Starting phenix.real_space_refine on Thu Jul 2 06:19:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8b9f_15930/07_2026/8b9f_15930.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b9f_15930/07_2026/8b9f_15930.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8b9f_15930/07_2026/8b9f_15930.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8b9f_15930/07_2026/8b9f_15930.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8b9f_15930/07_2026/8b9f_15930.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b9f_15930/07_2026/8b9f_15930.map" model { file = "/net/cci-nas-00/data/ceres_data/8b9f_15930/07_2026/8b9f_15930.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b9f_15930/07_2026/8b9f_15930.cif" } resolution = 3.93 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= 0.070 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1946 atoms to isotropic. 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 Se 1 7.20 5 S 47 5.16 5 C 3516 2.51 5 N 931 2.21 5 O 1038 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5533 Number of models: 1 Model: "" Number of chains: 5 Chain: "E" Number of atoms: 1946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1946 Classifications: {'peptide': 251} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 227} Chain: "B" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1579 Classifications: {'peptide': 204} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 194} Chain: "C" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1501 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 10, 'TRANS': 184} Chain: "A" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 486 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 5, 'TRANS': 53} Chain breaks: 1 Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'SPH': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.00, per 1000 atoms: 0.18 Number of scatterers: 5533 At special positions: 0 Unit cell: (74.55, 105, 137.55, 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) Se 1 33.99 S 47 16.00 O 1038 8.00 N 931 7.00 C 3516 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS E 36 " - pdb=" SG CYS E 81 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 94 " distance=2.03 Simple disulfide: pdb=" SG CYS E 98 " - pdb=" SG CYS E 145 " distance=2.03 Simple disulfide: pdb=" SG CYS E 129 " - pdb=" SG CYS E 158 " distance=2.04 Simple disulfide: pdb=" SG CYS E 163 " - pdb=" SG CYS E 204 " distance=2.03 Simple disulfide: pdb=" SG CYS E 190 " - pdb=" SG CYS E 220 " distance=2.03 Simple disulfide: pdb=" SG CYS E 225 " - pdb=" SG CYS E 267 " distance=2.02 Simple disulfide: pdb=" SG CYS E 253 " - pdb=" SG CYS E 283 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.35 Conformation dependent library (CDL) restraints added in 137.2 milliseconds 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1314 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 16 sheets defined 9.7% alpha, 30.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'E' and resid 112 through 116 Processing helix chain 'B' and resid 83 through 87 Processing helix chain 'B' and resid 89 through 99 Processing helix chain 'B' and resid 142 through 147 Processing helix chain 'B' and resid 178 through 185 removed outlier: 4.161A pdb=" N THR B 183 " --> pdb=" O GLY B 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 48 Processing helix chain 'C' and resid 65 through 69 Processing helix chain 'C' and resid 98 through 105 Processing helix chain 'C' and resid 144 through 150 removed outlier: 3.690A pdb=" N LEU C 150 " --> pdb=" O LYS C 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 108 Processing sheet with id=AA1, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.640A pdb=" N GLN E 86 " --> pdb=" O LEU E 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 70 through 71 Processing sheet with id=AA3, first strand: chain 'E' and resid 107 through 109 Processing sheet with id=AA4, first strand: chain 'E' and resid 133 through 135 Processing sheet with id=AA5, first strand: chain 'E' and resid 172 through 175 Processing sheet with id=AA6, first strand: chain 'E' and resid 194 through 197 Processing sheet with id=AA7, first strand: chain 'E' and resid 234 through 236 Processing sheet with id=AA8, first strand: chain 'E' and resid 258 through 260 Processing sheet with id=AA9, first strand: chain 'B' and resid 64 through 65 removed outlier: 4.495A pdb=" N VAL B 239 " --> pdb=" O TRP B 71 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 64 through 65 removed outlier: 4.105A pdb=" N ALA B 250 " --> pdb=" O ARG B 103 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ARG B 103 " --> pdb=" O ALA B 250 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N TYR B 252 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU B 101 " --> pdb=" O TYR B 252 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 153 through 154 removed outlier: 6.758A pdb=" N CYS B 121 " --> pdb=" O PHE B 226 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N SER B 228 " --> pdb=" O GLN B 119 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLN B 119 " --> pdb=" O SER B 228 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 51 through 52 Processing sheet with id=AB4, first strand: chain 'C' and resid 51 through 52 Processing sheet with id=AB5, first strand: chain 'C' and resid 83 through 86 removed outlier: 3.907A pdb=" N PHE C 83 " --> pdb=" O CYS C 192 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LYS C 129 " --> pdb=" O GLN C 195 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLY C 197 " --> pdb=" O THR C 127 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N THR C 127 " --> pdb=" O GLY C 197 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 177 through 178 removed outlier: 6.136A pdb=" N TYR C 107 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU C 225 " --> pdb=" O TYR C 107 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 110 through 112 removed outlier: 6.192A pdb=" N PHE A 110 " --> pdb=" O PRO A 250 " (cutoff:3.500A) 154 hydrogen bonds defined for protein. 369 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: 0.57 Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 1815 1.36 - 1.51: 1747 1.51 - 1.66: 2050 1.66 - 1.80: 39 1.80 - 1.95: 27 Bond restraints: 5678 Sorted by residual: bond pdb=" CA LYS E 161 " pdb=" C LYS E 161 " ideal model delta sigma weight residual 1.523 1.474 0.049 1.28e-02 6.10e+03 1.47e+01 bond pdb=" N ARG E 96 " pdb=" CA ARG E 96 " ideal model delta sigma weight residual 1.454 1.495 -0.041 1.16e-02 7.43e+03 1.24e+01 bond pdb=" N ILE C 70 " pdb=" CA ILE C 70 " ideal model delta sigma weight residual 1.461 1.490 -0.029 9.10e-03 1.21e+04 1.01e+01 bond pdb=" N SER E 162 " pdb=" CA SER E 162 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.17e-02 7.31e+03 9.77e+00 bond pdb=" N VAL B 141 " pdb=" CA VAL B 141 " ideal model delta sigma weight residual 1.457 1.491 -0.035 1.15e-02 7.56e+03 9.04e+00 ... (remaining 5673 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 7538 2.11 - 4.22: 174 4.22 - 6.34: 10 6.34 - 8.45: 2 8.45 - 10.56: 3 Bond angle restraints: 7727 Sorted by residual: angle pdb=" N MET C 65 " pdb=" CA MET C 65 " pdb=" C MET C 65 " ideal model delta sigma weight residual 113.23 104.79 8.44 1.24e+00 6.50e-01 4.63e+01 angle pdb=" N ARG E 96 " pdb=" CA ARG E 96 " pdb=" C ARG E 96 " ideal model delta sigma weight residual 110.46 119.01 -8.55 1.48e+00 4.57e-01 3.34e+01 angle pdb=" N SER E 97 " pdb=" CA SER E 97 " pdb=" C SER E 97 " ideal model delta sigma weight residual 108.07 116.92 -8.85 1.59e+00 3.96e-01 3.10e+01 angle pdb=" C THR C 64 " pdb=" CA THR C 64 " pdb=" CB THR C 64 " ideal model delta sigma weight residual 111.48 100.92 10.56 1.91e+00 2.74e-01 3.06e+01 angle pdb=" N LYS E 161 " pdb=" CA LYS E 161 " pdb=" C LYS E 161 " ideal model delta sigma weight residual 109.96 101.57 8.39 1.68e+00 3.54e-01 2.49e+01 ... (remaining 7722 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.34: 3251 24.34 - 48.68: 112 48.68 - 73.02: 22 73.02 - 97.36: 6 97.36 - 121.70: 1 Dihedral angle restraints: 3392 sinusoidal: 1345 harmonic: 2047 Sorted by residual: dihedral pdb=" CA PHE B 82 " pdb=" C PHE B 82 " pdb=" N PRO B 83 " pdb=" CA PRO B 83 " ideal model delta harmonic sigma weight residual 0.00 39.35 -39.35 0 5.00e+00 4.00e-02 6.19e+01 dihedral pdb=" C5 SPH A 300 " pdb=" C3 SPH A 300 " pdb=" C4 SPH A 300 " pdb=" O3 SPH A 300 " ideal model delta sinusoidal sigma weight residual -68.94 52.76 -121.70 1 2.00e+01 2.50e-03 3.66e+01 dihedral pdb=" C THR C 64 " pdb=" N THR C 64 " pdb=" CA THR C 64 " pdb=" CB THR C 64 " ideal model delta harmonic sigma weight residual -122.00 -110.86 -11.14 0 2.50e+00 1.60e-01 1.99e+01 ... (remaining 3389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 667 0.059 - 0.118: 144 0.118 - 0.176: 30 0.176 - 0.235: 7 0.235 - 0.294: 3 Chirality restraints: 851 Sorted by residual: chirality pdb=" CA THR C 64 " pdb=" N THR C 64 " pdb=" C THR C 64 " pdb=" CB THR C 64 " both_signs ideal model delta sigma weight residual False 2.53 2.82 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CB VAL A 101 " pdb=" CA VAL A 101 " pdb=" CG1 VAL A 101 " pdb=" CG2 VAL A 101 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA ILE C 70 " pdb=" N ILE C 70 " pdb=" C ILE C 70 " pdb=" CB ILE C 70 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 848 not shown) Planarity restraints: 994 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO C 54 " 0.018 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C PRO C 54 " -0.062 2.00e-02 2.50e+03 pdb=" O PRO C 54 " 0.024 2.00e-02 2.50e+03 pdb=" N VAL C 55 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS E 160 " -0.018 2.00e-02 2.50e+03 3.52e-02 1.24e+01 pdb=" C LYS E 160 " 0.061 2.00e-02 2.50e+03 pdb=" O LYS E 160 " -0.022 2.00e-02 2.50e+03 pdb=" N LYS E 161 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO E 177 " 0.014 2.00e-02 2.50e+03 2.69e-02 7.26e+00 pdb=" C PRO E 177 " -0.047 2.00e-02 2.50e+03 pdb=" O PRO E 177 " 0.017 2.00e-02 2.50e+03 pdb=" N GLY E 178 " 0.016 2.00e-02 2.50e+03 ... (remaining 991 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 349 2.73 - 3.27: 5311 3.27 - 3.81: 8990 3.81 - 4.36: 11662 4.36 - 4.90: 19253 Nonbonded interactions: 45565 Sorted by model distance: nonbonded pdb=" OG SER E 214 " pdb=" OD1 ASP E 215 " model vdw 2.185 3.040 nonbonded pdb=" OE1 GLU A 108 " pdb=" OH TYR A 258 " model vdw 2.238 3.040 nonbonded pdb=" OD1 ASP C 182 " pdb=" OG1 THR C 185 " model vdw 2.257 3.040 nonbonded pdb=" O GLY E 132 " pdb=" N LYS E 161 " model vdw 2.313 3.120 nonbonded pdb=" OG1 THR B 183 " pdb=" O ASP C 50 " model vdw 2.326 3.040 ... (remaining 45560 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.100 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6345 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 0.052 5686 Z= 0.319 Angle : 0.737 10.559 7743 Z= 0.460 Chirality : 0.056 0.294 851 Planarity : 0.005 0.047 994 Dihedral : 13.425 121.702 2054 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.29 % Allowed : 2.29 % Favored : 97.42 % Rotamer: Outliers : 1.45 % Allowed : 5.82 % Favored : 92.73 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.29), residues: 699 helix: -1.62 (0.67), residues: 43 sheet: 0.25 (0.38), residues: 174 loop : -1.27 (0.25), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 254 TYR 0.011 0.001 TYR A 258 PHE 0.015 0.002 PHE A 110 TRP 0.017 0.002 TRP E 276 HIS 0.005 0.001 HIS C 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.32 ( 5678) covalent geometry : angle 0.73610 / 0.46 ( 7727) SS BOND : bond 0.00472 / 0.24 ( 8) SS BOND : angle 1.15219 / 0.63 ( 16) hydrogen bonds : bond 0.19415 / 13.31 ( 150) hydrogen bonds : angle 8.93034 / 6.16 ( 369) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 246 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 42 VAL cc_start: -0.0379 (t) cc_final: -0.0762 (t) REVERT: E 71 LYS cc_start: 0.7813 (ptmt) cc_final: 0.7600 (mttm) REVERT: E 105 ASN cc_start: 0.7654 (m-40) cc_final: 0.7218 (m-40) REVERT: E 113 TYR cc_start: 0.7818 (m-80) cc_final: 0.7351 (m-80) REVERT: E 157 PHE cc_start: 0.5164 (p90) cc_final: 0.4903 (p90) REVERT: E 165 ASN cc_start: 0.8326 (t0) cc_final: 0.8055 (t0) REVERT: B 74 ASP cc_start: 0.8221 (p0) cc_final: 0.7705 (p0) REVERT: B 95 ASN cc_start: 0.8641 (m-40) cc_final: 0.8314 (m-40) REVERT: B 100 TYR cc_start: 0.7824 (t80) cc_final: 0.6470 (t80) REVERT: B 129 GLU cc_start: 0.6928 (mm-30) cc_final: 0.6639 (mm-30) REVERT: B 132 MET cc_start: 0.9229 (OUTLIER) cc_final: 0.8789 (mmm) REVERT: B 215 ARG cc_start: 0.7235 (ttp-170) cc_final: 0.4933 (mmt180) REVERT: B 219 PHE cc_start: 0.8713 (p90) cc_final: 0.8487 (p90) REVERT: B 256 ARG cc_start: 0.6342 (OUTLIER) cc_final: 0.5594 (ptp-170) REVERT: C 61 LYS cc_start: 0.8364 (mtmt) cc_final: 0.7737 (mttt) REVERT: C 179 VAL cc_start: 0.8318 (t) cc_final: 0.8024 (t) REVERT: C 195 GLN cc_start: 0.7618 (tp40) cc_final: 0.7319 (tp40) REVERT: A 265 ASN cc_start: 0.8065 (m-40) cc_final: 0.7831 (m-40) outliers start: 9 outliers final: 2 residues processed: 250 average time/residue: 0.0634 time to fit residues: 20.3212 Evaluate side-chains 166 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 162 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 225 CYS Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain A residue 277 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 181 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.218792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.153847 restraints weight = 6681.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.159120 restraints weight = 3837.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.162636 restraints weight = 2559.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.165311 restraints weight = 1915.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.166864 restraints weight = 1553.562| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5686 Z= 0.180 Angle : 0.606 5.742 7743 Z= 0.322 Chirality : 0.047 0.234 851 Planarity : 0.005 0.062 994 Dihedral : 6.984 108.101 785 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.68 % Allowed : 17.12 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -0.70 (0.29), residues: 699 helix: -0.58 (0.79), residues: 45 sheet: 0.39 (0.39), residues: 165 loop : -0.79 (0.24), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 254 TYR 0.037 0.002 TYR C 194 PHE 0.021 0.002 PHE B 226 TRP 0.023 0.002 TRP E 276 HIS 0.004 0.001 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 ( 5678) covalent geometry : angle 0.60589 / 0.32 ( 7727) SS BOND : bond 0.00146 / 0.07 ( 8) SS BOND : angle 0.47974 / 0.30 ( 16) hydrogen bonds : bond 0.03769 / 2.71 ( 150) hydrogen bonds : angle 6.48889 / 4.43 ( 369) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 71 LYS cc_start: 0.8161 (ptmt) cc_final: 0.7899 (mttm) REVERT: E 105 ASN cc_start: 0.8213 (m-40) cc_final: 0.7802 (m-40) REVERT: E 110 LYS cc_start: 0.7967 (ptmm) cc_final: 0.7763 (ptpt) REVERT: E 113 TYR cc_start: 0.8305 (m-80) cc_final: 0.7588 (m-10) REVERT: E 135 ARG cc_start: 0.6176 (ttt-90) cc_final: 0.5292 (tpp-160) REVERT: E 136 GLU cc_start: 0.7379 (tp30) cc_final: 0.6990 (tp30) REVERT: E 205 LEU cc_start: 0.6884 (mp) cc_final: 0.6631 (mm) REVERT: E 211 VAL cc_start: 0.7423 (OUTLIER) cc_final: 0.7010 (p) REVERT: B 64 TYR cc_start: 0.8566 (m-80) cc_final: 0.8294 (m-80) REVERT: B 70 THR cc_start: 0.9086 (m) cc_final: 0.8763 (p) REVERT: B 72 GLU cc_start: 0.8291 (mp0) cc_final: 0.8011 (mp0) REVERT: B 74 ASP cc_start: 0.8012 (p0) cc_final: 0.7748 (p0) REVERT: B 129 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6776 (mm-30) REVERT: B 132 MET cc_start: 0.9210 (mtt) cc_final: 0.8643 (mtt) REVERT: B 167 GLN cc_start: 0.7481 (tp-100) cc_final: 0.7057 (tp-100) REVERT: B 193 ARG cc_start: 0.9023 (ptm-80) cc_final: 0.8741 (ptm-80) REVERT: B 213 MET cc_start: 0.7713 (mmm) cc_final: 0.7399 (mtt) REVERT: B 215 ARG cc_start: 0.6917 (ttp-170) cc_final: 0.4762 (mmt180) REVERT: B 218 ASN cc_start: 0.8479 (m-40) cc_final: 0.7773 (m110) REVERT: B 256 ARG cc_start: 0.7435 (ppt90) cc_final: 0.6183 (mtp180) REVERT: C 44 MET cc_start: 0.7591 (mmt) cc_final: 0.7050 (tpp) REVERT: C 61 LYS cc_start: 0.8379 (mtmt) cc_final: 0.8075 (mtmt) REVERT: C 95 PHE cc_start: 0.6623 (m-80) cc_final: 0.5730 (m-10) REVERT: C 102 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7110 (mm-30) REVERT: C 134 TYR cc_start: 0.8248 (t80) cc_final: 0.7826 (t80) REVERT: C 224 LEU cc_start: 0.6773 (OUTLIER) cc_final: 0.6551 (tt) REVERT: A 98 ARG cc_start: 0.8184 (mtt180) cc_final: 0.7607 (mtt90) REVERT: A 103 MET cc_start: 0.8513 (tpp) cc_final: 0.8145 (tpp) REVERT: A 254 ARG cc_start: 0.8879 (mmm160) cc_final: 0.8499 (mmm160) REVERT: A 265 ASN cc_start: 0.8521 (m-40) cc_final: 0.8257 (m-40) outliers start: 29 outliers final: 18 residues processed: 190 average time/residue: 0.0693 time to fit residues: 16.9293 Evaluate side-chains 166 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 119 PHE Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 197 PHE Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 225 CYS Chi-restraints excluded: chain E residue 236 ILE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 231 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 6 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 0.0770 chunk 63 optimal weight: 0.0870 chunk 32 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 212 GLN E 271 ASN B 95 ASN ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.213620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.151546 restraints weight = 6414.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.156535 restraints weight = 3769.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.159677 restraints weight = 2529.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.162147 restraints weight = 1902.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.163592 restraints weight = 1546.864| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5686 Z= 0.129 Angle : 0.549 6.109 7743 Z= 0.290 Chirality : 0.045 0.172 851 Planarity : 0.004 0.031 994 Dihedral : 6.107 94.062 777 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 4.52 % Allowed : 18.42 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.29), residues: 699 helix: -0.39 (0.80), residues: 45 sheet: 0.53 (0.40), residues: 158 loop : -0.81 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 177 TYR 0.019 0.002 TYR E 118 PHE 0.028 0.002 PHE B 219 TRP 0.020 0.002 TRP E 276 HIS 0.005 0.001 HIS C 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 5678) covalent geometry : angle 0.54885 / 0.29 ( 7727) SS BOND : bond 0.00152 / 0.08 ( 8) SS BOND : angle 0.47507 / 0.30 ( 16) hydrogen bonds : bond 0.03410 / 2.40 ( 150) hydrogen bonds : angle 6.17705 / 4.25 ( 369) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 159 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 71 LYS cc_start: 0.8155 (ptmt) cc_final: 0.7889 (mttm) REVERT: E 82 LEU cc_start: 0.3759 (OUTLIER) cc_final: 0.3022 (tt) REVERT: E 105 ASN cc_start: 0.8182 (m-40) cc_final: 0.7780 (m-40) REVERT: E 110 LYS cc_start: 0.7741 (ptmm) cc_final: 0.7532 (ptpt) REVERT: E 113 TYR cc_start: 0.8133 (m-80) cc_final: 0.7273 (m-10) REVERT: E 135 ARG cc_start: 0.6175 (ttt-90) cc_final: 0.5236 (tpp-160) REVERT: E 136 GLU cc_start: 0.7128 (tp30) cc_final: 0.6776 (tp30) REVERT: E 205 LEU cc_start: 0.6787 (mp) cc_final: 0.6498 (mm) REVERT: B 70 THR cc_start: 0.9187 (m) cc_final: 0.8644 (p) REVERT: B 72 GLU cc_start: 0.8328 (mp0) cc_final: 0.7811 (mp0) REVERT: B 74 ASP cc_start: 0.7921 (p0) cc_final: 0.7594 (p0) REVERT: B 81 LYS cc_start: 0.8743 (mttm) cc_final: 0.8384 (mttt) REVERT: B 84 ASP cc_start: 0.7753 (t0) cc_final: 0.7451 (t0) REVERT: B 87 LYS cc_start: 0.8419 (pttt) cc_final: 0.7913 (ptpt) REVERT: B 129 GLU cc_start: 0.7378 (mm-30) cc_final: 0.6728 (mm-30) REVERT: B 132 MET cc_start: 0.9010 (mtt) cc_final: 0.8548 (mtt) REVERT: B 215 ARG cc_start: 0.6570 (ttp-170) cc_final: 0.4647 (mmt180) REVERT: B 256 ARG cc_start: 0.7438 (ppt90) cc_final: 0.6114 (mtp180) REVERT: C 44 MET cc_start: 0.7667 (mmt) cc_final: 0.7380 (tpp) REVERT: C 61 LYS cc_start: 0.8409 (mtmt) cc_final: 0.8130 (mtmt) REVERT: C 134 TYR cc_start: 0.8231 (t80) cc_final: 0.7869 (t80) REVERT: A 98 ARG cc_start: 0.8174 (mtt180) cc_final: 0.7692 (mtt90) REVERT: A 254 ARG cc_start: 0.8808 (mmm160) cc_final: 0.8606 (mmm160) REVERT: A 265 ASN cc_start: 0.8425 (m-40) cc_final: 0.8211 (m-40) outliers start: 28 outliers final: 16 residues processed: 177 average time/residue: 0.0735 time to fit residues: 16.6216 Evaluate side-chains 161 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 119 PHE Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 236 ILE Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 154 LYS Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 231 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 9 optimal weight: 9.9990 chunk 63 optimal weight: 0.0040 chunk 22 optimal weight: 20.0000 chunk 29 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 33 optimal weight: 0.1980 chunk 27 optimal weight: 1.9990 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 212 GLN E 271 ASN B 95 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.215087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.149881 restraints weight = 6625.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.154999 restraints weight = 3834.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.158620 restraints weight = 2571.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.160974 restraints weight = 1920.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.162709 restraints weight = 1570.474| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5686 Z= 0.156 Angle : 0.571 5.607 7743 Z= 0.301 Chirality : 0.046 0.175 851 Planarity : 0.004 0.033 994 Dihedral : 5.453 75.803 776 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 4.52 % Allowed : 20.52 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -0.72 (0.29), residues: 699 helix: -0.66 (0.77), residues: 46 sheet: 0.32 (0.39), residues: 164 loop : -0.76 (0.25), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 246 TYR 0.029 0.002 TYR C 194 PHE 0.027 0.002 PHE B 219 TRP 0.013 0.002 TRP E 276 HIS 0.005 0.001 HIS C 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 ( 5678) covalent geometry : angle 0.57025 / 0.30 ( 7727) SS BOND : bond 0.00236 / 0.12 ( 8) SS BOND : angle 0.76906 / 0.50 ( 16) hydrogen bonds : bond 0.03353 / 2.36 ( 150) hydrogen bonds : angle 6.09159 / 4.21 ( 369) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 71 LYS cc_start: 0.8225 (ptmt) cc_final: 0.7936 (mttm) REVERT: E 82 LEU cc_start: 0.3880 (OUTLIER) cc_final: 0.3283 (tt) REVERT: E 105 ASN cc_start: 0.8413 (m-40) cc_final: 0.7999 (m-40) REVERT: E 113 TYR cc_start: 0.8237 (m-80) cc_final: 0.7539 (m-10) REVERT: E 205 LEU cc_start: 0.6892 (mp) cc_final: 0.6596 (mm) REVERT: E 246 ARG cc_start: 0.7722 (ptp-170) cc_final: 0.7254 (ptp-170) REVERT: B 64 TYR cc_start: 0.8253 (m-80) cc_final: 0.7615 (m-80) REVERT: B 74 ASP cc_start: 0.8070 (p0) cc_final: 0.7747 (p0) REVERT: B 81 LYS cc_start: 0.8721 (mttm) cc_final: 0.8323 (mttt) REVERT: B 84 ASP cc_start: 0.7830 (t0) cc_final: 0.7473 (t0) REVERT: B 87 LYS cc_start: 0.8410 (pttt) cc_final: 0.7856 (ptpt) REVERT: B 96 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7739 (ttm) REVERT: B 129 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7037 (mm-30) REVERT: B 132 MET cc_start: 0.9027 (mtt) cc_final: 0.8499 (mtt) REVERT: B 213 MET cc_start: 0.7579 (mtt) cc_final: 0.6634 (mtt) REVERT: B 215 ARG cc_start: 0.6594 (ttp-170) cc_final: 0.4677 (mmt180) REVERT: B 256 ARG cc_start: 0.7635 (ppt90) cc_final: 0.6121 (mtp-110) REVERT: C 44 MET cc_start: 0.7679 (mmt) cc_final: 0.7354 (tpp) REVERT: C 61 LYS cc_start: 0.8320 (mtmt) cc_final: 0.8026 (mtmt) REVERT: C 134 TYR cc_start: 0.8386 (t80) cc_final: 0.8012 (t80) REVERT: A 98 ARG cc_start: 0.8302 (mtt180) cc_final: 0.7675 (mtt90) REVERT: A 254 ARG cc_start: 0.8888 (mmm160) cc_final: 0.8330 (mmm160) outliers start: 28 outliers final: 17 residues processed: 172 average time/residue: 0.0755 time to fit residues: 16.7189 Evaluate side-chains 159 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 119 PHE Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 236 ILE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 224 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 0 optimal weight: 20.0000 chunk 26 optimal weight: 4.9990 chunk 6 optimal weight: 30.0000 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 19 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 95 ASN ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.212534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.142658 restraints weight = 7175.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.147763 restraints weight = 4348.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.151026 restraints weight = 3008.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.153775 restraints weight = 2326.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.155339 restraints weight = 1927.216| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.4726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5686 Z= 0.160 Angle : 0.576 6.706 7743 Z= 0.305 Chirality : 0.046 0.167 851 Planarity : 0.004 0.034 994 Dihedral : 5.175 61.193 776 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 4.52 % Allowed : 20.19 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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 (0.29), residues: 699 helix: -0.98 (0.73), residues: 47 sheet: 0.19 (0.40), residues: 166 loop : -0.82 (0.25), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 105 TYR 0.035 0.002 TYR C 194 PHE 0.035 0.002 PHE B 219 TRP 0.014 0.002 TRP B 80 HIS 0.005 0.001 HIS C 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 ( 5678) covalent geometry : angle 0.57629 / 0.30 ( 7727) SS BOND : bond 0.00327 / 0.17 ( 8) SS BOND : angle 0.65064 / 0.45 ( 16) hydrogen bonds : bond 0.03279 / 2.30 ( 150) hydrogen bonds : angle 5.90663 / 4.10 ( 369) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 71 LYS cc_start: 0.8223 (ptmt) cc_final: 0.7919 (mttm) REVERT: E 82 LEU cc_start: 0.3926 (OUTLIER) cc_final: 0.3384 (tt) REVERT: E 105 ASN cc_start: 0.8500 (m-40) cc_final: 0.8031 (m-40) REVERT: E 113 TYR cc_start: 0.8217 (m-80) cc_final: 0.7878 (m-10) REVERT: E 205 LEU cc_start: 0.7043 (mp) cc_final: 0.6747 (mm) REVERT: B 64 TYR cc_start: 0.8270 (m-80) cc_final: 0.7422 (m-80) REVERT: B 72 GLU cc_start: 0.8481 (mp0) cc_final: 0.8266 (mp0) REVERT: B 74 ASP cc_start: 0.8098 (p0) cc_final: 0.7755 (p0) REVERT: B 84 ASP cc_start: 0.7716 (t0) cc_final: 0.7280 (t0) REVERT: B 87 LYS cc_start: 0.8409 (pttt) cc_final: 0.7827 (ptpt) REVERT: B 129 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7091 (mm-30) REVERT: B 132 MET cc_start: 0.9030 (mtt) cc_final: 0.8736 (mtt) REVERT: B 213 MET cc_start: 0.7696 (mtt) cc_final: 0.7329 (mpp) REVERT: B 215 ARG cc_start: 0.6648 (ttp-170) cc_final: 0.4608 (mmt180) REVERT: C 44 MET cc_start: 0.7961 (mmt) cc_final: 0.7644 (tpp) REVERT: C 61 LYS cc_start: 0.8250 (mtmt) cc_final: 0.7929 (mtmt) REVERT: C 88 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.7227 (mp10) REVERT: C 134 TYR cc_start: 0.8259 (t80) cc_final: 0.7894 (t80) REVERT: A 98 ARG cc_start: 0.8258 (mtt180) cc_final: 0.7769 (mtt90) REVERT: A 254 ARG cc_start: 0.8813 (mmm160) cc_final: 0.8207 (mmm160) outliers start: 28 outliers final: 21 residues processed: 170 average time/residue: 0.0644 time to fit residues: 14.4302 Evaluate side-chains 161 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 119 PHE Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 88 GLN Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain A residue 113 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 18 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 chunk 5 optimal weight: 5.9990 chunk 52 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 95 ASN ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN ** C 86 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 = 0.4371 r_free = 0.4371 target = 0.213905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.146159 restraints weight = 7083.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.151068 restraints weight = 4294.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.154435 restraints weight = 2974.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.156603 restraints weight = 2277.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.158379 restraints weight = 1898.317| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.5009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5686 Z= 0.192 Angle : 0.612 7.022 7743 Z= 0.324 Chirality : 0.047 0.211 851 Planarity : 0.004 0.032 994 Dihedral : 5.085 55.766 776 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 5.33 % Allowed : 21.16 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -0.87 (0.29), residues: 699 helix: -1.05 (0.73), residues: 47 sheet: 0.18 (0.39), residues: 169 loop : -0.83 (0.25), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 62 TYR 0.036 0.002 TYR C 194 PHE 0.037 0.002 PHE B 219 TRP 0.017 0.002 TRP B 80 HIS 0.005 0.001 HIS C 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 ( 5678) covalent geometry : angle 0.61210 / 0.32 ( 7727) SS BOND : bond 0.00435 / 0.23 ( 8) SS BOND : angle 0.56021 / 0.41 ( 16) hydrogen bonds : bond 0.03471 / 2.46 ( 150) hydrogen bonds : angle 5.97503 / 4.14 ( 369) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 152 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 71 LYS cc_start: 0.8224 (ptmt) cc_final: 0.7902 (mttm) REVERT: E 82 LEU cc_start: 0.3889 (OUTLIER) cc_final: 0.3331 (tt) REVERT: E 105 ASN cc_start: 0.8464 (m-40) cc_final: 0.8005 (m-40) REVERT: E 113 TYR cc_start: 0.8255 (m-80) cc_final: 0.7509 (m-10) REVERT: E 205 LEU cc_start: 0.7012 (mp) cc_final: 0.6727 (mm) REVERT: B 64 TYR cc_start: 0.8255 (m-80) cc_final: 0.7413 (m-80) REVERT: B 72 GLU cc_start: 0.8508 (mp0) cc_final: 0.8305 (mp0) REVERT: B 74 ASP cc_start: 0.8161 (p0) cc_final: 0.7811 (p0) REVERT: B 84 ASP cc_start: 0.7725 (t0) cc_final: 0.7362 (t0) REVERT: B 87 LYS cc_start: 0.8419 (pttt) cc_final: 0.7787 (ptpt) REVERT: B 96 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7607 (ttp) REVERT: B 129 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7255 (mm-30) REVERT: B 132 MET cc_start: 0.9036 (mtt) cc_final: 0.8510 (mtt) REVERT: B 213 MET cc_start: 0.7551 (mtt) cc_final: 0.7195 (mpp) REVERT: B 215 ARG cc_start: 0.7104 (ttp-170) cc_final: 0.4881 (mmt180) REVERT: B 256 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.6301 (mtt-85) REVERT: C 44 MET cc_start: 0.7928 (mmt) cc_final: 0.7620 (tpp) REVERT: C 61 LYS cc_start: 0.8198 (mtmt) cc_final: 0.7902 (mtmt) REVERT: C 88 GLN cc_start: 0.7521 (OUTLIER) cc_final: 0.6876 (mp10) REVERT: C 134 TYR cc_start: 0.8343 (t80) cc_final: 0.8009 (t80) REVERT: A 98 ARG cc_start: 0.8240 (mtt180) cc_final: 0.7591 (mtt90) REVERT: A 254 ARG cc_start: 0.9002 (mmm160) cc_final: 0.8314 (mmm160) outliers start: 33 outliers final: 25 residues processed: 170 average time/residue: 0.0711 time to fit residues: 15.6502 Evaluate side-chains 172 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 119 PHE Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 203 PHE Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 88 GLN Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain A residue 113 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 44 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 59 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 95 ASN ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN ** C 86 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 = 0.4362 r_free = 0.4362 target = 0.212819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.144545 restraints weight = 7220.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.149387 restraints weight = 4426.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.152597 restraints weight = 3086.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.155008 restraints weight = 2379.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.156483 restraints weight = 1977.653| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.5316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5686 Z= 0.200 Angle : 0.636 9.098 7743 Z= 0.335 Chirality : 0.047 0.202 851 Planarity : 0.004 0.032 994 Dihedral : 5.093 50.467 776 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 5.49 % Allowed : 21.32 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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 (0.30), residues: 699 helix: -0.85 (0.75), residues: 46 sheet: 0.21 (0.40), residues: 166 loop : -0.87 (0.26), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 246 TYR 0.039 0.002 TYR C 194 PHE 0.035 0.002 PHE B 219 TRP 0.018 0.002 TRP B 80 HIS 0.005 0.001 HIS C 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 ( 5678) covalent geometry : angle 0.63614 / 0.33 ( 7727) SS BOND : bond 0.00311 / 0.17 ( 8) SS BOND : angle 0.64846 / 0.48 ( 16) hydrogen bonds : bond 0.03505 / 2.47 ( 150) hydrogen bonds : angle 6.17255 / 4.30 ( 369) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 146 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 71 LYS cc_start: 0.8231 (ptmt) cc_final: 0.7899 (mttm) REVERT: E 82 LEU cc_start: 0.3904 (OUTLIER) cc_final: 0.3299 (tt) REVERT: E 105 ASN cc_start: 0.8438 (m-40) cc_final: 0.8009 (m-40) REVERT: E 113 TYR cc_start: 0.8130 (m-80) cc_final: 0.7067 (m-10) REVERT: E 157 PHE cc_start: 0.4709 (p90) cc_final: 0.4297 (p90) REVERT: E 205 LEU cc_start: 0.7031 (mp) cc_final: 0.6761 (mm) REVERT: E 247 GLN cc_start: 0.7971 (tt0) cc_final: 0.7647 (tm-30) REVERT: B 64 TYR cc_start: 0.8290 (m-80) cc_final: 0.7572 (m-80) REVERT: B 72 GLU cc_start: 0.8532 (mp0) cc_final: 0.8138 (mp0) REVERT: B 84 ASP cc_start: 0.7755 (t0) cc_final: 0.7352 (t0) REVERT: B 87 LYS cc_start: 0.8446 (pttt) cc_final: 0.7790 (ptpt) REVERT: B 96 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7725 (ttp) REVERT: B 129 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7270 (mm-30) REVERT: B 132 MET cc_start: 0.9051 (mtt) cc_final: 0.8244 (mtt) REVERT: B 213 MET cc_start: 0.7657 (mtt) cc_final: 0.6972 (mtt) REVERT: B 215 ARG cc_start: 0.7100 (ttp-170) cc_final: 0.5022 (mmt180) REVERT: B 256 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.6390 (mtt-85) REVERT: C 44 MET cc_start: 0.8049 (mmt) cc_final: 0.7758 (tpp) REVERT: C 88 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.7051 (mp10) REVERT: C 134 TYR cc_start: 0.8272 (t80) cc_final: 0.7985 (t80) REVERT: A 98 ARG cc_start: 0.8267 (mtt180) cc_final: 0.7654 (mtt90) REVERT: A 254 ARG cc_start: 0.8988 (mmm160) cc_final: 0.8404 (mmm160) outliers start: 34 outliers final: 27 residues processed: 165 average time/residue: 0.0779 time to fit residues: 16.3533 Evaluate side-chains 170 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 119 PHE Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 203 PHE Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 88 GLN Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain A residue 113 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 52 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 57 optimal weight: 0.1980 chunk 56 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 2 optimal weight: 0.0000 chunk 26 optimal weight: 2.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.216631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.148939 restraints weight = 7131.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.153992 restraints weight = 4320.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.157436 restraints weight = 2983.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.159682 restraints weight = 2286.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.161504 restraints weight = 1893.319| |-----------------------------------------------------------------------------| r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.5434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5686 Z= 0.131 Angle : 0.609 9.161 7743 Z= 0.321 Chirality : 0.046 0.189 851 Planarity : 0.004 0.036 994 Dihedral : 4.898 47.607 776 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 4.52 % Allowed : 23.26 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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 (0.30), residues: 699 helix: -0.50 (0.77), residues: 47 sheet: 0.11 (0.40), residues: 168 loop : -0.91 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 246 TYR 0.023 0.002 TYR B 100 PHE 0.025 0.002 PHE B 219 TRP 0.013 0.001 TRP B 78 HIS 0.007 0.001 HIS B 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 5678) covalent geometry : angle 0.60926 / 0.32 ( 7727) SS BOND : bond 0.00237 / 0.13 ( 8) SS BOND : angle 0.61196 / 0.43 ( 16) hydrogen bonds : bond 0.03299 / 2.38 ( 150) hydrogen bonds : angle 5.98557 / 4.14 ( 369) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 35 ASP cc_start: 0.3958 (OUTLIER) cc_final: 0.3372 (t70) REVERT: E 71 LYS cc_start: 0.8235 (ptmt) cc_final: 0.7931 (mttm) REVERT: E 82 LEU cc_start: 0.3898 (OUTLIER) cc_final: 0.3325 (tt) REVERT: E 105 ASN cc_start: 0.8398 (m-40) cc_final: 0.8028 (m-40) REVERT: E 113 TYR cc_start: 0.8115 (m-80) cc_final: 0.7163 (m-10) REVERT: E 205 LEU cc_start: 0.7067 (mp) cc_final: 0.6806 (mm) REVERT: E 247 GLN cc_start: 0.7837 (tt0) cc_final: 0.7500 (tm-30) REVERT: B 64 TYR cc_start: 0.8208 (m-80) cc_final: 0.7451 (m-80) REVERT: B 72 GLU cc_start: 0.8504 (mp0) cc_final: 0.8041 (mp0) REVERT: B 81 LYS cc_start: 0.8565 (mmtp) cc_final: 0.7881 (mttm) REVERT: B 84 ASP cc_start: 0.7747 (t0) cc_final: 0.7304 (t0) REVERT: B 87 LYS cc_start: 0.8379 (pttt) cc_final: 0.7725 (ptpt) REVERT: B 96 MET cc_start: 0.8042 (OUTLIER) cc_final: 0.7735 (ttp) REVERT: B 129 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7130 (mm-30) REVERT: B 132 MET cc_start: 0.9090 (mtt) cc_final: 0.8632 (mtt) REVERT: B 213 MET cc_start: 0.7587 (mtt) cc_final: 0.6819 (mtt) REVERT: B 215 ARG cc_start: 0.7034 (ttp-170) cc_final: 0.4869 (mmt180) REVERT: B 256 ARG cc_start: 0.7812 (ppt90) cc_final: 0.6282 (mtt-85) REVERT: C 44 MET cc_start: 0.8039 (mmt) cc_final: 0.7762 (tpp) REVERT: C 134 TYR cc_start: 0.8277 (t80) cc_final: 0.7937 (t80) REVERT: A 98 ARG cc_start: 0.8132 (mtt180) cc_final: 0.7525 (mtt90) REVERT: A 254 ARG cc_start: 0.8763 (mmm160) cc_final: 0.8300 (mmm160) outliers start: 28 outliers final: 21 residues processed: 166 average time/residue: 0.0833 time to fit residues: 17.7035 Evaluate side-chains 163 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 119 PHE Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 203 PHE Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 274 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 34 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 22 optimal weight: 20.0000 chunk 3 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 212 GLN ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 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 = 0.4369 r_free = 0.4369 target = 0.213574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.144835 restraints weight = 7275.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.149619 restraints weight = 4531.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.152729 restraints weight = 3198.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.155171 restraints weight = 2498.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.156590 restraints weight = 2083.947| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.5683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 5686 Z= 0.220 Angle : 0.691 9.475 7743 Z= 0.367 Chirality : 0.047 0.202 851 Planarity : 0.005 0.037 994 Dihedral : 5.141 44.301 776 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.85 % Allowed : 22.46 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -0.93 (0.30), residues: 699 helix: -0.24 (0.84), residues: 40 sheet: -0.06 (0.40), residues: 170 loop : -0.89 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 105 TYR 0.036 0.002 TYR C 194 PHE 0.033 0.002 PHE B 219 TRP 0.033 0.002 TRP B 78 HIS 0.005 0.001 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.22 ( 5678) covalent geometry : angle 0.69132 / 0.37 ( 7727) SS BOND : bond 0.00277 / 0.15 ( 8) SS BOND : angle 0.75163 / 0.56 ( 16) hydrogen bonds : bond 0.03642 / 2.61 ( 150) hydrogen bonds : angle 6.30383 / 4.39 ( 369) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 71 LYS cc_start: 0.8240 (ptmt) cc_final: 0.7931 (mttm) REVERT: E 82 LEU cc_start: 0.3920 (OUTLIER) cc_final: 0.3346 (tt) REVERT: E 105 ASN cc_start: 0.8467 (m-40) cc_final: 0.8078 (t0) REVERT: E 113 TYR cc_start: 0.8144 (m-80) cc_final: 0.7421 (m-10) REVERT: E 205 LEU cc_start: 0.7105 (mp) cc_final: 0.6804 (mm) REVERT: E 246 ARG cc_start: 0.7702 (ptp-170) cc_final: 0.7478 (tpp80) REVERT: E 247 GLN cc_start: 0.7884 (tt0) cc_final: 0.7648 (tt0) REVERT: B 64 TYR cc_start: 0.8372 (m-80) cc_final: 0.7703 (m-80) REVERT: B 72 GLU cc_start: 0.8496 (mp0) cc_final: 0.8201 (mp0) REVERT: B 84 ASP cc_start: 0.7785 (t0) cc_final: 0.7348 (t0) REVERT: B 87 LYS cc_start: 0.8477 (pttt) cc_final: 0.7830 (ptpt) REVERT: B 129 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7298 (mm-30) REVERT: B 132 MET cc_start: 0.9088 (mtt) cc_final: 0.8368 (mtt) REVERT: B 213 MET cc_start: 0.7642 (mtt) cc_final: 0.7302 (mtt) REVERT: B 215 ARG cc_start: 0.6621 (ttp-170) cc_final: 0.4791 (mmt180) REVERT: B 256 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.6296 (mtt-85) REVERT: C 44 MET cc_start: 0.8062 (mmt) cc_final: 0.7780 (tpp) REVERT: C 134 TYR cc_start: 0.8322 (t80) cc_final: 0.8012 (t80) REVERT: C 226 LYS cc_start: 0.6313 (OUTLIER) cc_final: 0.3715 (mmtt) REVERT: A 98 ARG cc_start: 0.8257 (mtt180) cc_final: 0.7541 (mtt90) REVERT: A 103 MET cc_start: 0.8252 (tpp) cc_final: 0.8019 (tpp) outliers start: 30 outliers final: 24 residues processed: 155 average time/residue: 0.0779 time to fit residues: 15.6818 Evaluate side-chains 161 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 119 PHE Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 203 PHE Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 226 LYS Chi-restraints excluded: chain A residue 113 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 37 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 27 optimal weight: 0.2980 chunk 7 optimal weight: 0.0770 chunk 51 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 46 optimal weight: 0.5980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN ** C 86 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 = 0.4418 r_free = 0.4418 target = 0.219860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.150722 restraints weight = 7430.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.156020 restraints weight = 4405.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.159716 restraints weight = 3022.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.162160 restraints weight = 2290.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.164029 restraints weight = 1889.685| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.5811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5686 Z= 0.139 Angle : 0.668 10.126 7743 Z= 0.347 Chirality : 0.046 0.184 851 Planarity : 0.004 0.035 994 Dihedral : 4.931 43.042 776 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.39 % Allowed : 24.23 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -0.94 (0.30), residues: 699 helix: -0.22 (0.79), residues: 46 sheet: -0.05 (0.41), residues: 171 loop : -0.91 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 105 TYR 0.024 0.002 TYR B 100 PHE 0.030 0.002 PHE B 219 TRP 0.031 0.002 TRP B 78 HIS 0.006 0.001 HIS C 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 5678) covalent geometry : angle 0.66831 / 0.35 ( 7727) SS BOND : bond 0.00202 / 0.11 ( 8) SS BOND : angle 0.59356 / 0.46 ( 16) hydrogen bonds : bond 0.03343 / 2.42 ( 150) hydrogen bonds : angle 6.14745 / 4.26 ( 369) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1398 Ramachandran restraints generated. 699 Oldfield, 0 Emsley, 699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 0.196 Fit side-chains revert: symmetry clash REVERT: E 35 ASP cc_start: 0.3985 (OUTLIER) cc_final: 0.3429 (t0) REVERT: E 71 LYS cc_start: 0.8212 (ptmt) cc_final: 0.7908 (mttm) REVERT: E 82 LEU cc_start: 0.4059 (OUTLIER) cc_final: 0.3534 (tt) REVERT: E 113 TYR cc_start: 0.8372 (m-80) cc_final: 0.7611 (m-10) REVERT: E 157 PHE cc_start: 0.4396 (p90) cc_final: 0.4086 (p90) REVERT: E 205 LEU cc_start: 0.7192 (mp) cc_final: 0.6935 (mm) REVERT: E 247 GLN cc_start: 0.7898 (tt0) cc_final: 0.7658 (tt0) REVERT: B 64 TYR cc_start: 0.8244 (m-80) cc_final: 0.7509 (m-80) REVERT: B 72 GLU cc_start: 0.8523 (mp0) cc_final: 0.8211 (mp0) REVERT: B 84 ASP cc_start: 0.7860 (t0) cc_final: 0.7467 (t0) REVERT: B 87 LYS cc_start: 0.8372 (pttt) cc_final: 0.7733 (ptpt) REVERT: B 96 MET cc_start: 0.7994 (ttp) cc_final: 0.7512 (ttp) REVERT: B 132 MET cc_start: 0.9030 (mtt) cc_final: 0.8518 (mtt) REVERT: B 213 MET cc_start: 0.7414 (mtt) cc_final: 0.6668 (mtt) REVERT: B 215 ARG cc_start: 0.6561 (ttp-170) cc_final: 0.4695 (mmt180) REVERT: B 256 ARG cc_start: 0.7707 (ppt90) cc_final: 0.6180 (mtt-85) REVERT: C 61 LYS cc_start: 0.7925 (mtmm) cc_final: 0.7700 (mtmm) REVERT: C 86 GLN cc_start: 0.8444 (mt0) cc_final: 0.8120 (pt0) REVERT: C 134 TYR cc_start: 0.8285 (t80) cc_final: 0.7936 (t80) REVERT: A 98 ARG cc_start: 0.8058 (mtt180) cc_final: 0.7371 (mtt90) REVERT: A 103 MET cc_start: 0.8152 (tpp) cc_final: 0.7755 (tpp) outliers start: 21 outliers final: 19 residues processed: 150 average time/residue: 0.0800 time to fit residues: 15.3964 Evaluate side-chains 157 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 119 PHE Chi-restraints excluded: chain E residue 203 PHE Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain A residue 113 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 65 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 16 optimal weight: 9.9990 chunk 61 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 10 optimal weight: 0.0020 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN ** C 86 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 = 0.4414 r_free = 0.4414 target = 0.219085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.150223 restraints weight = 7401.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.155487 restraints weight = 4424.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.159132 restraints weight = 3046.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.161680 restraints weight = 2322.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.163272 restraints weight = 1916.991| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.5829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 5686 Z= 0.235 Angle : 1.162 59.183 7743 Z= 0.702 Chirality : 0.046 0.185 851 Planarity : 0.005 0.052 994 Dihedral : 5.009 43.027 776 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.39 % Allowed : 24.07 % Favored : 72.54 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 4.26 % 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: -0.93 (0.30), residues: 699 helix: -0.23 (0.79), residues: 46 sheet: -0.04 (0.41), residues: 171 loop : -0.90 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 254 TYR 0.024 0.002 TYR A 258 PHE 0.031 0.002 PHE B 219 TRP 0.026 0.002 TRP E 276 HIS 0.007 0.001 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.24 ( 5678) covalent geometry : angle 1.16332 / 0.70 ( 7727) SS BOND : bond 0.00250 / 0.13 ( 8) SS BOND : angle 0.60788 / 0.48 ( 16) hydrogen bonds : bond 0.03349 / 2.42 ( 150) hydrogen bonds : angle 6.14476 / 4.26 ( 369) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1429.33 seconds wall clock time: 25 minutes 10.83 seconds (1510.83 seconds total)