Starting phenix.real_space_refine on Thu Jul 2 05:43:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8u4v_41899/07_2026/8u4v_41899.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u4v_41899/07_2026/8u4v_41899.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8u4v_41899/07_2026/8u4v_41899.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8u4v_41899/07_2026/8u4v_41899.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u4v_41899/07_2026/8u4v_41899.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u4v_41899/07_2026/8u4v_41899.map" model { file = "/net/cci-nas-00/data/ceres_data/8u4v_41899/07_2026/8u4v_41899.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u4v_41899/07_2026/8u4v_41899.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.018 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: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 4212 2.51 5 N 1102 2.21 5 O 1292 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6637 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1324 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 4, 'TRANS': 175} Chain: "B" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 970 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1620 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 202} Chain: "H" Number of atoms: 1735 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 228, 1724 Classifications: {'peptide': 228} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 215} Conformer: "B" Number of residues, atoms: 228, 1724 Classifications: {'peptide': 228} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 215} bond proxies already assigned to first conformer: 1761 Chain: "K" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 916 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "H" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'AV0': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 1.53, per 1000 atoms: 0.23 Number of scatterers: 6637 At special positions: 0 Unit cell: (77.964, 96.12, 129.228, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 31 16.00 O 1292 8.00 N 1102 7.00 C 4212 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 64 " distance=2.03 Simple disulfide: pdb=" SG CYS L 48 " - pdb=" SG CYS L 113 " distance=2.03 Simple disulfide: pdb=" SG CYS L 159 " - pdb=" SG CYS L 219 " distance=2.03 Simple disulfide: pdb=" SG CYS H 48 " - pdb=" SG CYS H 122 " distance=2.03 Simple disulfide: pdb=" SG CYS H 180 " - pdb=" SG CYS H 236 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.42 Conformation dependent library (CDL) restraints added in 360.6 milliseconds 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1588 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 17 sheets defined 20.6% alpha, 38.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 5 through 27 Processing helix chain 'A' and resid 69 through 73 removed outlier: 3.600A pdb=" N LEU A 73 " --> pdb=" O LEU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 101 removed outlier: 3.602A pdb=" N ALA A 79 " --> pdb=" O GLN A 75 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ALA A 80 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 149 Proline residue: A 135 - end of helix Processing helix chain 'A' and resid 161 through 183 removed outlier: 3.734A pdb=" N TYR A 165 " --> pdb=" O GLY A 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 217 Processing helix chain 'B' and resid 267 through 270 removed outlier: 3.666A pdb=" N ASN B 270 " --> pdb=" O ASN B 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 267 through 270' Processing helix chain 'L' and resid 104 through 108 removed outlier: 4.109A pdb=" N PHE L 108 " --> pdb=" O PRO L 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 146 through 153 Processing helix chain 'L' and resid 208 through 212 Processing helix chain 'H' and resid 54 through 57 removed outlier: 3.636A pdb=" N SER H 57 " --> pdb=" O ASN H 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 54 through 57' Processing helix chain 'H' and resid 113 through 117 Processing helix chain 'H' and resid 130 through 137 removed outlier: 3.588A pdb=" N LEU H 135 " --> pdb=" O TRP H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 198 No H-bonds generated for 'chain 'H' and resid 196 through 198' Processing helix chain 'H' and resid 225 through 229 removed outlier: 3.531A pdb=" N LEU H 229 " --> pdb=" O SER H 226 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 57 removed outlier: 4.147A pdb=" N GLY K 57 " --> pdb=" O SER K 54 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 66 Processing sheet with id=AA2, first strand: chain 'B' and resid 205 through 210 removed outlier: 7.133A pdb=" N ALA B 205 " --> pdb=" O ASN B 239 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N HIS B 241 " --> pdb=" O ALA B 205 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N GLU B 207 " --> pdb=" O HIS B 241 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N THR B 243 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU B 209 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N SER B 265 " --> pdb=" O LYS B 273 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N LYS B 273 " --> pdb=" O SER B 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 223 through 227 removed outlier: 3.912A pdb=" N GLN B 249 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS B 285 " --> pdb=" O ALA B 255 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 29 through 32 Processing sheet with id=AA5, first strand: chain 'L' and resid 35 through 38 removed outlier: 6.113A pdb=" N GLN L 62 " --> pdb=" O LEU L 71 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N LEU L 71 " --> pdb=" O GLN L 62 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 35 through 38 Processing sheet with id=AA7, first strand: chain 'L' and resid 139 through 143 removed outlier: 5.495A pdb=" N TYR L 198 " --> pdb=" O ASN L 163 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 169 through 174 Processing sheet with id=AA9, first strand: chain 'H' and resid 29 through 33 Processing sheet with id=AB1, first strand: chain 'H' and resid 37 through 38 removed outlier: 4.214A pdb=" N TRP H 125 " --> pdb=" O TYR H 59 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N TYR H 59 " --> pdb=" O TRP H 125 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ARG H 64 " --> pdb=" O TRP H 73 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N TRP H 73 " --> pdb=" O ARG H 64 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 37 through 38 Processing sheet with id=AB3, first strand: chain 'H' and resid 161 through 164 removed outlier: 3.584A pdb=" N SER H 220 " --> pdb=" O CYS H 180 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP H 184 " --> pdb=" O TYR H 216 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR H 216 " --> pdb=" O ASP H 184 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 161 through 164 removed outlier: 3.584A pdb=" N SER H 220 " --> pdb=" O CYS H 180 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP H 184 " --> pdb=" O TYR H 216 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR H 216 " --> pdb=" O ASP H 184 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 191 through 194 removed outlier: 4.792A pdb=" N TYR H 234 " --> pdb=" O VAL H 251 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 3 through 6 removed outlier: 6.055A pdb=" N GLY K 16 " --> pdb=" O SER K 85 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 59 through 60 removed outlier: 5.532A pdb=" N PHE K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ARG K 38 " --> pdb=" O PHE K 47 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA K 33 " --> pdb=" O ASP K 99 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 92 through 93 335 hydrogen bonds defined for protein. 891 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: 0.98 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1464 1.33 - 1.45: 1560 1.45 - 1.57: 3717 1.57 - 1.69: 0 1.69 - 1.81: 44 Bond restraints: 6785 Sorted by residual: bond pdb=" N GLY K 10 " pdb=" CA GLY K 10 " ideal model delta sigma weight residual 1.448 1.477 -0.029 9.20e-03 1.18e+04 9.94e+00 bond pdb=" N VAL K 50 " pdb=" CA VAL K 50 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.15e-02 7.56e+03 9.27e+00 bond pdb=" CCJ AV0 H 301 " pdb=" OBV AV0 H 301 " ideal model delta sigma weight residual 1.374 1.431 -0.057 2.00e-02 2.50e+03 8.11e+00 bond pdb=" CA SER L 35 " pdb=" CB SER L 35 " ideal model delta sigma weight residual 1.533 1.489 0.044 1.66e-02 3.63e+03 7.10e+00 bond pdb=" N ILE K 29 " pdb=" CA ILE K 29 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.35e-02 5.49e+03 7.09e+00 ... (remaining 6780 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.71: 9215 6.71 - 13.42: 9 13.42 - 20.13: 2 20.13 - 26.84: 3 26.84 - 33.55: 2 Bond angle restraints: 9231 Sorted by residual: angle pdb=" CBR AV0 H 301 " pdb=" CCM AV0 H 301 " pdb=" CBT AV0 H 301 " ideal model delta sigma weight residual 110.70 77.15 33.55 3.00e+00 1.11e-01 1.25e+02 angle pdb=" CBQ AV0 H 301 " pdb=" CCM AV0 H 301 " pdb=" CBS AV0 H 301 " ideal model delta sigma weight residual 110.52 81.56 28.96 3.00e+00 1.11e-01 9.32e+01 angle pdb=" C ARG K 38 " pdb=" CA ARG K 38 " pdb=" CB ARG K 38 " ideal model delta sigma weight residual 109.38 92.93 16.45 1.80e+00 3.09e-01 8.35e+01 angle pdb=" CBQ AV0 H 301 " pdb=" CCM AV0 H 301 " pdb=" CBR AV0 H 301 " ideal model delta sigma weight residual 107.79 81.90 25.89 3.00e+00 1.11e-01 7.45e+01 angle pdb=" CBS AV0 H 301 " pdb=" CCM AV0 H 301 " pdb=" CBT AV0 H 301 " ideal model delta sigma weight residual 105.72 80.28 25.44 3.00e+00 1.11e-01 7.19e+01 ... (remaining 9226 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 3553 17.76 - 35.52: 322 35.52 - 53.28: 80 53.28 - 71.05: 22 71.05 - 88.81: 6 Dihedral angle restraints: 3983 sinusoidal: 1497 harmonic: 2486 Sorted by residual: dihedral pdb=" C ARG K 38 " pdb=" N ARG K 38 " pdb=" CA ARG K 38 " pdb=" CB ARG K 38 " ideal model delta harmonic sigma weight residual -122.60 -101.94 -20.66 0 2.50e+00 1.60e-01 6.83e+01 dihedral pdb=" CB CYS H 180 " pdb=" SG CYS H 180 " pdb=" SG CYS H 236 " pdb=" CB CYS H 236 " ideal model delta sinusoidal sigma weight residual -86.00 -132.12 46.12 1 1.00e+01 1.00e-02 2.95e+01 dihedral pdb=" C ASN L 163 " pdb=" N ASN L 163 " pdb=" CA ASN L 163 " pdb=" CB ASN L 163 " ideal model delta harmonic sigma weight residual -122.60 -134.49 11.89 0 2.50e+00 1.60e-01 2.26e+01 ... (remaining 3980 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 985 0.111 - 0.222: 65 0.222 - 0.332: 4 0.332 - 0.443: 1 0.443 - 0.554: 1 Chirality restraints: 1056 Sorted by residual: chirality pdb=" CA ASN L 163 " pdb=" N ASN L 163 " pdb=" C ASN L 163 " pdb=" CB ASN L 163 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.67e+00 chirality pdb=" CA ARG K 38 " pdb=" N ARG K 38 " pdb=" C ARG K 38 " pdb=" CB ARG K 38 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" CA LYS A 157 " pdb=" N LYS A 157 " pdb=" C LYS A 157 " pdb=" CB LYS A 157 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 1053 not shown) Planarity restraints: 1153 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 73 " -0.039 5.00e-02 4.00e+02 5.99e-02 5.73e+00 pdb=" N PRO A 74 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 74 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 74 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 111 " 0.009 2.00e-02 2.50e+03 1.88e-02 3.52e+00 pdb=" CD GLU A 111 " -0.032 2.00e-02 2.50e+03 pdb=" OE1 GLU A 111 " 0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU A 111 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER L 184 " -0.008 2.00e-02 2.50e+03 1.57e-02 2.48e+00 pdb=" C SER L 184 " 0.027 2.00e-02 2.50e+03 pdb=" O SER L 184 " -0.010 2.00e-02 2.50e+03 pdb=" N GLN L 185 " -0.009 2.00e-02 2.50e+03 ... (remaining 1150 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 108 2.63 - 3.20: 5758 3.20 - 3.77: 10273 3.77 - 4.33: 14642 4.33 - 4.90: 24696 Nonbonded interactions: 55477 Sorted by model distance: nonbonded pdb=" O THR H 171 " pdb=" OG1 THR H 175 " model vdw 2.063 3.040 nonbonded pdb=" OG SER L 51 " pdb=" OE1 GLN L 52 " model vdw 2.199 3.040 nonbonded pdb=" O ALA L 178 " pdb=" NE2 GLN L 180 " model vdw 2.287 3.120 nonbonded pdb=" CBS AV0 H 301 " pdb=" OBV AV0 H 301 " model vdw 2.334 2.752 nonbonded pdb=" O SER L 119 " pdb=" OG SER H 85 " model vdw 2.354 3.040 ... (remaining 55472 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.47 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.800 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: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.940 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:5.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 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 : 0.006 0.057 6791 Z= 0.377 Angle : 1.120 33.548 9243 Z= 0.618 Chirality : 0.060 0.554 1056 Planarity : 0.004 0.060 1153 Dihedral : 15.094 88.806 2377 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.83 % Allowed : 21.47 % Favored : 77.70 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.30), residues: 853 helix: 2.16 (0.43), residues: 139 sheet: 0.22 (0.29), residues: 344 loop : 0.13 (0.35), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 53 TYR 0.007 0.001 TYR H 121 PHE 0.013 0.001 PHE K 37 TRP 0.015 0.001 TRP A 18 HIS 0.001 0.000 HIS B 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.38 ( 6785) covalent geometry : angle 1.12051 / 0.62 ( 9231) SS BOND : bond 0.00204 / 0.15 ( 6) SS BOND : angle 0.94701 / 0.72 ( 12) hydrogen bonds : bond 0.17811 / 12.24 ( 314) hydrogen bonds : angle 7.61977 / 5.44 ( 891) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 145 time to evaluate : 0.201 Fit side-chains REVERT: A 52 MET cc_start: 0.8997 (ptp) cc_final: 0.8581 (ptt) REVERT: A 78 GLN cc_start: 0.7249 (tt0) cc_final: 0.6797 (mt0) REVERT: B 250 LYS cc_start: 0.8210 (ttpt) cc_final: 0.7697 (tttp) REVERT: L 49 ARG cc_start: 0.7848 (ttp-170) cc_final: 0.7058 (ttp-110) REVERT: L 130 GLU cc_start: 0.8370 (mt-10) cc_final: 0.7976 (mt-10) REVERT: L 147 ASP cc_start: 0.8481 (p0) cc_final: 0.8261 (m-30) REVERT: L 210 ASP cc_start: 0.8229 (t0) cc_final: 0.7545 (t0) REVERT: H 250 LYS cc_start: 0.8816 (tttm) cc_final: 0.8561 (tptt) REVERT: H 252 GLU cc_start: 0.9152 (mt-10) cc_final: 0.8906 (mt-10) REVERT: K 89 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7310 (pm20) REVERT: K 101 ASP cc_start: 0.8254 (t0) cc_final: 0.7948 (t0) outliers start: 6 outliers final: 1 residues processed: 149 average time/residue: 0.4447 time to fit residues: 69.5415 Evaluate side-chains 114 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 112 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain K residue 89 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 295 GLN L 115 GLN ** L 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 185 GLN H 211 GLN K 3 GLN K 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.090379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.067695 restraints weight = 16876.407| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 2.55 r_work: 0.2597 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2457 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2457 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2462 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2462 r_free = 0.2462 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2462 r_free = 0.2462 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2462 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9080 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6791 Z= 0.176 Angle : 0.900 32.254 9243 Z= 0.380 Chirality : 0.043 0.144 1056 Planarity : 0.004 0.052 1153 Dihedral : 6.270 81.530 950 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.32 % Allowed : 19.81 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.30), residues: 853 helix: 2.33 (0.43), residues: 141 sheet: 0.56 (0.29), residues: 351 loop : 0.38 (0.36), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 72 TYR 0.012 0.001 TYR B 264 PHE 0.014 0.001 PHE B 261 TRP 0.011 0.001 TRP A 18 HIS 0.003 0.001 HIS H 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 ( 6785) covalent geometry : angle 0.89980 / 0.38 ( 9231) SS BOND : bond 0.00207 / 0.15 ( 6) SS BOND : angle 1.29542 / 0.84 ( 12) hydrogen bonds : bond 0.04115 / 2.74 ( 314) hydrogen bonds : angle 5.46500 / 3.81 ( 891) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.242 Fit side-chains REVERT: A 78 GLN cc_start: 0.8531 (tt0) cc_final: 0.8287 (mm-40) REVERT: A 130 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8823 (mm) REVERT: B 250 LYS cc_start: 0.9078 (ttpt) cc_final: 0.8751 (tttp) REVERT: B 295 GLN cc_start: 0.8780 (mm-40) cc_final: 0.8420 (mm-40) REVERT: L 49 ARG cc_start: 0.9056 (ttp-170) cc_final: 0.8605 (ttp-110) REVERT: L 91 ARG cc_start: 0.9066 (ttt180) cc_final: 0.8854 (ttt180) REVERT: L 95 ASP cc_start: 0.8951 (m-30) cc_final: 0.8332 (m-30) REVERT: L 175 VAL cc_start: 0.9183 (m) cc_final: 0.8853 (t) REVERT: L 210 ASP cc_start: 0.8632 (t0) cc_final: 0.8262 (t0) REVERT: H 178 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8783 (mp) REVERT: H 239 ASN cc_start: 0.9286 (t0) cc_final: 0.8991 (t0) REVERT: H 246 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8910 (mmmt) REVERT: K 89 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8193 (pm20) outliers start: 24 outliers final: 6 residues processed: 128 average time/residue: 0.4705 time to fit residues: 63.2343 Evaluate side-chains 115 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 264 TYR Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 246 LYS Chi-restraints excluded: chain K residue 89 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 64 optimal weight: 0.7980 chunk 52 optimal weight: 0.0670 chunk 17 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 69 optimal weight: 0.1980 chunk 4 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN H 244 ASN K 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.089727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.065916 restraints weight = 22359.154| |-----------------------------------------------------------------------------| r_work (start): 0.2696 rms_B_bonded: 3.03 r_work: 0.2557 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2567 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2567 r_free = 0.2567 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2567 r_free = 0.2567 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2567 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8995 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6791 Z= 0.148 Angle : 0.873 32.799 9243 Z= 0.361 Chirality : 0.042 0.141 1056 Planarity : 0.004 0.057 1153 Dihedral : 6.203 83.626 949 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.46 % Allowed : 21.05 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.30), residues: 853 helix: 2.55 (0.44), residues: 141 sheet: 0.74 (0.29), residues: 329 loop : 0.42 (0.35), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 53 TYR 0.009 0.001 TYR K 104 PHE 0.011 0.001 PHE B 261 TRP 0.009 0.001 TRP A 18 HIS 0.001 0.000 HIS B 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 6785) covalent geometry : angle 0.87284 / 0.36 ( 9231) SS BOND : bond 0.00188 / 0.14 ( 6) SS BOND : angle 0.99201 / 0.56 ( 12) hydrogen bonds : bond 0.03703 / 2.44 ( 314) hydrogen bonds : angle 5.09092 / 3.55 ( 891) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.163 Fit side-chains REVERT: A 130 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8716 (mm) REVERT: A 157 LYS cc_start: 0.8573 (tptm) cc_final: 0.8353 (tptp) REVERT: A 159 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8275 (mm-30) REVERT: B 250 LYS cc_start: 0.8994 (ttpt) cc_final: 0.8637 (tttp) REVERT: L 49 ARG cc_start: 0.8853 (ttp-170) cc_final: 0.8380 (ttp-110) REVERT: L 95 ASP cc_start: 0.8853 (m-30) cc_final: 0.8125 (m-30) REVERT: L 210 ASP cc_start: 0.8553 (t0) cc_final: 0.8194 (t0) REVERT: L 212 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8318 (mm-30) REVERT: H 239 ASN cc_start: 0.9163 (t0) cc_final: 0.8872 (t0) REVERT: H 246 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8850 (mmmt) REVERT: K 4 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7800 (pp) outliers start: 25 outliers final: 9 residues processed: 121 average time/residue: 0.4620 time to fit residues: 58.5946 Evaluate side-chains 116 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 246 LYS Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 62 ASP Chi-restraints excluded: chain K residue 74 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 81 optimal weight: 2.9990 chunk 68 optimal weight: 0.3980 chunk 2 optimal weight: 0.0870 chunk 9 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 39 GLN H 244 ASN K 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.090090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.066058 restraints weight = 22745.480| |-----------------------------------------------------------------------------| r_work (start): 0.2704 rms_B_bonded: 3.01 r_work: 0.2564 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2569 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2569 r_free = 0.2569 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2569 r_free = 0.2569 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2569 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8999 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6791 Z= 0.150 Angle : 0.873 32.445 9243 Z= 0.360 Chirality : 0.041 0.144 1056 Planarity : 0.004 0.048 1153 Dihedral : 6.086 84.046 946 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.46 % Allowed : 22.44 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.30), residues: 853 helix: 2.32 (0.44), residues: 145 sheet: 0.90 (0.30), residues: 317 loop : 0.28 (0.34), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 53 TYR 0.019 0.001 TYR A 67 PHE 0.011 0.001 PHE B 261 TRP 0.011 0.001 TRP A 18 HIS 0.001 0.000 HIS H 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 ( 6785) covalent geometry : angle 0.87254 / 0.36 ( 9231) SS BOND : bond 0.00198 / 0.14 ( 6) SS BOND : angle 0.97936 / 0.53 ( 12) hydrogen bonds : bond 0.03519 / 2.30 ( 314) hydrogen bonds : angle 4.94467 / 3.45 ( 891) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 0.178 Fit side-chains REVERT: A 130 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8749 (mm) REVERT: L 49 ARG cc_start: 0.8914 (ttp-170) cc_final: 0.8443 (ttp-110) REVERT: L 95 ASP cc_start: 0.8839 (m-30) cc_final: 0.8035 (m-30) REVERT: H 178 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8773 (mp) REVERT: H 239 ASN cc_start: 0.9165 (t0) cc_final: 0.8866 (t0) REVERT: K 4 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7752 (pp) outliers start: 25 outliers final: 11 residues processed: 118 average time/residue: 0.4528 time to fit residues: 56.0031 Evaluate side-chains 111 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 74 ASP Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 109 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 10 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 71 optimal weight: 0.2980 chunk 56 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 239 ASN H 244 ASN K 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.089630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.066504 restraints weight = 17360.636| |-----------------------------------------------------------------------------| r_work (start): 0.2710 rms_B_bonded: 2.66 r_work: 0.2577 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2439 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2439 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2446 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2446 r_free = 0.2446 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2446 r_free = 0.2446 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2446 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9065 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6791 Z= 0.165 Angle : 0.878 32.306 9243 Z= 0.364 Chirality : 0.042 0.144 1056 Planarity : 0.004 0.045 1153 Dihedral : 6.143 84.841 946 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.32 % Allowed : 22.71 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.31), residues: 853 helix: 2.32 (0.45), residues: 145 sheet: 0.80 (0.29), residues: 339 loop : 0.39 (0.36), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 53 TYR 0.012 0.001 TYR L 217 PHE 0.011 0.001 PHE B 261 TRP 0.010 0.001 TRP H 125 HIS 0.001 0.000 HIS B 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 ( 6785) covalent geometry : angle 0.87748 / 0.36 ( 9231) SS BOND : bond 0.00225 / 0.17 ( 6) SS BOND : angle 1.00053 / 0.54 ( 12) hydrogen bonds : bond 0.03542 / 2.32 ( 314) hydrogen bonds : angle 4.89229 / 3.42 ( 891) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: A 130 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8795 (mm) REVERT: L 49 ARG cc_start: 0.9027 (ttp-170) cc_final: 0.8567 (ttp-110) REVERT: L 95 ASP cc_start: 0.8931 (m-30) cc_final: 0.8199 (m-30) REVERT: L 190 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8590 (mm-30) REVERT: H 178 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8769 (mp) REVERT: H 239 ASN cc_start: 0.9231 (OUTLIER) cc_final: 0.8900 (m-40) REVERT: K 4 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7673 (pp) outliers start: 24 outliers final: 15 residues processed: 113 average time/residue: 0.4787 time to fit residues: 56.7707 Evaluate side-chains 114 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 239 ASN Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 62 ASP Chi-restraints excluded: chain K residue 74 ASP Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 109 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 76 optimal weight: 0.9980 chunk 34 optimal weight: 0.4980 chunk 72 optimal weight: 0.0070 chunk 49 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 39 GLN H 239 ASN H 244 ASN K 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.089760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.065828 restraints weight = 22438.769| |-----------------------------------------------------------------------------| r_work (start): 0.2693 rms_B_bonded: 3.03 r_work: 0.2552 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2553 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2553 r_free = 0.2553 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2553 r_free = 0.2553 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2553 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8996 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6791 Z= 0.156 Angle : 0.875 32.242 9243 Z= 0.361 Chirality : 0.042 0.145 1056 Planarity : 0.004 0.045 1153 Dihedral : 6.148 85.002 946 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.60 % Allowed : 22.58 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.31), residues: 853 helix: 2.34 (0.45), residues: 145 sheet: 0.85 (0.29), residues: 339 loop : 0.43 (0.36), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 53 TYR 0.009 0.001 TYR L 217 PHE 0.011 0.001 PHE B 261 TRP 0.010 0.001 TRP A 18 HIS 0.001 0.001 HIS H 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 ( 6785) covalent geometry : angle 0.87523 / 0.36 ( 9231) SS BOND : bond 0.00217 / 0.17 ( 6) SS BOND : angle 0.93596 / 0.49 ( 12) hydrogen bonds : bond 0.03439 / 2.25 ( 314) hydrogen bonds : angle 4.84160 / 3.38 ( 891) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: A 75 GLN cc_start: 0.7281 (tm-30) cc_final: 0.6888 (tm-30) REVERT: A 130 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8715 (mm) REVERT: L 49 ARG cc_start: 0.8868 (ttp-170) cc_final: 0.8413 (ttp-110) REVERT: L 95 ASP cc_start: 0.8856 (m-30) cc_final: 0.8034 (m-30) REVERT: H 178 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8717 (mp) REVERT: H 239 ASN cc_start: 0.9047 (OUTLIER) cc_final: 0.8794 (m-40) REVERT: K 4 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7768 (pp) outliers start: 26 outliers final: 13 residues processed: 114 average time/residue: 0.4752 time to fit residues: 56.8647 Evaluate side-chains 115 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 239 ASN Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 62 ASP Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 109 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 62 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 45 optimal weight: 0.4980 chunk 34 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 13 optimal weight: 0.0170 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 39 GLN H 239 ASN H 244 ASN K 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.089834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.065668 restraints weight = 22525.905| |-----------------------------------------------------------------------------| r_work (start): 0.2694 rms_B_bonded: 2.99 r_work: 0.2554 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2561 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2561 r_free = 0.2561 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2561 r_free = 0.2561 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2561 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9007 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6791 Z= 0.162 Angle : 0.878 32.220 9243 Z= 0.362 Chirality : 0.041 0.145 1056 Planarity : 0.004 0.043 1153 Dihedral : 6.154 85.199 946 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.32 % Allowed : 22.30 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.31), residues: 853 helix: 2.39 (0.45), residues: 145 sheet: 0.86 (0.29), residues: 339 loop : 0.42 (0.36), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 53 TYR 0.012 0.001 TYR L 217 PHE 0.011 0.001 PHE B 261 TRP 0.010 0.001 TRP A 18 HIS 0.001 0.000 HIS H 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 ( 6785) covalent geometry : angle 0.87796 / 0.36 ( 9231) SS BOND : bond 0.00237 / 0.18 ( 6) SS BOND : angle 0.96020 / 0.49 ( 12) hydrogen bonds : bond 0.03451 / 2.26 ( 314) hydrogen bonds : angle 4.82113 / 3.37 ( 891) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.154 Fit side-chains revert: symmetry clash REVERT: A 75 GLN cc_start: 0.7264 (tm-30) cc_final: 0.6849 (tm-30) REVERT: A 78 GLN cc_start: 0.8471 (tt0) cc_final: 0.8249 (mt0) REVERT: A 130 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8754 (mm) REVERT: L 49 ARG cc_start: 0.8896 (ttp-170) cc_final: 0.8451 (ttp-110) REVERT: L 95 ASP cc_start: 0.8857 (m-30) cc_final: 0.8040 (m-30) REVERT: H 178 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8739 (mp) REVERT: K 4 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7809 (pp) outliers start: 24 outliers final: 14 residues processed: 112 average time/residue: 0.4458 time to fit residues: 52.3945 Evaluate side-chains 113 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 62 ASP Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 109 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 64 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 24 optimal weight: 0.0020 chunk 26 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 39 GLN H 239 ASN H 244 ASN K 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.089759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.067380 restraints weight = 14481.779| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 2.41 r_work: 0.2599 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2458 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2458 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2470 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2470 r_free = 0.2470 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2470 r_free = 0.2470 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2470 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9052 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6791 Z= 0.155 Angle : 0.879 32.136 9243 Z= 0.362 Chirality : 0.041 0.145 1056 Planarity : 0.004 0.042 1153 Dihedral : 6.146 85.155 946 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.46 % Allowed : 22.30 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.31), residues: 853 helix: 2.43 (0.45), residues: 144 sheet: 0.87 (0.29), residues: 339 loop : 0.42 (0.36), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 53 TYR 0.009 0.001 TYR L 217 PHE 0.011 0.001 PHE B 261 TRP 0.011 0.001 TRP A 18 HIS 0.001 0.000 HIS H 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 ( 6785) covalent geometry : angle 0.87848 / 0.36 ( 9231) SS BOND : bond 0.00226 / 0.17 ( 6) SS BOND : angle 0.94246 / 0.50 ( 12) hydrogen bonds : bond 0.03413 / 2.24 ( 314) hydrogen bonds : angle 4.78234 / 3.35 ( 891) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.159 Fit side-chains revert: symmetry clash REVERT: A 75 GLN cc_start: 0.7318 (tm-30) cc_final: 0.6916 (tm-30) REVERT: A 78 GLN cc_start: 0.8547 (tt0) cc_final: 0.8335 (mt0) REVERT: A 130 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8789 (mm) REVERT: L 49 ARG cc_start: 0.8964 (ttp-170) cc_final: 0.8521 (ttp-110) REVERT: L 95 ASP cc_start: 0.8943 (m-30) cc_final: 0.8163 (m-30) REVERT: H 178 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8720 (mp) REVERT: K 4 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7807 (pp) outliers start: 25 outliers final: 11 residues processed: 116 average time/residue: 0.4885 time to fit residues: 59.4388 Evaluate side-chains 113 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 83 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 30 optimal weight: 3.9990 chunk 13 optimal weight: 0.0030 chunk 47 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 31 optimal weight: 0.1980 chunk 44 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 295 GLN H 39 GLN H 239 ASN H 244 ASN K 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.091116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.068498 restraints weight = 15165.205| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 2.51 r_work: 0.2617 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2477 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2477 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2485 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2485 r_free = 0.2485 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2485 r_free = 0.2485 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2485 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9059 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6791 Z= 0.128 Angle : 0.871 32.070 9243 Z= 0.357 Chirality : 0.041 0.146 1056 Planarity : 0.004 0.043 1153 Dihedral : 6.071 84.740 946 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.77 % Allowed : 22.85 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.31), residues: 853 helix: 2.48 (0.45), residues: 144 sheet: 1.09 (0.30), residues: 317 loop : 0.34 (0.34), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG K 31 TYR 0.008 0.001 TYR K 60 PHE 0.009 0.001 PHE B 316 TRP 0.013 0.001 TRP A 18 HIS 0.001 0.000 HIS H 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 6785) covalent geometry : angle 0.87128 / 0.36 ( 9231) SS BOND : bond 0.00155 / 0.12 ( 6) SS BOND : angle 0.79405 / 0.42 ( 12) hydrogen bonds : bond 0.03216 / 2.11 ( 314) hydrogen bonds : angle 4.68870 / 3.28 ( 891) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.177 Fit side-chains REVERT: A 75 GLN cc_start: 0.7314 (tm-30) cc_final: 0.6883 (tm-30) REVERT: A 130 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8768 (mm) REVERT: L 49 ARG cc_start: 0.8997 (ttp-170) cc_final: 0.8777 (ttp-170) REVERT: H 178 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8730 (mp) REVERT: K 4 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7827 (pp) outliers start: 20 outliers final: 9 residues processed: 117 average time/residue: 0.4763 time to fit residues: 58.4381 Evaluate side-chains 110 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 43 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 54 optimal weight: 2.9990 chunk 2 optimal weight: 0.3980 chunk 9 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 53 optimal weight: 0.0170 chunk 28 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 39 GLN H 239 ASN H 244 ASN K 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.090201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.066484 restraints weight = 20507.576| |-----------------------------------------------------------------------------| r_work (start): 0.2708 rms_B_bonded: 2.89 r_work: 0.2572 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2579 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2579 r_free = 0.2579 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2579 r_free = 0.2579 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2579 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8972 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6791 Z= 0.153 Angle : 0.895 32.069 9243 Z= 0.372 Chirality : 0.042 0.145 1056 Planarity : 0.004 0.043 1153 Dihedral : 6.118 84.732 946 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.94 % Allowed : 24.24 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.31), residues: 853 helix: 2.68 (0.45), residues: 141 sheet: 1.01 (0.29), residues: 330 loop : 0.44 (0.35), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 53 TYR 0.010 0.001 TYR L 217 PHE 0.011 0.001 PHE B 261 TRP 0.013 0.001 TRP A 18 HIS 0.001 0.000 HIS H 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.15 ( 6785) covalent geometry : angle 0.89510 / 0.37 ( 9231) SS BOND : bond 0.00211 / 0.16 ( 6) SS BOND : angle 0.92833 / 0.49 ( 12) hydrogen bonds : bond 0.03357 / 2.21 ( 314) hydrogen bonds : angle 4.71236 / 3.31 ( 891) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.251 Fit side-chains REVERT: A 75 GLN cc_start: 0.7274 (tm-30) cc_final: 0.6852 (tm-30) REVERT: A 130 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8690 (mm) REVERT: L 49 ARG cc_start: 0.8855 (ttp-170) cc_final: 0.8635 (ttp-170) REVERT: H 178 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8664 (mp) REVERT: K 4 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7802 (pp) outliers start: 14 outliers final: 8 residues processed: 104 average time/residue: 0.5142 time to fit residues: 55.8766 Evaluate side-chains 107 residues out of total 721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 43 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 9 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 20 optimal weight: 0.0010 chunk 21 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 69 optimal weight: 0.7980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 39 GLN H 239 ASN K 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.090838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.068477 restraints weight = 14007.637| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 2.40 r_work: 0.2617 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2477 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2477 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2485 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2485 r_free = 0.2485 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2485 r_free = 0.2485 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2485 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9039 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6791 Z= 0.136 Angle : 0.884 32.005 9243 Z= 0.365 Chirality : 0.042 0.145 1056 Planarity : 0.004 0.043 1153 Dihedral : 6.085 84.507 946 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.52 % Allowed : 24.52 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.31), residues: 853 helix: 2.67 (0.45), residues: 141 sheet: 1.18 (0.30), residues: 309 loop : 0.38 (0.34), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 53 TYR 0.009 0.001 TYR L 217 PHE 0.009 0.001 PHE B 316 TRP 0.015 0.001 TRP A 18 HIS 0.001 0.000 HIS H 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 6785) covalent geometry : angle 0.88431 / 0.37 ( 9231) SS BOND : bond 0.00171 / 0.13 ( 6) SS BOND : angle 0.85628 / 0.47 ( 12) hydrogen bonds : bond 0.03280 / 2.17 ( 314) hydrogen bonds : angle 4.66129 / 3.27 ( 891) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2090.41 seconds wall clock time: 36 minutes 24.64 seconds (2184.64 seconds total)