Starting phenix.real_space_refine on Fri Aug 22 18:05:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8spb_40678/08_2025/8spb_40678.cif Found real_map, /net/cci-nas-00/data/ceres_data/8spb_40678/08_2025/8spb_40678.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8spb_40678/08_2025/8spb_40678.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8spb_40678/08_2025/8spb_40678.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8spb_40678/08_2025/8spb_40678.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8spb_40678/08_2025/8spb_40678.map" } resolution = 3.2 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= 0.065 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 50 5.16 5 C 4264 2.51 5 N 1134 2.21 5 O 1278 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6726 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1332 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 7, 'TRANS': 158} Chain: "B" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 731 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 4, 'TRANS': 83} Chain: "C" Number of atoms: 1300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1300 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 4, 'TRANS': 155} Chain breaks: 1 Chain: "a" Number of atoms: 1332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1332 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 7, 'TRANS': 158} Chain: "b" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 731 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 4, 'TRANS': 83} Chain: "c" Number of atoms: 1300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1300 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 4, 'TRANS': 155} Chain breaks: 1 Time building chain proxies: 1.52, per 1000 atoms: 0.23 Number of scatterers: 6726 At special positions: 0 Unit cell: (72.21, 138.61, 78.02, 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 50 16.00 O 1278 8.00 N 1134 7.00 C 4264 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.45 Conformation dependent library (CDL) restraints added in 269.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1596 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 16 sheets defined 22.2% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 110 through 119 removed outlier: 3.885A pdb=" N PHE A 114 " --> pdb=" O PRO A 110 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 115 " --> pdb=" O HIS A 111 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N CYS A 118 " --> pdb=" O PHE A 114 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LYS A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 169 Processing helix chain 'A' and resid 180 through 193 Processing helix chain 'A' and resid 194 through 198 Processing helix chain 'A' and resid 231 through 238 removed outlier: 3.597A pdb=" N PHE A 238 " --> pdb=" O ILE A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 247 removed outlier: 3.872A pdb=" N LYS A 247 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 334 Processing helix chain 'B' and resid 338 through 350 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'a' and resid 110 through 121 removed outlier: 3.520A pdb=" N CYS a 118 " --> pdb=" O PHE a 114 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS a 119 " --> pdb=" O LEU a 115 " (cutoff:3.500A) Processing helix chain 'a' and resid 154 through 169 Processing helix chain 'a' and resid 180 through 193 Processing helix chain 'a' and resid 194 through 200 removed outlier: 3.522A pdb=" N LYS a 198 " --> pdb=" O PRO a 195 " (cutoff:3.500A) Processing helix chain 'a' and resid 231 through 238 Processing helix chain 'a' and resid 243 through 247 Processing helix chain 'b' and resid 321 through 334 Processing helix chain 'b' and resid 338 through 350 Processing helix chain 'c' and resid 112 through 116 Processing sheet with id=AA1, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.792A pdb=" N ALA A 138 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE A 204 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N THR A 203 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ILE A 254 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU A 205 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N GLN A 256 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU A 207 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 215 through 217 Processing sheet with id=AA3, first strand: chain 'A' and resid 266 through 269 Processing sheet with id=AA4, first strand: chain 'B' and resid 291 through 294 Processing sheet with id=AA5, first strand: chain 'B' and resid 319 through 320 Processing sheet with id=AA6, first strand: chain 'C' and resid 24 through 25 removed outlier: 3.697A pdb=" N ALA C 162 " --> pdb=" O ILE C 173 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 45 through 46 removed outlier: 3.526A pdb=" N SER C 46 " --> pdb=" O MET C 186 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 85 through 88 removed outlier: 5.954A pdb=" N ILE C 100 " --> pdb=" O LEU C 110 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 85 through 88 removed outlier: 3.603A pdb=" N MET C 149 " --> pdb=" O VAL C 189 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'a' and resid 172 through 176 removed outlier: 3.832A pdb=" N ALA a 138 " --> pdb=" O SER a 172 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N LEU a 137 " --> pdb=" O PHE a 204 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N VAL a 206 " --> pdb=" O LEU a 137 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU a 139 " --> pdb=" O VAL a 206 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N MET a 208 " --> pdb=" O LEU a 139 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE a 141 " --> pdb=" O MET a 208 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE b 301 " --> pdb=" O LYS a 251 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'a' and resid 215 through 217 Processing sheet with id=AB3, first strand: chain 'b' and resid 319 through 320 Processing sheet with id=AB4, first strand: chain 'c' and resid 18 through 19 removed outlier: 6.153A pdb=" N LEU c 23 " --> pdb=" O LEU c 172 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU c 172 " --> pdb=" O LEU c 23 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE c 25 " --> pdb=" O PHE c 170 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA c 162 " --> pdb=" O ILE c 173 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'c' and resid 45 through 46 removed outlier: 3.508A pdb=" N SER c 46 " --> pdb=" O MET c 186 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'c' and resid 84 through 88 removed outlier: 6.122A pdb=" N ILE c 100 " --> pdb=" O LEU c 110 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'c' and resid 84 through 88 removed outlier: 3.918A pdb=" N MET c 149 " --> pdb=" O VAL c 189 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL c 189 " --> pdb=" O MET c 149 " (cutoff:3.500A) 219 hydrogen bonds defined for protein. 561 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: 0.81 Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2190 1.34 - 1.46: 942 1.46 - 1.57: 3650 1.57 - 1.69: 0 1.69 - 1.81: 74 Bond restraints: 6856 Sorted by residual: bond pdb=" N ILE C 11 " pdb=" CA ILE C 11 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.02e+01 bond pdb=" N LYS a 249 " pdb=" CA LYS a 249 " ideal model delta sigma weight residual 1.453 1.487 -0.035 1.18e-02 7.18e+03 8.67e+00 bond pdb=" N LYS c 148 " pdb=" CA LYS c 148 " ideal model delta sigma weight residual 1.454 1.485 -0.032 1.18e-02 7.18e+03 7.21e+00 bond pdb=" N LYS C 148 " pdb=" CA LYS C 148 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.25e-02 6.40e+03 7.15e+00 bond pdb=" N ILE a 140 " pdb=" CA ILE a 140 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.28e-02 6.10e+03 6.49e+00 ... (remaining 6851 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.23: 9164 3.23 - 6.45: 56 6.45 - 9.68: 8 9.68 - 12.91: 0 12.91 - 16.14: 2 Bond angle restraints: 9230 Sorted by residual: angle pdb=" N ASN C 12 " pdb=" CA ASN C 12 " pdb=" C ASN C 12 " ideal model delta sigma weight residual 108.17 124.31 -16.14 1.85e+00 2.92e-01 7.61e+01 angle pdb=" N ASN C 12 " pdb=" CA ASN C 12 " pdb=" CB ASN C 12 " ideal model delta sigma weight residual 110.46 101.21 9.25 1.42e+00 4.96e-01 4.24e+01 angle pdb=" N ILE C 11 " pdb=" CA ILE C 11 " pdb=" C ILE C 11 " ideal model delta sigma weight residual 109.34 122.27 -12.93 2.08e+00 2.31e-01 3.86e+01 angle pdb=" C ARG C 167 " pdb=" CA ARG C 167 " pdb=" CB ARG C 167 " ideal model delta sigma weight residual 117.23 110.34 6.89 1.36e+00 5.41e-01 2.57e+01 angle pdb=" C ARG c 167 " pdb=" CA ARG c 167 " pdb=" CB ARG c 167 " ideal model delta sigma weight residual 117.23 110.39 6.84 1.36e+00 5.41e-01 2.53e+01 ... (remaining 9225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 3573 17.99 - 35.97: 465 35.97 - 53.96: 132 53.96 - 71.94: 17 71.94 - 89.93: 9 Dihedral angle restraints: 4196 sinusoidal: 1756 harmonic: 2440 Sorted by residual: dihedral pdb=" CA VAL c 47 " pdb=" C VAL c 47 " pdb=" N ILE c 48 " pdb=" CA ILE c 48 " ideal model delta harmonic sigma weight residual -180.00 -158.96 -21.04 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA VAL C 47 " pdb=" C VAL C 47 " pdb=" N ILE C 48 " pdb=" CA ILE C 48 " ideal model delta harmonic sigma weight residual -180.00 -159.54 -20.46 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA TYR c 37 " pdb=" C TYR c 37 " pdb=" N PHE c 38 " pdb=" CA PHE c 38 " ideal model delta harmonic sigma weight residual -180.00 -161.85 -18.15 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 4193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 818 0.055 - 0.109: 162 0.109 - 0.164: 30 0.164 - 0.218: 3 0.218 - 0.273: 3 Chirality restraints: 1016 Sorted by residual: chirality pdb=" CA ASN C 12 " pdb=" N ASN C 12 " pdb=" C ASN C 12 " pdb=" CB ASN C 12 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA THR c 188 " pdb=" N THR c 188 " pdb=" C THR c 188 " pdb=" CB THR c 188 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA ILE C 11 " pdb=" N ILE C 11 " pdb=" C ILE C 11 " pdb=" CB ILE C 11 " both_signs ideal model delta sigma weight residual False 2.43 2.21 0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 1013 not shown) Planarity restraints: 1192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR b 307 " -0.044 5.00e-02 4.00e+02 6.61e-02 6.99e+00 pdb=" N PRO b 308 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO b 308 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO b 308 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 124 " 0.041 5.00e-02 4.00e+02 6.16e-02 6.08e+00 pdb=" N PRO C 125 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO C 125 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 125 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR c 37 " 0.007 2.00e-02 2.50e+03 1.20e-02 2.88e+00 pdb=" CG TYR c 37 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR c 37 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR c 37 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR c 37 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR c 37 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR c 37 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR c 37 " 0.000 2.00e-02 2.50e+03 ... (remaining 1189 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 985 2.76 - 3.30: 6429 3.30 - 3.83: 10700 3.83 - 4.37: 12308 4.37 - 4.90: 21335 Nonbonded interactions: 51757 Sorted by model distance: nonbonded pdb=" N GLU C 31 " pdb=" OE1 GLU C 31 " model vdw 2.227 3.120 nonbonded pdb=" OG SER c 86 " pdb=" OG1 THR c 99 " model vdw 2.237 3.040 nonbonded pdb=" OG SER C 86 " pdb=" OG1 THR C 99 " model vdw 2.261 3.040 nonbonded pdb=" O THR A 135 " pdb=" OG1 THR A 135 " model vdw 2.268 3.040 nonbonded pdb=" O PHE B 330 " pdb=" OG SER B 334 " model vdw 2.278 3.040 ... (remaining 51752 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'a' } ncs_group { reference = chain 'B' selection = chain 'b' } ncs_group { reference = chain 'C' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.140 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.430 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 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 : 0.003 0.044 6856 Z= 0.190 Angle : 0.731 16.137 9230 Z= 0.430 Chirality : 0.047 0.273 1016 Planarity : 0.004 0.066 1192 Dihedral : 17.299 89.931 2600 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.18 % Allowed : 25.79 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.37 (0.28), residues: 812 helix: 0.53 (0.41), residues: 148 sheet: -0.38 (0.42), residues: 160 loop : -1.61 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG c 49 TYR 0.028 0.001 TYR c 37 PHE 0.017 0.001 PHE c 170 TRP 0.022 0.002 TRP b 335 HIS 0.003 0.001 HIS A 148 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 6856) covalent geometry : angle 0.73088 ( 9230) hydrogen bonds : bond 0.25721 ( 209) hydrogen bonds : angle 8.28406 ( 561) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 238 time to evaluate : 0.279 Fit side-chains REVERT: C 138 PHE cc_start: 0.6988 (m-80) cc_final: 0.6609 (m-80) REVERT: C 152 GLU cc_start: 0.3870 (tp30) cc_final: 0.3668 (tp30) REVERT: a 182 ARG cc_start: 0.8132 (mmp80) cc_final: 0.7921 (mmt180) REVERT: c 103 LYS cc_start: 0.5659 (tttt) cc_final: 0.5165 (tttp) outliers start: 9 outliers final: 4 residues processed: 244 average time/residue: 0.0784 time to fit residues: 25.0265 Evaluate side-chains 218 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 214 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 229 LEU Chi-restraints excluded: chain b residue 341 GLU Chi-restraints excluded: chain c residue 119 PHE Chi-restraints excluded: chain c residue 160 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN C 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.191158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.121199 restraints weight = 7365.815| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 3.35 r_work: 0.3245 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 6856 Z= 0.210 Angle : 0.617 6.991 9230 Z= 0.332 Chirality : 0.044 0.152 1016 Planarity : 0.004 0.046 1192 Dihedral : 6.048 54.474 899 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 5.26 % Allowed : 26.05 % Favored : 68.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.28), residues: 812 helix: 0.69 (0.39), residues: 152 sheet: -0.23 (0.42), residues: 160 loop : -1.62 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 269 TYR 0.018 0.001 TYR c 37 PHE 0.021 0.002 PHE C 13 TRP 0.013 0.002 TRP b 335 HIS 0.003 0.001 HIS B 295 Details of bonding type rmsd covalent geometry : bond 0.00491 ( 6856) covalent geometry : angle 0.61652 ( 9230) hydrogen bonds : bond 0.04883 ( 209) hydrogen bonds : angle 5.93430 ( 561) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 213 time to evaluate : 0.275 Fit side-chains REVERT: B 373 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8235 (mm) REVERT: C 45 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7800 (pp) REVERT: C 123 ASN cc_start: 0.7863 (OUTLIER) cc_final: 0.7506 (m110) REVERT: a 223 GLU cc_start: 0.8323 (mm-30) cc_final: 0.7806 (pm20) outliers start: 40 outliers final: 22 residues processed: 234 average time/residue: 0.0657 time to fit residues: 20.5866 Evaluate side-chains 236 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 211 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 112 CYS Chi-restraints excluded: chain C residue 123 ASN Chi-restraints excluded: chain a residue 156 ASP Chi-restraints excluded: chain a residue 228 VAL Chi-restraints excluded: chain a residue 229 LEU Chi-restraints excluded: chain a residue 268 VAL Chi-restraints excluded: chain b residue 312 SER Chi-restraints excluded: chain b residue 341 GLU Chi-restraints excluded: chain b residue 342 VAL Chi-restraints excluded: chain b residue 349 SER Chi-restraints excluded: chain c residue 26 ILE Chi-restraints excluded: chain c residue 46 SER Chi-restraints excluded: chain c residue 104 CYS Chi-restraints excluded: chain c residue 112 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 26 optimal weight: 0.0020 chunk 38 optimal weight: 0.0470 chunk 62 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 78 optimal weight: 0.3980 chunk 44 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 0.3980 chunk 28 optimal weight: 6.9990 overall best weight: 0.3086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN b 310 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.197908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.127759 restraints weight = 7272.679| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 3.39 r_work: 0.3323 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6856 Z= 0.105 Angle : 0.570 8.798 9230 Z= 0.297 Chirality : 0.042 0.142 1016 Planarity : 0.003 0.035 1192 Dihedral : 5.234 47.313 895 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 4.21 % Allowed : 27.11 % Favored : 68.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.28), residues: 812 helix: 1.04 (0.39), residues: 152 sheet: -0.23 (0.42), residues: 164 loop : -1.56 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG c 49 TYR 0.011 0.001 TYR c 37 PHE 0.015 0.001 PHE C 13 TRP 0.013 0.002 TRP b 335 HIS 0.003 0.001 HIS A 148 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 6856) covalent geometry : angle 0.57006 ( 9230) hydrogen bonds : bond 0.03830 ( 209) hydrogen bonds : angle 5.28250 ( 561) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 224 time to evaluate : 0.188 Fit side-chains REVERT: B 314 ARG cc_start: 0.7267 (OUTLIER) cc_final: 0.6876 (ttp-110) REVERT: B 373 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8246 (mm) REVERT: C 45 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7860 (pp) REVERT: a 214 GLU cc_start: 0.7945 (mp0) cc_final: 0.7541 (mp0) REVERT: a 223 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7821 (pm20) REVERT: c 165 LYS cc_start: 0.7426 (tptt) cc_final: 0.7168 (ttmm) REVERT: c 166 GLU cc_start: 0.7015 (mp0) cc_final: 0.6673 (mp0) REVERT: c 168 ASP cc_start: 0.7156 (t0) cc_final: 0.6920 (t0) outliers start: 32 outliers final: 20 residues processed: 235 average time/residue: 0.0778 time to fit residues: 23.8154 Evaluate side-chains 236 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 213 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain a residue 108 LEU Chi-restraints excluded: chain a residue 156 ASP Chi-restraints excluded: chain a residue 228 VAL Chi-restraints excluded: chain a residue 229 LEU Chi-restraints excluded: chain b residue 341 GLU Chi-restraints excluded: chain b residue 349 SER Chi-restraints excluded: chain c residue 99 THR Chi-restraints excluded: chain c residue 104 CYS Chi-restraints excluded: chain c residue 116 ILE Chi-restraints excluded: chain c residue 123 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 64 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 34 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.191174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.120419 restraints weight = 7421.608| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 3.35 r_work: 0.3228 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 6856 Z= 0.207 Angle : 0.601 7.394 9230 Z= 0.321 Chirality : 0.044 0.146 1016 Planarity : 0.004 0.038 1192 Dihedral : 5.339 46.753 895 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 5.66 % Allowed : 25.79 % Favored : 68.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.36 (0.28), residues: 812 helix: 0.73 (0.39), residues: 154 sheet: -0.48 (0.41), residues: 164 loop : -1.67 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 49 TYR 0.028 0.002 TYR c 37 PHE 0.013 0.001 PHE C 13 TRP 0.015 0.002 TRP b 335 HIS 0.004 0.001 HIS B 338 Details of bonding type rmsd covalent geometry : bond 0.00485 ( 6856) covalent geometry : angle 0.60114 ( 9230) hydrogen bonds : bond 0.04143 ( 209) hydrogen bonds : angle 5.50423 ( 561) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 218 time to evaluate : 0.261 Fit side-chains REVERT: A 131 ARG cc_start: 0.7654 (tpt-90) cc_final: 0.7451 (tpt90) REVERT: A 223 GLU cc_start: 0.8425 (mp0) cc_final: 0.8027 (pm20) REVERT: B 373 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8271 (mm) REVERT: C 45 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7846 (pp) REVERT: C 123 ASN cc_start: 0.7889 (OUTLIER) cc_final: 0.7554 (m110) REVERT: C 184 SER cc_start: 0.4629 (m) cc_final: 0.4113 (t) REVERT: a 223 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7952 (pm20) REVERT: a 227 ASP cc_start: 0.8139 (t70) cc_final: 0.7871 (t0) REVERT: b 373 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8472 (mm) REVERT: c 103 LYS cc_start: 0.5135 (tttt) cc_final: 0.4931 (ttmt) outliers start: 43 outliers final: 30 residues processed: 233 average time/residue: 0.0787 time to fit residues: 24.1385 Evaluate side-chains 242 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 208 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 112 CYS Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 123 ASN Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain a residue 156 ASP Chi-restraints excluded: chain a residue 228 VAL Chi-restraints excluded: chain a residue 229 LEU Chi-restraints excluded: chain a residue 236 GLN Chi-restraints excluded: chain a residue 268 VAL Chi-restraints excluded: chain b residue 312 SER Chi-restraints excluded: chain b residue 340 GLU Chi-restraints excluded: chain b residue 349 SER Chi-restraints excluded: chain b residue 373 LEU Chi-restraints excluded: chain c residue 52 ASN Chi-restraints excluded: chain c residue 99 THR Chi-restraints excluded: chain c residue 104 CYS Chi-restraints excluded: chain c residue 110 LEU Chi-restraints excluded: chain c residue 116 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 35 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.193716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.122444 restraints weight = 7474.403| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 3.39 r_work: 0.3267 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6856 Z= 0.137 Angle : 0.589 8.104 9230 Z= 0.306 Chirality : 0.042 0.137 1016 Planarity : 0.003 0.034 1192 Dihedral : 4.809 44.956 892 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 5.00 % Allowed : 27.50 % Favored : 67.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.28), residues: 812 helix: 0.88 (0.39), residues: 154 sheet: -0.59 (0.41), residues: 164 loop : -1.65 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 49 TYR 0.017 0.001 TYR c 37 PHE 0.012 0.001 PHE C 13 TRP 0.016 0.002 TRP b 335 HIS 0.004 0.001 HIS B 338 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 6856) covalent geometry : angle 0.58912 ( 9230) hydrogen bonds : bond 0.03649 ( 209) hydrogen bonds : angle 5.15659 ( 561) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 213 time to evaluate : 0.197 Fit side-chains REVERT: A 223 GLU cc_start: 0.8430 (mp0) cc_final: 0.8009 (pm20) REVERT: B 373 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8287 (mm) REVERT: C 45 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7814 (pp) REVERT: a 123 GLU cc_start: 0.8592 (pm20) cc_final: 0.8303 (pm20) REVERT: a 223 GLU cc_start: 0.8357 (mm-30) cc_final: 0.7961 (pm20) REVERT: a 227 ASP cc_start: 0.8095 (t70) cc_final: 0.7835 (t0) REVERT: c 87 MET cc_start: 0.6343 (ppp) cc_final: 0.6116 (pmm) REVERT: c 103 LYS cc_start: 0.5101 (tttt) cc_final: 0.4895 (ttmt) REVERT: c 165 LYS cc_start: 0.7425 (tptt) cc_final: 0.7113 (ttmm) REVERT: c 168 ASP cc_start: 0.7198 (t0) cc_final: 0.6955 (t0) outliers start: 38 outliers final: 28 residues processed: 226 average time/residue: 0.0705 time to fit residues: 21.0799 Evaluate side-chains 235 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 205 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 112 CYS Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain a residue 156 ASP Chi-restraints excluded: chain a residue 186 SER Chi-restraints excluded: chain a residue 228 VAL Chi-restraints excluded: chain a residue 229 LEU Chi-restraints excluded: chain a residue 236 GLN Chi-restraints excluded: chain b residue 312 SER Chi-restraints excluded: chain b residue 349 SER Chi-restraints excluded: chain c residue 19 ILE Chi-restraints excluded: chain c residue 99 THR Chi-restraints excluded: chain c residue 104 CYS Chi-restraints excluded: chain c residue 110 LEU Chi-restraints excluded: chain c residue 116 ILE Chi-restraints excluded: chain c residue 123 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 47 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 68 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 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 262 ASN C 123 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.196011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.123465 restraints weight = 7391.418| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 3.44 r_work: 0.3282 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6856 Z= 0.123 Angle : 0.570 8.388 9230 Z= 0.299 Chirality : 0.042 0.136 1016 Planarity : 0.003 0.033 1192 Dihedral : 4.762 43.974 892 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.90 % Favored : 92.98 % Rotamer: Outliers : 4.74 % Allowed : 27.76 % Favored : 67.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.28), residues: 812 helix: 1.05 (0.39), residues: 154 sheet: -0.62 (0.40), residues: 170 loop : -1.64 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 49 TYR 0.020 0.001 TYR c 37 PHE 0.011 0.001 PHE c 13 TRP 0.017 0.002 TRP b 335 HIS 0.003 0.001 HIS A 148 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 6856) covalent geometry : angle 0.57004 ( 9230) hydrogen bonds : bond 0.03421 ( 209) hydrogen bonds : angle 4.94922 ( 561) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 210 time to evaluate : 0.189 Fit side-chains REVERT: A 223 GLU cc_start: 0.8440 (mp0) cc_final: 0.8013 (pm20) REVERT: B 373 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8287 (mm) REVERT: C 122 MET cc_start: 0.7582 (mmt) cc_final: 0.6790 (tpt) REVERT: a 123 GLU cc_start: 0.8543 (pm20) cc_final: 0.8302 (pm20) REVERT: a 223 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7928 (pm20) REVERT: a 227 ASP cc_start: 0.8096 (t70) cc_final: 0.7776 (t0) REVERT: c 87 MET cc_start: 0.6340 (ppp) cc_final: 0.6110 (pmm) outliers start: 36 outliers final: 29 residues processed: 224 average time/residue: 0.0790 time to fit residues: 23.2047 Evaluate side-chains 227 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 197 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 112 CYS Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain a residue 156 ASP Chi-restraints excluded: chain a residue 228 VAL Chi-restraints excluded: chain a residue 229 LEU Chi-restraints excluded: chain a residue 236 GLN Chi-restraints excluded: chain a residue 256 GLN Chi-restraints excluded: chain a residue 268 VAL Chi-restraints excluded: chain b residue 312 SER Chi-restraints excluded: chain b residue 340 GLU Chi-restraints excluded: chain b residue 349 SER Chi-restraints excluded: chain b residue 368 THR Chi-restraints excluded: chain c residue 19 ILE Chi-restraints excluded: chain c residue 46 SER Chi-restraints excluded: chain c residue 99 THR Chi-restraints excluded: chain c residue 116 ILE Chi-restraints excluded: chain c residue 123 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 52 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.191571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.120984 restraints weight = 7289.728| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 3.24 r_work: 0.3251 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 6856 Z= 0.194 Angle : 0.621 7.810 9230 Z= 0.326 Chirality : 0.044 0.149 1016 Planarity : 0.003 0.037 1192 Dihedral : 4.984 43.786 892 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.90 % Favored : 92.98 % Rotamer: Outliers : 5.66 % Allowed : 27.89 % Favored : 66.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.43 (0.28), residues: 812 helix: 0.77 (0.39), residues: 154 sheet: -0.76 (0.41), residues: 170 loop : -1.65 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 49 TYR 0.022 0.001 TYR c 37 PHE 0.010 0.001 PHE C 13 TRP 0.020 0.003 TRP b 335 HIS 0.003 0.001 HIS b 295 Details of bonding type rmsd covalent geometry : bond 0.00459 ( 6856) covalent geometry : angle 0.62060 ( 9230) hydrogen bonds : bond 0.03717 ( 209) hydrogen bonds : angle 5.21862 ( 561) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 203 time to evaluate : 0.263 Fit side-chains REVERT: A 170 ASP cc_start: 0.7907 (t0) cc_final: 0.7648 (m-30) REVERT: A 223 GLU cc_start: 0.8426 (mp0) cc_final: 0.8140 (pm20) REVERT: A 227 ASP cc_start: 0.8232 (t0) cc_final: 0.7792 (t0) REVERT: B 373 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8315 (mm) REVERT: a 123 GLU cc_start: 0.8617 (pm20) cc_final: 0.8369 (pm20) REVERT: a 223 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8080 (pm20) REVERT: a 227 ASP cc_start: 0.8160 (t70) cc_final: 0.7934 (t0) REVERT: c 87 MET cc_start: 0.6580 (ppp) cc_final: 0.6340 (pmm) outliers start: 43 outliers final: 33 residues processed: 223 average time/residue: 0.0724 time to fit residues: 21.7795 Evaluate side-chains 234 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 200 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 112 CYS Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain a residue 108 LEU Chi-restraints excluded: chain a residue 156 ASP Chi-restraints excluded: chain a residue 186 SER Chi-restraints excluded: chain a residue 228 VAL Chi-restraints excluded: chain a residue 229 LEU Chi-restraints excluded: chain a residue 236 GLN Chi-restraints excluded: chain a residue 244 LEU Chi-restraints excluded: chain a residue 268 VAL Chi-restraints excluded: chain b residue 312 SER Chi-restraints excluded: chain b residue 340 GLU Chi-restraints excluded: chain b residue 349 SER Chi-restraints excluded: chain b residue 368 THR Chi-restraints excluded: chain c residue 19 ILE Chi-restraints excluded: chain c residue 38 PHE Chi-restraints excluded: chain c residue 46 SER Chi-restraints excluded: chain c residue 52 ASN Chi-restraints excluded: chain c residue 99 THR Chi-restraints excluded: chain c residue 116 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 10.0000 chunk 50 optimal weight: 0.6980 chunk 63 optimal weight: 0.5980 chunk 69 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 16 optimal weight: 0.0980 chunk 48 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN B 310 ASN ** B 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.195952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.125155 restraints weight = 7341.772| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 3.34 r_work: 0.3313 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6856 Z= 0.119 Angle : 0.613 8.465 9230 Z= 0.314 Chirality : 0.042 0.138 1016 Planarity : 0.003 0.033 1192 Dihedral : 4.762 42.939 892 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.77 % Favored : 93.10 % Rotamer: Outliers : 4.34 % Allowed : 28.29 % Favored : 67.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.28), residues: 812 helix: 1.09 (0.39), residues: 154 sheet: -0.66 (0.41), residues: 158 loop : -1.59 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 49 TYR 0.019 0.001 TYR c 37 PHE 0.010 0.001 PHE C 13 TRP 0.019 0.002 TRP b 335 HIS 0.003 0.001 HIS A 148 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 6856) covalent geometry : angle 0.61276 ( 9230) hydrogen bonds : bond 0.03279 ( 209) hydrogen bonds : angle 4.86735 ( 561) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 203 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: A 170 ASP cc_start: 0.7857 (t0) cc_final: 0.7595 (m-30) REVERT: A 223 GLU cc_start: 0.8401 (mp0) cc_final: 0.7986 (pm20) REVERT: B 373 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8282 (mm) REVERT: C 122 MET cc_start: 0.7546 (mmt) cc_final: 0.6907 (tpt) REVERT: a 123 GLU cc_start: 0.8723 (pm20) cc_final: 0.8446 (pm20) REVERT: a 223 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8054 (mp0) REVERT: a 227 ASP cc_start: 0.8143 (t70) cc_final: 0.7919 (t0) REVERT: c 31 GLU cc_start: 0.8537 (pm20) cc_final: 0.8328 (pm20) outliers start: 33 outliers final: 25 residues processed: 216 average time/residue: 0.0747 time to fit residues: 21.4742 Evaluate side-chains 221 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 195 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain a residue 156 ASP Chi-restraints excluded: chain a residue 186 SER Chi-restraints excluded: chain a residue 228 VAL Chi-restraints excluded: chain a residue 229 LEU Chi-restraints excluded: chain a residue 236 GLN Chi-restraints excluded: chain a residue 268 VAL Chi-restraints excluded: chain b residue 349 SER Chi-restraints excluded: chain b residue 368 THR Chi-restraints excluded: chain c residue 19 ILE Chi-restraints excluded: chain c residue 116 ILE Chi-restraints excluded: chain c residue 123 ASN Chi-restraints excluded: chain c residue 188 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 65 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 63 optimal weight: 0.1980 chunk 72 optimal weight: 0.3980 chunk 43 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN ** B 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.195782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.125525 restraints weight = 7376.083| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 3.32 r_work: 0.3316 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6856 Z= 0.124 Angle : 0.617 8.346 9230 Z= 0.318 Chirality : 0.043 0.143 1016 Planarity : 0.003 0.033 1192 Dihedral : 4.737 43.270 892 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.77 % Favored : 93.10 % Rotamer: Outliers : 4.08 % Allowed : 29.34 % Favored : 66.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.28), residues: 812 helix: 1.22 (0.39), residues: 154 sheet: -0.71 (0.41), residues: 162 loop : -1.55 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 49 TYR 0.031 0.001 TYR c 37 PHE 0.009 0.001 PHE C 13 TRP 0.022 0.002 TRP b 335 HIS 0.003 0.001 HIS A 148 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 6856) covalent geometry : angle 0.61686 ( 9230) hydrogen bonds : bond 0.03193 ( 209) hydrogen bonds : angle 4.77186 ( 561) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 200 time to evaluate : 0.175 Fit side-chains REVERT: A 170 ASP cc_start: 0.7869 (t0) cc_final: 0.7592 (m-30) REVERT: A 223 GLU cc_start: 0.8396 (mp0) cc_final: 0.7976 (pm20) REVERT: A 227 ASP cc_start: 0.8038 (t70) cc_final: 0.7680 (t0) REVERT: B 314 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.6030 (ttp80) REVERT: B 373 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8324 (mm) REVERT: C 122 MET cc_start: 0.7532 (mmt) cc_final: 0.6999 (tpt) REVERT: a 123 GLU cc_start: 0.8733 (pm20) cc_final: 0.8461 (pm20) REVERT: a 223 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8047 (mp0) REVERT: a 227 ASP cc_start: 0.8154 (t70) cc_final: 0.7918 (t0) REVERT: c 31 GLU cc_start: 0.8549 (pm20) cc_final: 0.8340 (pm20) outliers start: 31 outliers final: 29 residues processed: 214 average time/residue: 0.0734 time to fit residues: 20.5841 Evaluate side-chains 230 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 199 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain a residue 156 ASP Chi-restraints excluded: chain a residue 186 SER Chi-restraints excluded: chain a residue 228 VAL Chi-restraints excluded: chain a residue 229 LEU Chi-restraints excluded: chain a residue 236 GLN Chi-restraints excluded: chain a residue 256 GLN Chi-restraints excluded: chain a residue 268 VAL Chi-restraints excluded: chain b residue 312 SER Chi-restraints excluded: chain b residue 349 SER Chi-restraints excluded: chain b residue 368 THR Chi-restraints excluded: chain c residue 19 ILE Chi-restraints excluded: chain c residue 38 PHE Chi-restraints excluded: chain c residue 116 ILE Chi-restraints excluded: chain c residue 123 ASN Chi-restraints excluded: chain c residue 188 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 44 optimal weight: 0.5980 chunk 37 optimal weight: 0.3980 chunk 47 optimal weight: 5.9990 chunk 26 optimal weight: 0.4980 chunk 39 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN ** B 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.196369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.125784 restraints weight = 7347.090| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 3.31 r_work: 0.3324 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6856 Z= 0.124 Angle : 0.633 8.524 9230 Z= 0.324 Chirality : 0.043 0.151 1016 Planarity : 0.003 0.032 1192 Dihedral : 4.730 43.220 892 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.53 % Favored : 93.35 % Rotamer: Outliers : 3.82 % Allowed : 29.87 % Favored : 66.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.28), residues: 812 helix: 1.23 (0.39), residues: 154 sheet: -0.68 (0.41), residues: 162 loop : -1.56 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 369 TYR 0.029 0.001 TYR c 37 PHE 0.011 0.001 PHE B 330 TRP 0.023 0.002 TRP b 335 HIS 0.003 0.001 HIS A 148 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 6856) covalent geometry : angle 0.63259 ( 9230) hydrogen bonds : bond 0.03169 ( 209) hydrogen bonds : angle 4.74542 ( 561) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 202 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: A 170 ASP cc_start: 0.7867 (t0) cc_final: 0.7593 (m-30) REVERT: A 223 GLU cc_start: 0.8373 (mp0) cc_final: 0.7958 (pm20) REVERT: A 227 ASP cc_start: 0.8025 (t70) cc_final: 0.7676 (t0) REVERT: B 314 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.6030 (ttp80) REVERT: B 373 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8313 (mm) REVERT: C 122 MET cc_start: 0.7516 (mmt) cc_final: 0.6980 (tpt) REVERT: a 123 GLU cc_start: 0.8742 (pm20) cc_final: 0.8503 (pm20) REVERT: a 223 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8089 (mp0) REVERT: a 227 ASP cc_start: 0.8171 (t70) cc_final: 0.7941 (t0) REVERT: c 31 GLU cc_start: 0.8552 (pm20) cc_final: 0.8342 (pm20) outliers start: 29 outliers final: 25 residues processed: 215 average time/residue: 0.0765 time to fit residues: 22.0564 Evaluate side-chains 221 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 194 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain a residue 156 ASP Chi-restraints excluded: chain a residue 186 SER Chi-restraints excluded: chain a residue 228 VAL Chi-restraints excluded: chain a residue 229 LEU Chi-restraints excluded: chain a residue 236 GLN Chi-restraints excluded: chain a residue 256 GLN Chi-restraints excluded: chain a residue 268 VAL Chi-restraints excluded: chain b residue 312 SER Chi-restraints excluded: chain b residue 349 SER Chi-restraints excluded: chain b residue 368 THR Chi-restraints excluded: chain c residue 19 ILE Chi-restraints excluded: chain c residue 188 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 35 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 48 optimal weight: 0.9980 chunk 70 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 29 optimal weight: 0.0020 chunk 49 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.196173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.126126 restraints weight = 7353.476| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 3.30 r_work: 0.3328 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6856 Z= 0.124 Angle : 0.626 8.665 9230 Z= 0.322 Chirality : 0.043 0.148 1016 Planarity : 0.003 0.032 1192 Dihedral : 4.702 43.298 892 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.65 % Favored : 93.23 % Rotamer: Outliers : 4.21 % Allowed : 29.74 % Favored : 66.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.28), residues: 812 helix: 1.24 (0.39), residues: 154 sheet: -0.59 (0.42), residues: 162 loop : -1.53 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 369 TYR 0.028 0.001 TYR c 37 PHE 0.010 0.001 PHE B 330 TRP 0.023 0.002 TRP b 335 HIS 0.003 0.001 HIS A 148 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 6856) covalent geometry : angle 0.62550 ( 9230) hydrogen bonds : bond 0.03118 ( 209) hydrogen bonds : angle 4.69306 ( 561) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2090.62 seconds wall clock time: 36 minutes 21.17 seconds (2181.17 seconds total)