bond 0.00325 ( 7) SS BOND : angle 0.60025 ( 14) covalent geometry : bond 0.00246 ( 6146) covalent geometry : angle 0.49649 ( 8338) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4437.53 seconds wall clock time: 76 minutes 30.76 seconds (4590.76 seconds total)