Starting phenix.real_space_refine on Wed May 14 15:53:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dpe_47104/05_2025/9dpe_47104_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dpe_47104/05_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_47104/05_2025/9dpe_47104.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dpe_47104/05_2025/9dpe_47104.map" model { file = "/net/cci-nas-00/data/ceres_data/9dpe_47104/05_2025/9dpe_47104_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dpe_47104/05_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-5687/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: 6.05, per 1000 atoms: 0.51 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: 3.02 Conformation dependent library (CDL) restraints added in 971.8 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: 1.21 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: 3.97 Time building geometry restraints manager: 3.61 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: 2.670 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: 0.190 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 27.190 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: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.430 ------------------------------------------------------------------------------- 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 : 1.372 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: 0.6237 time to fit residues: 73.8489 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 : 0.859 ------------------------------------------------------------------------------- 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 = 37)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.030875 restraints weight = 111860.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.032801 restraints weight = 45894.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.034159 restraints weight = 25216.717| |-----------------------------------------------------------------------------| r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 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 1.04552 ( 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 : 0.983 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: 0.9096 (tt0) cc_final: 0.8790 (pt0) REVERT: A 99 PHE cc_start: 0.9138 (m-80) cc_final: 0.8884 (m-80) REVERT: A 184 LYS cc_start: 0.9609 (ptmt) cc_final: 0.9151 (ttmt) REVERT: A 202 LYS cc_start: 0.8868 (mmtp) cc_final: 0.8544 (mttt) REVERT: L 122 ASP cc_start: 0.9695 (m-30) cc_final: 0.9475 (p0) REVERT: L 213 GLU cc_start: 0.8514 (tt0) cc_final: 0.7938 (tm-30) REVERT: N 43 MET cc_start: 0.8546 (mmm) cc_final: 0.8292 (mpp) outliers start: 5 outliers final: 3 residues processed: 71 average time/residue: 0.6408 time to fit residues: 54.2811 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 : 0.941 ------------------------------------------------------------------------------- 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: 3.9990 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: 3.9990 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 = 0.3155 r_free = 0.3155 target = 0.038712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.029416 restraints weight = 117805.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.031266 restraints weight = 49716.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.032561 restraints weight = 27837.900| |-----------------------------------------------------------------------------| r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 6157 Z= 0.302 Angle : 0.590 5.232 8364 Z= 0.318 Chirality : 0.041 0.146 935 Planarity : 0.005 0.038 1068 Dihedral : 5.639 51.625 937 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.66 % Allowed : 6.04 % 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: 0.05 (0.30), residues: 771 helix: -1.81 (0.94), residues: 20 sheet: 0.24 (0.26), residues: 364 loop : 0.07 (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 0.001 PHE A 207 TYR 0.018 0.002 TYR L 140 ARG 0.004 0.001 ARG A 103 Details of bonding type rmsd link_NAG-ASN : bond 0.00446 ( 4) link_NAG-ASN : angle 1.13564 ( 12) hydrogen bonds : bond 0.03448 ( 246) hydrogen bonds : angle 5.59968 ( 654) SS BOND : bond 0.00448 ( 7) SS BOND : angle 1.19987 ( 14) covalent geometry : bond 0.00606 ( 6146) covalent geometry : angle 0.58715 ( 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 : 0.839 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: 0.9114 (tt0) cc_final: 0.8896 (pt0) REVERT: A 184 LYS cc_start: 0.9571 (ptmt) cc_final: 0.9342 (ptmm) REVERT: H 83 MET cc_start: 0.8240 (mpp) cc_final: 0.7923 (mpp) REVERT: L 122 ASP cc_start: 0.9692 (m-30) cc_final: 0.9481 (p0) REVERT: L 213 GLU cc_start: 0.8731 (tt0) cc_final: 0.8119 (tm-30) outliers start: 11 outliers final: 8 residues processed: 63 average time/residue: 0.6598 time to fit residues: 49.6305 Evaluate side-chains 63 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 76 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 = 0.3149 r_free = 0.3149 target = 0.038427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.029301 restraints weight = 117979.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.031119 restraints weight = 49589.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.032410 restraints weight = 27725.875| |-----------------------------------------------------------------------------| r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2949 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= 0.252 Angle : 0.542 4.909 8364 Z= 0.290 Chirality : 0.041 0.134 935 Planarity : 0.004 0.034 1068 Dihedral : 5.510 48.895 937 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % 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: -0.21 (0.30), residues: 771 helix: -2.28 (1.07), residues: 14 sheet: 0.05 (0.26), residues: 363 loop : -0.10 (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 0.003 0.000 ARG L 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00281 ( 4) link_NAG-ASN : angle 1.02422 ( 12) hydrogen bonds : bond 0.02946 ( 246) hydrogen bonds : angle 5.45447 ( 654) SS BOND : bond 0.00315 ( 7) SS BOND : angle 0.94962 ( 14) covalent geometry : bond 0.00500 ( 6146) covalent geometry : angle 0.54025 ( 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 65 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 1.178 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: A 32 GLU cc_start: 0.9087 (tt0) cc_final: 0.8883 (pt0) REVERT: L 105 GLU cc_start: 0.8660 (mp0) cc_final: 0.8378 (mp0) REVERT: L 213 GLU cc_start: 0.8833 (tt0) cc_final: 0.8211 (tm-30) outliers start: 10 outliers final: 10 residues processed: 61 average time/residue: 0.6251 time to fit residues: 46.1793 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 : 0.953 ------------------------------------------------------------------------------- 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: 6.9990 chunk 21 optimal weight: 5.9990 chunk 25 optimal weight: 0.4980 chunk 49 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3163 r_free = 0.3163 target = 0.038615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.029482 restraints weight = 114447.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.031325 restraints weight = 47945.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.032624 restraints weight = 26594.708| |-----------------------------------------------------------------------------| r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6157 Z= 0.134 Angle : 0.487 5.421 8364 Z= 0.257 Chirality : 0.042 0.133 935 Planarity : 0.004 0.035 1068 Dihedral : 5.099 44.077 937 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.51 % Allowed : 7.25 % Favored : 91.24 % 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: -2.01 (1.23), residues: 14 sheet: 0.02 (0.26), residues: 365 loop : 0.07 (0.32), 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 0.005 0.001 PHE N 68 TYR 0.008 0.001 TYR L 140 ARG 0.002 0.000 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00121 ( 4) link_NAG-ASN : angle 0.86437 ( 12) hydrogen bonds : bond 0.02585 ( 246) hydrogen bonds : angle 5.15868 ( 654) SS BOND : bond 0.00259 ( 7) SS BOND : angle 0.64463 ( 14) covalent geometry : bond 0.00277 ( 6146) covalent geometry : angle 0.48601 ( 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 57 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 1.033 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 32 GLU cc_start: 0.9104 (tt0) cc_final: 0.8872 (pt0) REVERT: A 99 PHE cc_start: 0.9202 (m-80) cc_final: 0.8872 (m-80) REVERT: A 184 LYS cc_start: 0.9564 (ptmt) cc_final: 0.9363 (mmtt) REVERT: L 105 GLU cc_start: 0.8703 (mp0) cc_final: 0.8391 (mp0) REVERT: L 118 PHE cc_start: 0.8308 (m-80) cc_final: 0.8086 (m-80) REVERT: L 213 GLU cc_start: 0.8821 (tt0) cc_final: 0.8173 (tm-30) outliers start: 10 outliers final: 10 residues processed: 53 average time/residue: 0.5771 time to fit residues: 37.6044 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 : 0.907 ------------------------------------------------------------------------------- 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 204 ILE 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: 4.9990 chunk 53 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 64 optimal weight: 0.0000 chunk 67 optimal weight: 0.9990 overall best weight: 1.3390 ------------------------------------------------------------------------------- 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 = 0.3162 r_free = 0.3162 target = 0.038526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.029404 restraints weight = 116845.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.031249 restraints weight = 48713.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.032546 restraints weight = 26862.305| |-----------------------------------------------------------------------------| r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6157 Z= 0.172 Angle : 0.493 6.050 8364 Z= 0.260 Chirality : 0.042 0.130 935 Planarity : 0.004 0.034 1068 Dihedral : 5.068 43.010 937 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.66 % Allowed : 7.25 % Favored : 91.09 % 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: -0.20 (0.30), residues: 771 helix: -2.03 (1.22), residues: 14 sheet: -0.08 (0.26), residues: 366 loop : 0.05 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 142 HIS 0.003 0.001 HIS A 111 PHE 0.010 0.001 PHE L 98 TYR 0.010 0.001 TYR L 140 ARG 0.003 0.000 ARG N 40 Details of bonding type rmsd link_NAG-ASN : bond 0.00176 ( 4) link_NAG-ASN : angle 0.92264 ( 12) hydrogen bonds : bond 0.02647 ( 246) hydrogen bonds : angle 5.11892 ( 654) SS BOND : bond 0.00371 ( 7) SS BOND : angle 0.70268 ( 14) covalent geometry : bond 0.00351 ( 6146) covalent geometry : angle 0.49197 ( 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 57 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.989 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 32 GLU cc_start: 0.9083 (tt0) cc_final: 0.8869 (pt0) REVERT: A 99 PHE cc_start: 0.9187 (m-80) cc_final: 0.8872 (m-80) REVERT: L 105 GLU cc_start: 0.8716 (mp0) cc_final: 0.8384 (mp0) REVERT: L 118 PHE cc_start: 0.8282 (m-80) cc_final: 0.8074 (m-80) REVERT: L 213 GLU cc_start: 0.8676 (tt0) cc_final: 0.7992 (tm-30) outliers start: 11 outliers final: 10 residues processed: 53 average time/residue: 0.5440 time to fit residues: 36.5801 Evaluate side-chains 54 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 37 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 14 optimal weight: 0.2980 chunk 63 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 71 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3162 r_free = 0.3162 target = 0.038491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.029320 restraints weight = 116064.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.031167 restraints weight = 48856.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.032468 restraints weight = 27189.003| |-----------------------------------------------------------------------------| r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6157 Z= 0.143 Angle : 0.494 6.383 8364 Z= 0.257 Chirality : 0.042 0.131 935 Planarity : 0.004 0.034 1068 Dihedral : 4.902 40.150 937 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % 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 (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: -0.13 (0.30), residues: 771 helix: -1.91 (1.25), residues: 14 sheet: -0.07 (0.26), residues: 366 loop : 0.14 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 150 HIS 0.002 0.001 HIS H 209 PHE 0.005 0.001 PHE L 98 TYR 0.007 0.001 TYR L 140 ARG 0.002 0.000 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00127 ( 4) link_NAG-ASN : angle 0.86346 ( 12) hydrogen bonds : bond 0.02514 ( 246) hydrogen bonds : angle 5.02119 ( 654) SS BOND : bond 0.00352 ( 7) SS BOND : angle 0.67016 ( 14) covalent geometry : bond 0.00298 ( 6146) covalent geometry : angle 0.49277 ( 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 57 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.963 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 32 GLU cc_start: 0.9083 (tt0) cc_final: 0.8866 (pt0) REVERT: A 61 MET cc_start: 0.8480 (mtp) cc_final: 0.8277 (mtp) REVERT: A 99 PHE cc_start: 0.9168 (m-80) cc_final: 0.8862 (m-80) REVERT: A 125 MET cc_start: 0.5841 (tmm) cc_final: 0.5628 (tmm) REVERT: L 105 GLU cc_start: 0.8718 (mp0) cc_final: 0.8439 (mp0) REVERT: L 118 PHE cc_start: 0.8268 (m-80) cc_final: 0.8066 (m-80) REVERT: L 213 GLU cc_start: 0.8641 (tt0) cc_final: 0.7937 (tm-30) outliers start: 12 outliers final: 11 residues processed: 53 average time/residue: 0.5035 time to fit residues: 33.6575 Evaluate side-chains 54 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.850 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain N residue 107 ILE 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: 1.9990 chunk 65 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 43 optimal weight: 8.9990 chunk 54 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.3155 r_free = 0.3155 target = 0.038321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.029149 restraints weight = 117141.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.030987 restraints weight = 49567.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.032270 restraints weight = 27705.462| |-----------------------------------------------------------------------------| r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3611 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= 0.184 Angle : 0.516 10.906 8364 Z= 0.267 Chirality : 0.041 0.132 935 Planarity : 0.004 0.037 1068 Dihedral : 5.012 40.178 937 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.96 % Allowed : 8.01 % 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: -0.23 (0.30), residues: 771 helix: -2.01 (1.21), residues: 14 sheet: -0.13 (0.26), residues: 366 loop : 0.06 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 142 HIS 0.003 0.001 HIS A 111 PHE 0.007 0.001 PHE A 207 TYR 0.011 0.001 TYR L 140 ARG 0.002 0.000 ARG A 126 Details of bonding type rmsd link_NAG-ASN : bond 0.00195 ( 4) link_NAG-ASN : angle 0.91886 ( 12) hydrogen bonds : bond 0.02662 ( 246) hydrogen bonds : angle 5.08383 ( 654) SS BOND : bond 0.00366 ( 7) SS BOND : angle 0.71028 ( 14) covalent geometry : bond 0.00376 ( 6146) covalent geometry : angle 0.51502 ( 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 56 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.878 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 32 GLU cc_start: 0.9109 (tt0) cc_final: 0.8902 (pt0) REVERT: L 105 GLU cc_start: 0.8696 (mp0) cc_final: 0.8350 (mp0) REVERT: L 213 GLU cc_start: 0.8657 (tt0) cc_final: 0.7928 (tm-30) outliers start: 13 outliers final: 11 residues processed: 51 average time/residue: 0.4796 time to fit residues: 31.0288 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 : 0.868 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 5 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3158 r_free = 0.3158 target = 0.038360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.029166 restraints weight = 115717.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.031001 restraints weight = 49231.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.032295 restraints weight = 27555.070| |-----------------------------------------------------------------------------| r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3680 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= 0.151 Angle : 0.498 9.671 8364 Z= 0.258 Chirality : 0.042 0.129 935 Planarity : 0.004 0.040 1068 Dihedral : 4.860 37.353 937 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.81 % Allowed : 8.31 % 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: -0.16 (0.30), residues: 771 helix: -1.90 (1.24), residues: 14 sheet: -0.13 (0.26), residues: 366 loop : 0.16 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 142 HIS 0.002 0.001 HIS H 209 PHE 0.012 0.001 PHE H 109 TYR 0.008 0.001 TYR L 140 ARG 0.002 0.000 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00131 ( 4) link_NAG-ASN : angle 0.86742 ( 12) hydrogen bonds : bond 0.02571 ( 246) hydrogen bonds : angle 5.03762 ( 654) SS BOND : bond 0.00344 ( 7) SS BOND : angle 0.65562 ( 14) covalent geometry : bond 0.00314 ( 6146) covalent geometry : angle 0.49704 ( 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 54 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 1.024 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: 0.9160 (m-80) cc_final: 0.8870 (m-80) REVERT: L 105 GLU cc_start: 0.8683 (mp0) cc_final: 0.8455 (mp0) REVERT: L 213 GLU cc_start: 0.8594 (tt0) cc_final: 0.7858 (tm-30) outliers start: 12 outliers final: 12 residues processed: 49 average time/residue: 0.5249 time to fit residues: 32.3699 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 : 0.968 ------------------------------------------------------------------------------- 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 A residue 162 LYS 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 37 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 15 optimal weight: 0.0870 chunk 49 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- 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 = 0.3162 r_free = 0.3162 target = 0.038487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.029281 restraints weight = 114979.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.031137 restraints weight = 48523.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.032452 restraints weight = 27063.072| |-----------------------------------------------------------------------------| r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6157 Z= 0.117 Angle : 0.497 11.583 8364 Z= 0.254 Chirality : 0.042 0.133 935 Planarity : 0.004 0.040 1068 Dihedral : 4.696 34.662 937 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.36 % Allowed : 8.61 % 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: -0.04 (0.30), residues: 771 helix: -1.81 (1.26), residues: 14 sheet: -0.10 (0.26), residues: 366 loop : 0.31 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 163 HIS 0.002 0.001 HIS H 209 PHE 0.010 0.001 PHE H 109 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 0.00100 ( 4) link_NAG-ASN : angle 0.83087 ( 12) hydrogen bonds : bond 0.02465 ( 246) hydrogen bonds : angle 4.89546 ( 654) SS BOND : bond 0.00338 ( 7) SS BOND : angle 0.61159 ( 14) covalent geometry : bond 0.00254 ( 6146) covalent geometry : angle 0.49569 ( 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 52 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.888 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: 0.9152 (m-80) cc_final: 0.8851 (m-80) REVERT: L 105 GLU cc_start: 0.8644 (mp0) cc_final: 0.8425 (mp0) REVERT: L 213 GLU cc_start: 0.8583 (tt0) cc_final: 0.7799 (tm-30) outliers start: 9 outliers final: 9 residues processed: 49 average time/residue: 0.5322 time to fit residues: 32.6046 Evaluate side-chains 51 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 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 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: 0.9980 chunk 5 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 48 optimal weight: 0.3980 chunk 54 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 56 optimal weight: 0.0970 chunk 34 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3168 r_free = 0.3168 target = 0.038590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.029431 restraints weight = 114521.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.031304 restraints weight = 47822.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.032618 restraints weight = 26489.182| |-----------------------------------------------------------------------------| r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6157 Z= 0.107 Angle : 0.488 11.153 8364 Z= 0.249 Chirality : 0.043 0.134 935 Planarity : 0.004 0.040 1068 Dihedral : 4.507 32.325 937 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.36 % Allowed : 8.46 % 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: 0.13 (0.31), residues: 771 helix: -1.66 (1.29), residues: 14 sheet: 0.01 (0.26), residues: 366 loop : 0.44 (0.34), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 163 HIS 0.003 0.001 HIS H 209 PHE 0.008 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 0.00098 ( 4) link_NAG-ASN : angle 0.85242 ( 12) hydrogen bonds : bond 0.02380 ( 246) hydrogen bonds : angle 4.76709 ( 654) SS BOND : bond 0.00330 ( 7) SS BOND : angle 0.60753 ( 14) covalent geometry : bond 0.00237 ( 6146) covalent geometry : angle 0.48682 ( 8338) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4136.21 seconds wall clock time: 72 minutes 17.94 seconds (4337.94 seconds total)