Starting phenix.real_space_refine on Wed Mar 4 06:19:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sk9_25177/03_2026/7sk9_25177_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sk9_25177/03_2026/7sk9_25177.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sk9_25177/03_2026/7sk9_25177_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sk9_25177/03_2026/7sk9_25177_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sk9_25177/03_2026/7sk9_25177.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sk9_25177/03_2026/7sk9_25177.map" } resolution = 3.7 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= 0.001 sd= 0.056 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 29 5.16 5 C 3711 2.51 5 N 918 2.21 5 O 1042 1.98 5 H 5561 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11261 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4674 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 282, 4660 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 9, 'TRANS': 272} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 282, 4660 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 9, 'TRANS': 272} Chain breaks: 1 bond proxies already assigned to first conformer: 4712 Chain: "F" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 3280 Classifications: {'peptide': 222} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 209} Chain breaks: 1 Chain: "E" Number of atoms: 3213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 3213 Classifications: {'peptide': 212} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 200} Chain: "A" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 94 Unusual residues: {'CLR': 2, 'GJ9': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N HIS A 291 " occ=0.50 ... (29 atoms not shown) pdb=" HE2BHIS A 291 " occ=0.50 Time building chain proxies: 2.89, per 1000 atoms: 0.26 Number of scatterers: 11261 At special positions: 0 Unit cell: (60.48, 64.8, 145.8, 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 29 16.00 O 1042 8.00 N 918 7.00 C 3711 6.00 H 5561 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 25 " - pdb=" SG CYS F 99 " distance=2.04 Simple disulfide: pdb=" SG CYS F 157 " - pdb=" SG CYS F 213 " distance=2.03 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 89 " distance=2.04 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 195 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 423.1 milliseconds 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1358 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 12 sheets defined 39.4% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 40 through 73 removed outlier: 4.211A pdb=" N LYS A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 106 removed outlier: 3.580A pdb=" N LEU A 84 " --> pdb=" O HIS A 80 " (cutoff:3.500A) Proline residue: A 98 - end of helix Processing helix chain 'A' and resid 113 through 148 removed outlier: 3.760A pdb=" N SER A 125 " --> pdb=" O HIS A 121 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL A 140 " --> pdb=" O THR A 136 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE A 146 " --> pdb=" O ARG A 142 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR A 147 " --> pdb=" O TYR A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 152 removed outlier: 3.851A pdb=" N THR A 152 " --> pdb=" O PHE A 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 149 through 152' Processing helix chain 'A' and resid 153 through 182 Proline residue: A 178 - end of helix removed outlier: 3.730A pdb=" N TYR A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 219 Processing helix chain 'A' and resid 221 through 242 Processing helix chain 'A' and resid 243 through 249 removed outlier: 4.065A pdb=" N LYS A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N HIS A 248 " --> pdb=" O ASP A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 280 removed outlier: 4.018A pdb=" N PHE A 261 " --> pdb=" O TYR A 257 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU A 262 " --> pdb=" O VAL A 258 " (cutoff:3.500A) Proline residue: A 267 - end of helix Processing helix chain 'A' and resid 286 through 305 removed outlier: 3.612A pdb=" N LEU A 305 " --> pdb=" O GLN A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.907A pdb=" N CYS A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 316 Processing helix chain 'A' and resid 319 through 329 Processing helix chain 'F' and resid 31 through 35 Processing helix chain 'F' and resid 65 through 68 Processing helix chain 'F' and resid 90 through 94 removed outlier: 3.885A pdb=" N THR F 94 " --> pdb=" O ALA F 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 84 removed outlier: 4.179A pdb=" N PHE E 84 " --> pdb=" O PRO E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 129 removed outlier: 3.949A pdb=" N LYS E 127 " --> pdb=" O ASP E 123 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER E 128 " --> pdb=" O SER E 124 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY E 129 " --> pdb=" O GLN E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 190 Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 79 removed outlier: 3.561A pdb=" N SER F 112 " --> pdb=" O ASP A 78 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 184 Processing sheet with id=AA3, first strand: chain 'F' and resid 20 through 26 Processing sheet with id=AA4, first strand: chain 'F' and resid 62 through 63 removed outlier: 6.741A pdb=" N TRP F 39 " --> pdb=" O VAL F 51 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N SER F 53 " --> pdb=" O ILE F 37 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE F 37 " --> pdb=" O SER F 53 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER F 36 " --> pdb=" O VAL F 102 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA F 95 " --> pdb=" O VAL F 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 137 through 141 removed outlier: 6.095A pdb=" N TYR F 193 " --> pdb=" O ASP F 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 137 through 141 removed outlier: 6.095A pdb=" N TYR F 193 " --> pdb=" O ASP F 161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 168 through 171 removed outlier: 3.741A pdb=" N THR F 168 " --> pdb=" O ASN F 216 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN F 216 " --> pdb=" O THR F 168 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N TYR F 211 " --> pdb=" O VAL F 228 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 6 through 8 removed outlier: 4.070A pdb=" N THR E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 11 through 13 removed outlier: 3.796A pdb=" N GLU E 106 " --> pdb=" O LEU E 12 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 54 through 55 removed outlier: 5.969A pdb=" N LEU E 47 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLN E 38 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 115 through 119 removed outlier: 3.637A pdb=" N ALA E 131 " --> pdb=" O LEU E 182 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN E 139 " --> pdb=" O TYR E 174 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N TYR E 174 " --> pdb=" O ASN E 139 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 154 through 156 removed outlier: 4.670A pdb=" N TRP E 149 " --> pdb=" O GLN E 156 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS E 150 " --> pdb=" O ALA E 194 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA E 194 " --> pdb=" O LYS E 150 " (cutoff:3.500A) 305 hydrogen bonds defined for protein. 851 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.20 Time building geometry restraints manager: 1.37 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: 5552 1.03 - 1.23: 29 1.23 - 1.42: 2489 1.42 - 1.62: 3314 1.62 - 1.82: 39 Bond restraints: 11423 Sorted by residual: bond pdb=" C14 GJ9 A 401 " pdb=" N13 GJ9 A 401 " ideal model delta sigma weight residual 1.416 1.492 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C09 GJ9 A 401 " pdb=" N10 GJ9 A 401 " ideal model delta sigma weight residual 1.495 1.558 -0.063 2.00e-02 2.50e+03 9.80e+00 bond pdb=" C32 GJ9 A 401 " pdb=" N13 GJ9 A 401 " ideal model delta sigma weight residual 1.457 1.517 -0.060 2.00e-02 2.50e+03 8.85e+00 bond pdb=" C12 GJ9 A 401 " pdb=" N13 GJ9 A 401 " ideal model delta sigma weight residual 1.446 1.505 -0.059 2.00e-02 2.50e+03 8.84e+00 bond pdb=" C11 GJ9 A 401 " pdb=" N10 GJ9 A 401 " ideal model delta sigma weight residual 1.497 1.551 -0.054 2.00e-02 2.50e+03 7.32e+00 ... (remaining 11418 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 20226 1.56 - 3.13: 272 3.13 - 4.69: 43 4.69 - 6.26: 8 6.26 - 7.82: 8 Bond angle restraints: 20557 Sorted by residual: angle pdb=" C22 CLR A 403 " pdb=" C23 CLR A 403 " pdb=" C24 CLR A 403 " ideal model delta sigma weight residual 111.95 104.13 7.82 3.00e+00 1.11e-01 6.80e+00 angle pdb=" C22 CLR A 402 " pdb=" C23 CLR A 402 " pdb=" C24 CLR A 402 " ideal model delta sigma weight residual 111.95 104.37 7.58 3.00e+00 1.11e-01 6.39e+00 angle pdb=" C33 GJ9 A 401 " pdb=" C32 GJ9 A 401 " pdb=" N13 GJ9 A 401 " ideal model delta sigma weight residual 112.14 119.71 -7.57 3.00e+00 1.11e-01 6.37e+00 angle pdb=" C08 GJ9 A 401 " pdb=" C09 GJ9 A 401 " pdb=" N10 GJ9 A 401 " ideal model delta sigma weight residual 108.48 116.01 -7.53 3.00e+00 1.11e-01 6.29e+00 angle pdb=" C06 GJ9 A 401 " pdb=" N05 GJ9 A 401 " pdb=" C37 GJ9 A 401 " ideal model delta sigma weight residual 121.17 114.07 7.10 3.00e+00 1.11e-01 5.61e+00 ... (remaining 20552 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.04: 5377 29.04 - 58.08: 206 58.08 - 87.12: 5 87.12 - 116.16: 6 116.16 - 145.19: 5 Dihedral angle restraints: 5599 sinusoidal: 3008 harmonic: 2591 Sorted by residual: dihedral pdb=" CB CYS A 117 " pdb=" SG CYS A 117 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 178.86 -85.86 1 1.00e+01 1.00e-02 8.91e+01 dihedral pdb=" N10 GJ9 A 401 " pdb=" C11 GJ9 A 401 " pdb=" C12 GJ9 A 401 " pdb=" N13 GJ9 A 401 " ideal model delta sinusoidal sigma weight residual -73.26 71.93 -145.19 1 3.00e+01 1.11e-03 1.94e+01 dihedral pdb=" C11 GJ9 A 401 " pdb=" C12 GJ9 A 401 " pdb=" N13 GJ9 A 401 " pdb=" C14 GJ9 A 401 " ideal model delta sinusoidal sigma weight residual 193.62 60.62 133.00 1 3.00e+01 1.11e-03 1.79e+01 ... (remaining 5596 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 846 0.075 - 0.151: 67 0.151 - 0.226: 1 0.226 - 0.301: 2 0.301 - 0.376: 6 Chirality restraints: 922 Sorted by residual: chirality pdb=" C17 CLR A 403 " pdb=" C13 CLR A 403 " pdb=" C16 CLR A 403 " pdb=" C20 CLR A 403 " both_signs ideal model delta sigma weight residual False 2.55 2.93 -0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" N10 GJ9 A 401 " pdb=" C09 GJ9 A 401 " pdb=" C11 GJ9 A 401 " pdb=" C34 GJ9 A 401 " both_signs ideal model delta sigma weight residual False -2.23 -2.59 0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" C17 CLR A 402 " pdb=" C13 CLR A 402 " pdb=" C16 CLR A 402 " pdb=" C20 CLR A 402 " both_signs ideal model delta sigma weight residual False 2.55 2.87 -0.32 2.00e-01 2.50e+01 2.57e+00 ... (remaining 919 not shown) Planarity restraints: 1646 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 209 " 0.009 2.00e-02 2.50e+03 1.79e-02 3.22e+00 pdb=" C LEU A 209 " -0.031 2.00e-02 2.50e+03 pdb=" O LEU A 209 " 0.012 2.00e-02 2.50e+03 pdb=" N ILE A 210 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 225 " 0.011 2.00e-02 2.50e+03 6.79e-03 1.39e+00 pdb=" CG PHE A 225 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE A 225 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 225 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 225 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 225 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 225 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE A 225 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE A 225 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE A 225 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE A 225 " 0.003 2.00e-02 2.50e+03 pdb=" HZ PHE A 225 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU F 165 " -0.019 5.00e-02 4.00e+02 2.91e-02 1.35e+00 pdb=" N PRO F 166 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO F 166 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO F 166 " -0.015 5.00e-02 4.00e+02 ... (remaining 1643 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 1428 2.25 - 2.84: 24621 2.84 - 3.42: 27440 3.42 - 4.01: 38245 4.01 - 4.60: 58028 Nonbonded interactions: 149762 Sorted by model distance: nonbonded pdb=" O GLN A 106 " pdb=" H GLN A 109 " model vdw 1.662 2.450 nonbonded pdb=" O HIS E 190 " pdb=" HE ARG E 212 " model vdw 1.706 2.450 nonbonded pdb=" O ASP E 83 " pdb=" HH TYR E 87 " model vdw 1.731 2.450 nonbonded pdb=" O THR A 147 " pdb=" HG SER F 57 " model vdw 1.744 2.450 nonbonded pdb=" H ILE F 32 " pdb=" OD1 ASN F 80 " model vdw 1.745 2.450 ... (remaining 149757 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=0.50 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: 0.060 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.440 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 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 : 0.005 0.076 5867 Z= 0.224 Angle : 0.620 7.825 8016 Z= 0.288 Chirality : 0.050 0.376 922 Planarity : 0.003 0.029 966 Dihedral : 15.645 145.195 2177 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % 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: 1.15 (0.35), residues: 707 helix: 2.71 (0.36), residues: 222 sheet: 0.15 (0.41), residues: 198 loop : -0.29 (0.41), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 101 TYR 0.018 0.001 TYR A 181 PHE 0.020 0.001 PHE A 225 TRP 0.008 0.001 TRP F 171 HIS 0.004 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00469 ( 5862) covalent geometry : angle 0.62009 ( 8006) SS BOND : bond 0.00394 ( 5) SS BOND : angle 0.49826 ( 10) hydrogen bonds : bond 0.14656 ( 290) hydrogen bonds : angle 5.87488 ( 851) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.301 Fit side-chains REVERT: E 25 ARG cc_start: 0.7710 (mtp85) cc_final: 0.7382 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1395 time to fit residues: 16.8596 Evaluate side-chains 69 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN F 42 GLN E 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.115500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.095375 restraints weight = 29819.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.099409 restraints weight = 15761.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.102006 restraints weight = 10148.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.103804 restraints weight = 7416.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.104987 restraints weight = 5880.328| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3252 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3251 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5867 Z= 0.187 Angle : 0.566 5.759 8016 Z= 0.295 Chirality : 0.041 0.148 922 Planarity : 0.004 0.035 966 Dihedral : 12.303 142.036 946 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.47 % Allowed : 6.77 % Favored : 92.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % 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: 0.85 (0.34), residues: 707 helix: 2.46 (0.34), residues: 233 sheet: 0.10 (0.39), residues: 203 loop : -0.72 (0.40), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 70 TYR 0.017 0.001 TYR A 181 PHE 0.018 0.001 PHE A 225 TRP 0.010 0.001 TRP F 171 HIS 0.004 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 5862) covalent geometry : angle 0.56450 ( 8006) SS BOND : bond 0.00749 ( 5) SS BOND : angle 1.34531 ( 10) hydrogen bonds : bond 0.04862 ( 290) hydrogen bonds : angle 4.86185 ( 851) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.277 Fit side-chains REVERT: E 25 ARG cc_start: 0.7654 (mtp85) cc_final: 0.7258 (ttm-80) outliers start: 3 outliers final: 3 residues processed: 72 average time/residue: 0.1462 time to fit residues: 14.5185 Evaluate side-chains 71 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 68 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain F residue 214 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 13 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.115623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.094456 restraints weight = 35734.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.098848 restraints weight = 17526.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.101787 restraints weight = 10835.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.103732 restraints weight = 7679.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.104989 restraints weight = 5973.193| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3252 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3252 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5867 Z= 0.152 Angle : 0.535 7.441 8016 Z= 0.274 Chirality : 0.040 0.141 922 Planarity : 0.003 0.035 966 Dihedral : 9.079 126.864 946 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.10 % Allowed : 7.40 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % 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: 0.86 (0.34), residues: 707 helix: 2.44 (0.34), residues: 237 sheet: 0.13 (0.39), residues: 203 loop : -0.76 (0.41), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 161 TYR 0.013 0.001 TYR F 162 PHE 0.017 0.001 PHE A 225 TRP 0.010 0.001 TRP F 171 HIS 0.003 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 5862) covalent geometry : angle 0.53422 ( 8006) SS BOND : bond 0.00440 ( 5) SS BOND : angle 0.96022 ( 10) hydrogen bonds : bond 0.04549 ( 290) hydrogen bonds : angle 4.66281 ( 851) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.314 Fit side-chains REVERT: E 25 ARG cc_start: 0.7730 (mtp85) cc_final: 0.7386 (ttm-80) outliers start: 7 outliers final: 6 residues processed: 72 average time/residue: 0.1371 time to fit residues: 13.6112 Evaluate side-chains 73 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain F residue 206 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 17 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS E 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.115832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.094254 restraints weight = 38127.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.098813 restraints weight = 18317.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.101820 restraints weight = 11172.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.103850 restraints weight = 7875.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.105115 restraints weight = 6063.776| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3254 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3254 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5867 Z= 0.148 Angle : 0.530 7.269 8016 Z= 0.271 Chirality : 0.039 0.139 922 Planarity : 0.003 0.034 966 Dihedral : 5.824 58.131 946 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.79 % Allowed : 8.82 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % 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: 0.88 (0.34), residues: 707 helix: 2.46 (0.34), residues: 237 sheet: 0.16 (0.39), residues: 203 loop : -0.77 (0.41), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 161 TYR 0.016 0.001 TYR A 181 PHE 0.019 0.001 PHE A 225 TRP 0.010 0.001 TRP F 171 HIS 0.003 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 5862) covalent geometry : angle 0.52930 ( 8006) SS BOND : bond 0.00439 ( 5) SS BOND : angle 0.89238 ( 10) hydrogen bonds : bond 0.04313 ( 290) hydrogen bonds : angle 4.53914 ( 851) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.283 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 71 average time/residue: 0.1334 time to fit residues: 13.2915 Evaluate side-chains 71 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain F residue 206 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 17 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.115950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.094806 restraints weight = 36041.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.099264 restraints weight = 17650.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.102208 restraints weight = 10884.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.104009 restraints weight = 7696.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.105412 restraints weight = 6048.754| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3255 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3255 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5867 Z= 0.141 Angle : 0.506 4.826 8016 Z= 0.263 Chirality : 0.039 0.138 922 Planarity : 0.003 0.035 966 Dihedral : 5.476 60.971 946 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.94 % Allowed : 9.45 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % 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: 0.91 (0.34), residues: 707 helix: 2.51 (0.34), residues: 237 sheet: 0.16 (0.39), residues: 203 loop : -0.78 (0.41), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 25 TYR 0.013 0.001 TYR A 181 PHE 0.019 0.001 PHE A 225 TRP 0.010 0.001 TRP F 171 HIS 0.003 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 5862) covalent geometry : angle 0.50544 ( 8006) SS BOND : bond 0.00433 ( 5) SS BOND : angle 0.83774 ( 10) hydrogen bonds : bond 0.04216 ( 290) hydrogen bonds : angle 4.46640 ( 851) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.270 Fit side-chains REVERT: E 25 ARG cc_start: 0.7756 (mtp85) cc_final: 0.7376 (ttm-80) outliers start: 6 outliers final: 5 residues processed: 70 average time/residue: 0.1520 time to fit residues: 14.5880 Evaluate side-chains 70 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain F residue 206 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 1 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3405 r_free = 0.3405 target = 0.115601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.094801 restraints weight = 34815.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.099158 restraints weight = 17152.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.102071 restraints weight = 10615.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.104010 restraints weight = 7516.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.105310 restraints weight = 5802.470| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3257 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3257 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5867 Z= 0.143 Angle : 0.507 4.549 8016 Z= 0.263 Chirality : 0.039 0.139 922 Planarity : 0.003 0.035 966 Dihedral : 5.364 62.724 946 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.94 % Allowed : 10.24 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % 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: 0.92 (0.34), residues: 707 helix: 2.53 (0.34), residues: 237 sheet: 0.15 (0.39), residues: 203 loop : -0.77 (0.41), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 161 TYR 0.012 0.001 TYR F 162 PHE 0.019 0.001 PHE A 225 TRP 0.010 0.001 TRP F 171 HIS 0.003 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 5862) covalent geometry : angle 0.50630 ( 8006) SS BOND : bond 0.00443 ( 5) SS BOND : angle 0.83936 ( 10) hydrogen bonds : bond 0.04184 ( 290) hydrogen bonds : angle 4.42663 ( 851) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.311 Fit side-chains REVERT: E 25 ARG cc_start: 0.7779 (mtp85) cc_final: 0.7439 (ttm-80) outliers start: 6 outliers final: 6 residues processed: 66 average time/residue: 0.1604 time to fit residues: 14.4562 Evaluate side-chains 71 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain F residue 206 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 39 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 13 optimal weight: 0.0770 chunk 63 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 = 0.3420 r_free = 0.3420 target = 0.116691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.094661 restraints weight = 42812.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.099477 restraints weight = 19559.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.102665 restraints weight = 11604.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.104628 restraints weight = 8018.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.106130 restraints weight = 6193.302| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3266 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3266 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5867 Z= 0.114 Angle : 0.489 4.566 8016 Z= 0.252 Chirality : 0.039 0.137 922 Planarity : 0.003 0.034 966 Dihedral : 5.202 59.615 946 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.94 % Allowed : 10.39 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % 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: 1.05 (0.34), residues: 707 helix: 2.67 (0.34), residues: 237 sheet: 0.22 (0.39), residues: 203 loop : -0.72 (0.42), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 161 TYR 0.015 0.001 TYR A 181 PHE 0.019 0.001 PHE A 225 TRP 0.009 0.001 TRP F 171 HIS 0.003 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 5862) covalent geometry : angle 0.48859 ( 8006) SS BOND : bond 0.00383 ( 5) SS BOND : angle 0.72512 ( 10) hydrogen bonds : bond 0.03887 ( 290) hydrogen bonds : angle 4.32642 ( 851) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.300 Fit side-chains REVERT: E 25 ARG cc_start: 0.7804 (mtp85) cc_final: 0.7485 (ttm-80) outliers start: 6 outliers final: 6 residues processed: 75 average time/residue: 0.1583 time to fit residues: 16.1091 Evaluate side-chains 74 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain F residue 206 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 39 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 18 optimal weight: 0.2980 chunk 1 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 11 optimal weight: 0.4980 chunk 59 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- 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 = 0.3422 r_free = 0.3422 target = 0.116779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.095656 restraints weight = 35950.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.100114 restraints weight = 17580.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.103102 restraints weight = 10851.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.105084 restraints weight = 7655.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.106338 restraints weight = 5894.964| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3271 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3271 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5867 Z= 0.117 Angle : 0.490 4.503 8016 Z= 0.253 Chirality : 0.039 0.137 922 Planarity : 0.003 0.034 966 Dihedral : 5.128 58.766 946 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.10 % Allowed : 10.87 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % 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 (0.34), residues: 707 helix: 2.70 (0.34), residues: 237 sheet: 0.24 (0.39), residues: 203 loop : -0.71 (0.42), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 161 TYR 0.018 0.001 TYR A 181 PHE 0.019 0.001 PHE A 225 TRP 0.010 0.001 TRP F 171 HIS 0.002 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 5862) covalent geometry : angle 0.48919 ( 8006) SS BOND : bond 0.00392 ( 5) SS BOND : angle 0.73170 ( 10) hydrogen bonds : bond 0.03811 ( 290) hydrogen bonds : angle 4.27914 ( 851) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.291 Fit side-chains REVERT: E 25 ARG cc_start: 0.7825 (mtp85) cc_final: 0.7500 (ttm-80) outliers start: 7 outliers final: 6 residues processed: 73 average time/residue: 0.1552 time to fit residues: 15.5914 Evaluate side-chains 76 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain F residue 206 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 59 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3406 r_free = 0.3406 target = 0.115621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.094721 restraints weight = 35404.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.099110 restraints weight = 17444.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.102056 restraints weight = 10800.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.103861 restraints weight = 7647.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.105220 restraints weight = 5992.475| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3253 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3253 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5867 Z= 0.146 Angle : 0.508 4.572 8016 Z= 0.264 Chirality : 0.039 0.140 922 Planarity : 0.003 0.035 966 Dihedral : 5.286 61.773 946 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.94 % Allowed : 10.87 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % 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: 0.99 (0.34), residues: 707 helix: 2.62 (0.34), residues: 237 sheet: 0.19 (0.39), residues: 203 loop : -0.77 (0.42), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 161 TYR 0.020 0.001 TYR A 181 PHE 0.021 0.001 PHE A 225 TRP 0.010 0.001 TRP F 171 HIS 0.004 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 5862) covalent geometry : angle 0.50733 ( 8006) SS BOND : bond 0.00445 ( 5) SS BOND : angle 0.82569 ( 10) hydrogen bonds : bond 0.04078 ( 290) hydrogen bonds : angle 4.32660 ( 851) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.293 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 71 average time/residue: 0.1519 time to fit residues: 14.9174 Evaluate side-chains 74 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain F residue 206 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 54 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 55 optimal weight: 0.4980 chunk 50 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.115931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.094465 restraints weight = 39023.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.099019 restraints weight = 18490.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.102004 restraints weight = 11238.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.104084 restraints weight = 7905.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.105424 restraints weight = 6059.960| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3255 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3255 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5867 Z= 0.131 Angle : 0.500 4.512 8016 Z= 0.258 Chirality : 0.039 0.139 922 Planarity : 0.003 0.034 966 Dihedral : 5.220 60.890 946 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.94 % Allowed : 10.87 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % 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: 1.04 (0.34), residues: 707 helix: 2.67 (0.34), residues: 237 sheet: 0.20 (0.39), residues: 203 loop : -0.73 (0.42), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 25 TYR 0.016 0.001 TYR A 181 PHE 0.021 0.001 PHE A 225 TRP 0.009 0.001 TRP F 171 HIS 0.003 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 5862) covalent geometry : angle 0.49919 ( 8006) SS BOND : bond 0.00427 ( 5) SS BOND : angle 0.73662 ( 10) hydrogen bonds : bond 0.03962 ( 290) hydrogen bonds : angle 4.29264 ( 851) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.290 Fit side-chains REVERT: E 25 ARG cc_start: 0.7844 (mtp85) cc_final: 0.7490 (ttm-80) outliers start: 6 outliers final: 6 residues processed: 72 average time/residue: 0.1432 time to fit residues: 14.2758 Evaluate side-chains 76 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain F residue 206 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 61 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 51 optimal weight: 0.3980 chunk 66 optimal weight: 0.7980 chunk 13 optimal weight: 0.4980 chunk 9 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 45 optimal weight: 0.2980 chunk 56 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3425 r_free = 0.3425 target = 0.117158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.098018 restraints weight = 26571.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.101813 restraints weight = 14227.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.104165 restraints weight = 9296.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.105966 restraints weight = 6921.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.107096 restraints weight = 5470.293| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3280 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3280 r_free = 0.3280 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3280 r_free = 0.3280 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3280 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5867 Z= 0.105 Angle : 0.482 4.641 8016 Z= 0.247 Chirality : 0.039 0.136 922 Planarity : 0.003 0.033 966 Dihedral : 5.029 57.003 946 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.94 % Allowed : 10.87 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % 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: 1.19 (0.35), residues: 707 helix: 2.81 (0.34), residues: 237 sheet: 0.27 (0.39), residues: 202 loop : -0.65 (0.42), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 25 TYR 0.013 0.001 TYR A 181 PHE 0.020 0.001 PHE A 225 TRP 0.009 0.001 TRP F 171 HIS 0.003 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 5862) covalent geometry : angle 0.48145 ( 8006) SS BOND : bond 0.00369 ( 5) SS BOND : angle 0.62502 ( 10) hydrogen bonds : bond 0.03661 ( 290) hydrogen bonds : angle 4.20279 ( 851) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2143.67 seconds wall clock time: 37 minutes 16.81 seconds (2236.81 seconds total)