Starting phenix.real_space_refine on Tue Aug 4 22:54:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8h87_34531/08_2026/8h87_34531.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h87_34531/08_2026/8h87_34531.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8h87_34531/08_2026/8h87_34531.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h87_34531/08_2026/8h87_34531.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8h87_34531/08_2026/8h87_34531.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h87_34531/08_2026/8h87_34531.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8h87_34531/08_2026/8h87_34531.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8h87_34531/08_2026/8h87_34531.cif" } resolution = 2.53 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= 0.009 sd= 0.430 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 48 5.16 5 C 4830 2.51 5 N 978 2.21 5 O 1224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7083 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2097 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 16, 'TRANS': 242} Chain: "A" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 264 Unusual residues: {'PLM': 9, 'PSC': 6, 'RET': 1} Classifications: {'undetermined': 16, 'water': 49} Link IDs: {None: 64} Unresolved non-hydrogen bonds: 280 Unresolved non-hydrogen angles: 331 Unresolved non-hydrogen dihedrals: 222 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'RET:plan-5': 1, 'PSC:plan-1': 4, 'PSC:plan-2': 4, 'PSC:plan-3': 4, 'PSC:plan-4': 4, 'PLM:plan-1': 8} Unresolved non-hydrogen planarities: 84 Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "C" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Restraints were copied for chains: B, C Time building chain proxies: 1.08, per 1000 atoms: 0.15 Number of scatterers: 7083 At special positions: 0 Unit cell: (78.02, 77.19, 84.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 P 3 15.00 O 1224 8.00 N 978 7.00 C 4830 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.51 Conformation dependent library (CDL) restraints added in 245.9 milliseconds 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1440 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 0 sheets defined 72.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 21 through 48 Processing helix chain 'A' and resid 64 through 67 Processing helix chain 'A' and resid 68 through 90 Processing helix chain 'A' and resid 105 through 122 removed outlier: 4.182A pdb=" N THR A 109 " --> pdb=" O ASP A 105 " (cutoff:3.500A) Proline residue: A 111 - end of helix Processing helix chain 'A' and resid 125 through 146 Processing helix chain 'A' and resid 149 through 177 removed outlier: 3.878A pdb=" N ALA A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TRP A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Proline residue: A 164 - end of helix Processing helix chain 'A' and resid 181 through 199 removed outlier: 3.521A pdb=" N TRP A 190 " --> pdb=" O ARG A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 207 removed outlier: 3.986A pdb=" N ILE A 207 " --> pdb=" O PRO A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 233 Processing helix chain 'A' and resid 233 through 252 Processing helix chain 'B' and resid 21 through 48 Processing helix chain 'B' and resid 64 through 67 Processing helix chain 'B' and resid 68 through 90 Processing helix chain 'B' and resid 105 through 122 removed outlier: 4.182A pdb=" N THR B 109 " --> pdb=" O ASP B 105 " (cutoff:3.500A) Proline residue: B 111 - end of helix Processing helix chain 'B' and resid 125 through 146 Processing helix chain 'B' and resid 149 through 177 removed outlier: 3.878A pdb=" N ALA B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TRP B 161 " --> pdb=" O LEU B 157 " (cutoff:3.500A) Proline residue: B 164 - end of helix Processing helix chain 'B' and resid 181 through 199 removed outlier: 3.521A pdb=" N TRP B 190 " --> pdb=" O ARG B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 207 removed outlier: 3.986A pdb=" N ILE B 207 " --> pdb=" O PRO B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 233 Processing helix chain 'B' and resid 233 through 252 Processing helix chain 'C' and resid 21 through 48 Processing helix chain 'C' and resid 64 through 67 Processing helix chain 'C' and resid 68 through 90 Processing helix chain 'C' and resid 105 through 122 removed outlier: 4.182A pdb=" N THR C 109 " --> pdb=" O ASP C 105 " (cutoff:3.500A) Proline residue: C 111 - end of helix Processing helix chain 'C' and resid 125 through 146 Processing helix chain 'C' and resid 149 through 177 removed outlier: 3.878A pdb=" N ALA C 153 " --> pdb=" O ALA C 149 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TRP C 161 " --> pdb=" O LEU C 157 " (cutoff:3.500A) Proline residue: C 164 - end of helix Processing helix chain 'C' and resid 181 through 199 removed outlier: 3.521A pdb=" N TRP C 190 " --> pdb=" O ARG C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 207 removed outlier: 3.986A pdb=" N ILE C 207 " --> pdb=" O PRO C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 233 Processing helix chain 'C' and resid 233 through 252 414 hydrogen bonds defined for protein. 1233 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: 0.88 Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1169 1.33 - 1.46: 2602 1.46 - 1.59: 3288 1.59 - 1.72: 6 1.72 - 1.85: 63 Bond restraints: 7128 Sorted by residual: bond pdb=" C6 PSC A 404 " pdb=" C7 PSC A 404 " ideal model delta sigma weight residual 1.523 1.314 0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C6 PSC C 404 " pdb=" C7 PSC C 404 " ideal model delta sigma weight residual 1.523 1.314 0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C6 PSC B 404 " pdb=" C7 PSC B 404 " ideal model delta sigma weight residual 1.523 1.314 0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" CA SER A 217 " pdb=" CB SER A 217 " ideal model delta sigma weight residual 1.528 1.461 0.067 1.61e-02 3.86e+03 1.75e+01 bond pdb=" CA SER C 217 " pdb=" CB SER C 217 " ideal model delta sigma weight residual 1.528 1.461 0.067 1.61e-02 3.86e+03 1.72e+01 ... (remaining 7123 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.08: 9373 4.08 - 8.16: 101 8.16 - 12.24: 12 12.24 - 16.32: 12 16.32 - 20.41: 3 Bond angle restraints: 9501 Sorted by residual: angle pdb=" C01 PSC B 402 " pdb=" C02 PSC B 402 " pdb=" O01 PSC B 402 " ideal model delta sigma weight residual 107.00 127.41 -20.41 3.00e+00 1.11e-01 4.63e+01 angle pdb=" C01 PSC C 402 " pdb=" C02 PSC C 402 " pdb=" O01 PSC C 402 " ideal model delta sigma weight residual 107.00 127.40 -20.40 3.00e+00 1.11e-01 4.62e+01 angle pdb=" C01 PSC A 402 " pdb=" C02 PSC A 402 " pdb=" O01 PSC A 402 " ideal model delta sigma weight residual 107.00 127.39 -20.39 3.00e+00 1.11e-01 4.62e+01 angle pdb=" N PRO C 182 " pdb=" CA PRO C 182 " pdb=" C PRO C 182 " ideal model delta sigma weight residual 113.75 121.44 -7.69 1.49e+00 4.50e-01 2.67e+01 angle pdb=" N PRO A 182 " pdb=" CA PRO A 182 " pdb=" C PRO A 182 " ideal model delta sigma weight residual 113.75 121.44 -7.69 1.49e+00 4.50e-01 2.66e+01 ... (remaining 9496 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.13: 3888 32.13 - 64.27: 204 64.27 - 96.40: 9 96.40 - 128.53: 3 128.53 - 160.67: 3 Dihedral angle restraints: 4107 sinusoidal: 1845 harmonic: 2262 Sorted by residual: dihedral pdb=" N PSC A 402 " pdb=" C04 PSC A 402 " pdb=" C05 PSC A 402 " pdb=" O12 PSC A 402 " ideal model delta sinusoidal sigma weight residual -70.45 90.22 -160.67 1 3.00e+01 1.11e-03 2.07e+01 dihedral pdb=" N PSC B 402 " pdb=" C04 PSC B 402 " pdb=" C05 PSC B 402 " pdb=" O12 PSC B 402 " ideal model delta sinusoidal sigma weight residual -70.45 90.21 -160.66 1 3.00e+01 1.11e-03 2.07e+01 dihedral pdb=" N PSC C 402 " pdb=" C04 PSC C 402 " pdb=" C05 PSC C 402 " pdb=" O12 PSC C 402 " ideal model delta sinusoidal sigma weight residual -70.45 90.20 -160.65 1 3.00e+01 1.11e-03 2.07e+01 ... (remaining 4104 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 460 0.049 - 0.098: 261 0.098 - 0.147: 139 0.147 - 0.196: 43 0.196 - 0.245: 24 Chirality restraints: 927 Sorted by residual: chirality pdb=" CB VAL B 17 " pdb=" CA VAL B 17 " pdb=" CG1 VAL B 17 " pdb=" CG2 VAL B 17 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CB VAL C 17 " pdb=" CA VAL C 17 " pdb=" CG1 VAL C 17 " pdb=" CG2 VAL C 17 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB VAL A 17 " pdb=" CA VAL A 17 " pdb=" CG1 VAL A 17 " pdb=" CG2 VAL A 17 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 924 not shown) Planarity restraints: 1137 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 PSC A 402 " -0.246 2.00e-02 2.50e+03 1.85e-01 3.43e+02 pdb=" C11 PSC A 402 " 0.088 2.00e-02 2.50e+03 pdb=" C8 PSC A 402 " -0.089 2.00e-02 2.50e+03 pdb=" C9 PSC A 402 " 0.247 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 PSC C 402 " 0.246 2.00e-02 2.50e+03 1.85e-01 3.43e+02 pdb=" C11 PSC C 402 " -0.088 2.00e-02 2.50e+03 pdb=" C8 PSC C 402 " 0.089 2.00e-02 2.50e+03 pdb=" C9 PSC C 402 " -0.247 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 PSC B 402 " 0.246 2.00e-02 2.50e+03 1.85e-01 3.42e+02 pdb=" C11 PSC B 402 " -0.088 2.00e-02 2.50e+03 pdb=" C8 PSC B 402 " 0.089 2.00e-02 2.50e+03 pdb=" C9 PSC B 402 " -0.247 2.00e-02 2.50e+03 ... (remaining 1134 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2114 2.82 - 3.34: 6640 3.34 - 3.86: 12755 3.86 - 4.38: 16441 4.38 - 4.90: 25046 Nonbonded interactions: 62996 Sorted by model distance: nonbonded pdb=" OH TYR A 180 " pdb=" O HOH A 501 " model vdw 2.300 3.040 nonbonded pdb=" OH TYR C 180 " pdb=" O HOH C 501 " model vdw 2.301 3.040 nonbonded pdb=" OH TYR B 180 " pdb=" O HOH B 501 " model vdw 2.301 3.040 nonbonded pdb=" N GLY A 52 " pdb=" OE1 GLU A 248 " model vdw 2.333 3.120 nonbonded pdb=" N GLY B 52 " pdb=" OE1 GLU B 248 " model vdw 2.333 3.120 ... (remaining 62991 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.990 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 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 : 0.011 0.209 7131 Z= 0.729 Angle : 1.547 20.406 9501 Z= 0.941 Chirality : 0.080 0.245 927 Planarity : 0.017 0.185 1137 Dihedral : 18.620 160.666 2667 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.91 % Allowed : 1.82 % Favored : 97.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.27), residues: 771 helix: -1.08 (0.18), residues: 516 sheet: None (None), residues: 0 loop : 0.02 (0.42), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARG B 46 TYR 0.043 0.010 TYR A 101 PHE 0.050 0.010 PHE A 150 TRP 0.049 0.011 TRP C 42 HIS 0.012 0.006 HIS C 225 Details of bonding type rmsd/Z covalent geometry : bond 0.01079 / 0.65 ( 7128) covalent geometry : angle 1.54697 / 0.94 ( 9501) hydrogen bonds : bond 0.17238 / 11.53 ( 414) hydrogen bonds : angle 7.56513 / 5.38 ( 1233) Misc. bond : bond 0.16257 / 10.20 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 ASP cc_start: 0.8294 (m-30) cc_final: 0.7947 (m-30) REVERT: A 171 ARG cc_start: 0.7193 (ttt-90) cc_final: 0.6401 (ttp-170) REVERT: A 174 LYS cc_start: 0.7676 (mtpm) cc_final: 0.7077 (mtmt) REVERT: A 186 ARG cc_start: 0.8078 (ttt180) cc_final: 0.7023 (ttm110) REVERT: A 204 LEU cc_start: 0.7840 (tp) cc_final: 0.7525 (mt) REVERT: A 235 ILE cc_start: 0.7628 (mm) cc_final: 0.7405 (mt) REVERT: B 4 TYR cc_start: 0.8153 (t80) cc_final: 0.7940 (t80) REVERT: B 5 ASP cc_start: 0.8288 (m-30) cc_final: 0.8018 (m-30) REVERT: B 14 ARG cc_start: 0.7816 (mtp-110) cc_final: 0.6862 (mmp-170) REVERT: B 171 ARG cc_start: 0.7391 (ttt-90) cc_final: 0.6602 (ttp-170) REVERT: B 174 LYS cc_start: 0.7774 (mtpm) cc_final: 0.7222 (mtmp) REVERT: B 204 LEU cc_start: 0.7739 (tp) cc_final: 0.7474 (mt) REVERT: C 5 ASP cc_start: 0.8412 (m-30) cc_final: 0.8078 (m-30) REVERT: C 43 MET cc_start: 0.7930 (mtt) cc_final: 0.7695 (mtt) REVERT: C 171 ARG cc_start: 0.7205 (ttt-90) cc_final: 0.6382 (ttp-170) REVERT: C 174 LYS cc_start: 0.7698 (mtpm) cc_final: 0.7172 (mtmp) REVERT: C 186 ARG cc_start: 0.7992 (ttt180) cc_final: 0.6898 (ttm110) REVERT: C 204 LEU cc_start: 0.7704 (tp) cc_final: 0.7489 (mt) REVERT: C 230 LEU cc_start: 0.7623 (tp) cc_final: 0.7392 (tp) outliers start: 6 outliers final: 2 residues processed: 89 average time/residue: 0.5298 time to fit residues: 49.4448 Evaluate side-chains 82 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 80 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 165 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.0870 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.125815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.118662 restraints weight = 6533.121| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 0.45 r_work: 0.3175 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7131 Z= 0.145 Angle : 0.598 6.988 9501 Z= 0.303 Chirality : 0.041 0.151 927 Planarity : 0.005 0.034 1137 Dihedral : 20.815 150.963 1276 Min Nonbonded Distance : 2.682 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 2.42 % Allowed : 6.36 % Favored : 91.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.29), residues: 771 helix: 1.81 (0.21), residues: 519 sheet: None (None), residues: 0 loop : 0.60 (0.42), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 218 TYR 0.013 0.002 TYR B 103 PHE 0.013 0.002 PHE B 238 TRP 0.020 0.002 TRP B 42 HIS 0.002 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 ( 7128) covalent geometry : angle 0.59828 / 0.30 ( 9501) hydrogen bonds : bond 0.05744 / 3.86 ( 414) hydrogen bonds : angle 4.58284 / 3.22 ( 1233) Misc. bond : bond 0.00089 / 0.06 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.188 Fit side-chains REVERT: A 171 ARG cc_start: 0.8022 (ttt-90) cc_final: 0.7430 (ttp-170) REVERT: A 174 LYS cc_start: 0.8705 (mtpm) cc_final: 0.8350 (mtmp) REVERT: A 186 ARG cc_start: 0.8704 (ttt180) cc_final: 0.8169 (ttm110) REVERT: A 229 ASP cc_start: 0.8380 (m-30) cc_final: 0.8158 (m-30) REVERT: B 171 ARG cc_start: 0.8033 (ttt-90) cc_final: 0.7402 (ttp-170) REVERT: B 174 LYS cc_start: 0.8748 (mtpm) cc_final: 0.8437 (mtmp) REVERT: C 43 MET cc_start: 0.8815 (mtt) cc_final: 0.8525 (mtt) REVERT: C 171 ARG cc_start: 0.8042 (ttt-90) cc_final: 0.7561 (ttp-170) REVERT: C 174 LYS cc_start: 0.8777 (mtpm) cc_final: 0.8409 (mtmp) REVERT: C 244 ARG cc_start: 0.8905 (mtt90) cc_final: 0.8626 (mtm110) outliers start: 16 outliers final: 4 residues processed: 96 average time/residue: 0.6453 time to fit residues: 64.7988 Evaluate side-chains 81 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 165 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 45 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 38 optimal weight: 9.9990 chunk 37 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.131910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.126400 restraints weight = 6671.279| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 0.35 r_work: 0.3285 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7131 Z= 0.190 Angle : 0.664 7.891 9501 Z= 0.330 Chirality : 0.044 0.196 927 Planarity : 0.005 0.040 1137 Dihedral : 20.221 148.915 1276 Min Nonbonded Distance : 2.656 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.88 % Allowed : 6.97 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.29), residues: 771 helix: 1.89 (0.21), residues: 525 sheet: None (None), residues: 0 loop : 0.74 (0.42), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 46 TYR 0.016 0.002 TYR A 81 PHE 0.018 0.003 PHE B 208 TRP 0.018 0.003 TRP C 42 HIS 0.004 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 ( 7128) covalent geometry : angle 0.66419 / 0.33 ( 9501) hydrogen bonds : bond 0.06393 / 4.30 ( 414) hydrogen bonds : angle 4.49116 / 3.15 ( 1233) Misc. bond : bond 0.00084 / 0.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.266 Fit side-chains REVERT: A 171 ARG cc_start: 0.8138 (ttt-90) cc_final: 0.7543 (ttp-170) REVERT: A 174 LYS cc_start: 0.8742 (mtpm) cc_final: 0.8403 (mtmp) REVERT: A 175 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8374 (mtmt) REVERT: A 186 ARG cc_start: 0.8730 (ttt180) cc_final: 0.8264 (ttm110) REVERT: B 5 ASP cc_start: 0.8646 (m-30) cc_final: 0.8439 (m-30) REVERT: B 171 ARG cc_start: 0.8171 (ttt-90) cc_final: 0.7382 (ttp-170) REVERT: B 174 LYS cc_start: 0.8823 (mtpm) cc_final: 0.8527 (mtmp) REVERT: B 175 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.7872 (mttp) REVERT: C 43 MET cc_start: 0.8858 (mtt) cc_final: 0.8623 (mtt) REVERT: C 171 ARG cc_start: 0.8145 (ttt-90) cc_final: 0.7737 (ttp-170) REVERT: C 174 LYS cc_start: 0.8743 (mtpm) cc_final: 0.8419 (mtmp) outliers start: 19 outliers final: 6 residues processed: 86 average time/residue: 0.5656 time to fit residues: 51.1206 Evaluate side-chains 83 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 165 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 64 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 31 optimal weight: 0.1980 chunk 10 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 3 optimal weight: 20.0000 chunk 12 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.130558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.123735 restraints weight = 6489.386| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 0.43 r_work: 0.3247 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7131 Z= 0.108 Angle : 0.494 7.134 9501 Z= 0.245 Chirality : 0.038 0.127 927 Planarity : 0.005 0.038 1137 Dihedral : 18.567 143.481 1276 Min Nonbonded Distance : 2.654 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 1.36 % Allowed : 8.18 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.85 (0.30), residues: 771 helix: 2.43 (0.22), residues: 525 sheet: None (None), residues: 0 loop : 0.79 (0.42), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 171 TYR 0.008 0.001 TYR C 221 PHE 0.011 0.001 PHE C 134 TRP 0.014 0.001 TRP B 42 HIS 0.001 0.000 HIS C 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 ( 7128) covalent geometry : angle 0.49368 / 0.25 ( 9501) hydrogen bonds : bond 0.04337 / 2.91 ( 414) hydrogen bonds : angle 4.08838 / 2.86 ( 1233) Misc. bond : bond 0.00010 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.253 Fit side-chains REVERT: A 171 ARG cc_start: 0.7885 (ttt-90) cc_final: 0.7306 (ttp-170) REVERT: A 174 LYS cc_start: 0.8650 (mtpm) cc_final: 0.8283 (mtmp) REVERT: A 186 ARG cc_start: 0.8621 (ttt180) cc_final: 0.8053 (ttm110) REVERT: B 171 ARG cc_start: 0.7873 (ttt-90) cc_final: 0.7279 (ttp-170) REVERT: B 174 LYS cc_start: 0.8748 (mtpm) cc_final: 0.8349 (mtmm) REVERT: C 171 ARG cc_start: 0.7885 (ttt-90) cc_final: 0.7406 (ttp-170) REVERT: C 174 LYS cc_start: 0.8683 (mtpm) cc_final: 0.8300 (mtmp) REVERT: C 244 ARG cc_start: 0.8869 (mtt90) cc_final: 0.8536 (mtm110) outliers start: 9 outliers final: 3 residues processed: 92 average time/residue: 0.5954 time to fit residues: 57.2833 Evaluate side-chains 86 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 83 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 165 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 0.6980 chunk 45 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN B 125 GLN C 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.125361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.118423 restraints weight = 6519.441| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 0.44 r_work: 0.3140 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7131 Z= 0.159 Angle : 0.588 7.790 9501 Z= 0.293 Chirality : 0.041 0.158 927 Planarity : 0.005 0.039 1137 Dihedral : 18.840 144.364 1276 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 1.97 % Allowed : 7.27 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.61 (0.29), residues: 771 helix: 2.25 (0.21), residues: 525 sheet: None (None), residues: 0 loop : 0.72 (0.41), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 244 TYR 0.013 0.002 TYR C 81 PHE 0.015 0.002 PHE A 134 TRP 0.014 0.002 TRP B 42 HIS 0.004 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 ( 7128) covalent geometry : angle 0.58821 / 0.29 ( 9501) hydrogen bonds : bond 0.05611 / 3.79 ( 414) hydrogen bonds : angle 4.25659 / 2.99 ( 1233) Misc. bond : bond 0.00013 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.203 Fit side-chains REVERT: A 171 ARG cc_start: 0.8119 (ttt-90) cc_final: 0.7508 (ttp-170) REVERT: A 174 LYS cc_start: 0.8800 (mtpm) cc_final: 0.8418 (mtmp) REVERT: A 186 ARG cc_start: 0.8771 (ttt180) cc_final: 0.8172 (ttm110) REVERT: B 171 ARG cc_start: 0.8123 (ttt-90) cc_final: 0.7476 (ttp-170) REVERT: B 174 LYS cc_start: 0.8855 (mtpm) cc_final: 0.8443 (mtmm) REVERT: C 76 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8580 (mt) REVERT: C 171 ARG cc_start: 0.8136 (ttt-90) cc_final: 0.7657 (ttp-170) REVERT: C 174 LYS cc_start: 0.8837 (mtpm) cc_final: 0.8463 (mtmp) outliers start: 13 outliers final: 6 residues processed: 86 average time/residue: 0.5652 time to fit residues: 51.0652 Evaluate side-chains 79 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 230 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 50 optimal weight: 0.3980 chunk 73 optimal weight: 5.9990 chunk 63 optimal weight: 20.0000 chunk 29 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.129549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.122737 restraints weight = 6487.295| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 0.43 r_work: 0.3232 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7131 Z= 0.114 Angle : 0.500 7.180 9501 Z= 0.249 Chirality : 0.038 0.129 927 Planarity : 0.005 0.036 1137 Dihedral : 17.872 141.095 1276 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 1.52 % Allowed : 8.48 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.84 (0.30), residues: 771 helix: 2.44 (0.21), residues: 525 sheet: None (None), residues: 0 loop : 0.75 (0.42), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 171 TYR 0.008 0.001 TYR C 81 PHE 0.012 0.001 PHE A 134 TRP 0.013 0.001 TRP C 42 HIS 0.002 0.000 HIS C 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 7128) covalent geometry : angle 0.49968 / 0.25 ( 9501) hydrogen bonds : bond 0.04568 / 3.07 ( 414) hydrogen bonds : angle 4.06443 / 2.85 ( 1233) Misc. bond : bond 0.00010 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.279 Fit side-chains REVERT: A 171 ARG cc_start: 0.7954 (ttt-90) cc_final: 0.7356 (ttp-170) REVERT: A 174 LYS cc_start: 0.8671 (mtpm) cc_final: 0.8294 (mtmp) REVERT: B 171 ARG cc_start: 0.7935 (ttt-90) cc_final: 0.7324 (ttp-170) REVERT: B 174 LYS cc_start: 0.8738 (mtpm) cc_final: 0.8336 (mtmm) REVERT: B 175 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.7951 (mtmt) REVERT: C 171 ARG cc_start: 0.7929 (ttt-90) cc_final: 0.7457 (ttp-170) REVERT: C 174 LYS cc_start: 0.8714 (mtpm) cc_final: 0.8330 (mtmp) outliers start: 10 outliers final: 6 residues processed: 87 average time/residue: 0.5775 time to fit residues: 52.6726 Evaluate side-chains 86 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 230 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 56 optimal weight: 3.9990 chunk 50 optimal weight: 0.0870 chunk 26 optimal weight: 0.0000 chunk 64 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 32 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 overall best weight: 0.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN B 125 GLN C 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.149264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.144465 restraints weight = 6581.240| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 0.32 r_work: 0.3525 rms_B_bonded: 1.09 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 2.30 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7131 Z= 0.102 Angle : 0.476 7.004 9501 Z= 0.234 Chirality : 0.037 0.125 927 Planarity : 0.004 0.034 1137 Dihedral : 16.707 138.851 1276 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.97 % Allowed : 8.48 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.10 (0.30), residues: 771 helix: 2.62 (0.22), residues: 528 sheet: None (None), residues: 0 loop : 0.86 (0.42), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 171 TYR 0.007 0.001 TYR A 221 PHE 0.011 0.001 PHE A 134 TRP 0.012 0.001 TRP B 42 HIS 0.001 0.000 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 ( 7128) covalent geometry : angle 0.47606 / 0.23 ( 9501) hydrogen bonds : bond 0.03983 / 2.68 ( 414) hydrogen bonds : angle 3.88793 / 2.73 ( 1233) Misc. bond : bond 0.00002 / 0.00 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.153 Fit side-chains REVERT: A 171 ARG cc_start: 0.7893 (ttt-90) cc_final: 0.7298 (ttp-170) REVERT: A 174 LYS cc_start: 0.8651 (mtpm) cc_final: 0.8283 (mtmp) REVERT: B 171 ARG cc_start: 0.7905 (ttt-90) cc_final: 0.7326 (ttp-170) REVERT: B 174 LYS cc_start: 0.8749 (mtpm) cc_final: 0.8362 (mtmm) REVERT: B 175 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8304 (mtmt) REVERT: C 76 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8520 (mt) REVERT: C 171 ARG cc_start: 0.7863 (ttt-90) cc_final: 0.7421 (ttp-170) outliers start: 13 outliers final: 5 residues processed: 92 average time/residue: 0.5299 time to fit residues: 51.2380 Evaluate side-chains 80 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 165 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 59 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 25 optimal weight: 0.0030 chunk 66 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 overall best weight: 2.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 125 GLN C 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.127284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.120265 restraints weight = 6554.551| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 0.45 r_work: 0.3156 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7131 Z= 0.142 Angle : 0.549 7.649 9501 Z= 0.275 Chirality : 0.040 0.146 927 Planarity : 0.005 0.035 1137 Dihedral : 17.181 140.872 1276 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 1.82 % Allowed : 8.79 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.76 (0.29), residues: 771 helix: 2.37 (0.21), residues: 525 sheet: None (None), residues: 0 loop : 0.73 (0.42), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 218 TYR 0.011 0.002 TYR C 81 PHE 0.016 0.002 PHE A 134 TRP 0.011 0.002 TRP B 42 HIS 0.004 0.001 HIS C 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 7128) covalent geometry : angle 0.54947 / 0.27 ( 9501) hydrogen bonds : bond 0.05170 / 3.48 ( 414) hydrogen bonds : angle 4.11570 / 2.89 ( 1233) Misc. bond : bond 0.00006 / 0.00 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.152 Fit side-chains REVERT: A 171 ARG cc_start: 0.8054 (ttt-90) cc_final: 0.7437 (ttp-170) REVERT: A 174 LYS cc_start: 0.8765 (mtpm) cc_final: 0.8380 (mtmp) REVERT: B 171 ARG cc_start: 0.8120 (ttt-90) cc_final: 0.7471 (ttp-170) REVERT: B 174 LYS cc_start: 0.8816 (mtpm) cc_final: 0.8411 (mtmm) REVERT: B 175 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8024 (mtmt) REVERT: C 76 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8568 (mt) REVERT: C 171 ARG cc_start: 0.8100 (ttt-90) cc_final: 0.7660 (ttp-170) outliers start: 12 outliers final: 5 residues processed: 80 average time/residue: 0.5852 time to fit residues: 49.0123 Evaluate side-chains 83 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 165 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 51 optimal weight: 0.0060 chunk 7 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 56 optimal weight: 0.4980 chunk 32 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.9002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.127754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.120800 restraints weight = 6509.216| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 0.45 r_work: 0.3150 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7131 Z= 0.133 Angle : 0.532 7.491 9501 Z= 0.266 Chirality : 0.039 0.135 927 Planarity : 0.005 0.036 1137 Dihedral : 17.129 141.151 1276 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 1.21 % Allowed : 9.39 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.70 (0.29), residues: 771 helix: 2.38 (0.21), residues: 522 sheet: None (None), residues: 0 loop : 0.61 (0.41), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 46 TYR 0.010 0.002 TYR C 81 PHE 0.015 0.001 PHE A 134 TRP 0.012 0.002 TRP C 42 HIS 0.003 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 7128) covalent geometry : angle 0.53163 / 0.27 ( 9501) hydrogen bonds : bond 0.05018 / 3.38 ( 414) hydrogen bonds : angle 4.10473 / 2.88 ( 1233) Misc. bond : bond 0.00010 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.169 Fit side-chains REVERT: A 171 ARG cc_start: 0.8078 (ttt-90) cc_final: 0.7734 (ttp80) REVERT: A 174 LYS cc_start: 0.8782 (mtpm) cc_final: 0.8406 (mtmp) REVERT: B 171 ARG cc_start: 0.8079 (ttt-90) cc_final: 0.7454 (ttp-170) REVERT: B 174 LYS cc_start: 0.8844 (mtpm) cc_final: 0.8438 (mtmm) REVERT: B 175 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8060 (mtmt) REVERT: C 76 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8559 (mt) REVERT: C 171 ARG cc_start: 0.8098 (ttt-90) cc_final: 0.7637 (ttp-170) outliers start: 8 outliers final: 5 residues processed: 83 average time/residue: 0.5629 time to fit residues: 48.9877 Evaluate side-chains 81 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 165 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 64 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.124826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.117863 restraints weight = 6534.134| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 0.45 r_work: 0.3121 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7131 Z= 0.174 Angle : 0.607 7.971 9501 Z= 0.304 Chirality : 0.042 0.183 927 Planarity : 0.005 0.038 1137 Dihedral : 17.727 143.262 1276 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.21 % Allowed : 8.94 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.42 (0.29), residues: 771 helix: 2.15 (0.21), residues: 522 sheet: None (None), residues: 0 loop : 0.54 (0.41), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 46 TYR 0.014 0.002 TYR B 81 PHE 0.015 0.002 PHE A 134 TRP 0.012 0.002 TRP C 42 HIS 0.004 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 ( 7128) covalent geometry : angle 0.60667 / 0.30 ( 9501) hydrogen bonds : bond 0.05885 / 3.98 ( 414) hydrogen bonds : angle 4.28821 / 3.01 ( 1233) Misc. bond : bond 0.00012 / 0.01 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.192 Fit side-chains REVERT: A 171 ARG cc_start: 0.8135 (ttt-90) cc_final: 0.7564 (ttp-170) REVERT: A 174 LYS cc_start: 0.8799 (mtpm) cc_final: 0.8424 (mtmp) REVERT: B 171 ARG cc_start: 0.8192 (ttt-90) cc_final: 0.7529 (ttp-170) REVERT: B 174 LYS cc_start: 0.8858 (mtpm) cc_final: 0.8450 (mtmm) REVERT: B 175 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8023 (mtmt) REVERT: C 171 ARG cc_start: 0.8182 (ttt-90) cc_final: 0.7725 (ttp-170) outliers start: 8 outliers final: 5 residues processed: 79 average time/residue: 0.5421 time to fit residues: 44.8383 Evaluate side-chains 80 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 165 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 chunk 69 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.125904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.119002 restraints weight = 6529.768| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 0.45 r_work: 0.3140 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7131 Z= 0.150 Angle : 0.566 7.723 9501 Z= 0.284 Chirality : 0.041 0.153 927 Planarity : 0.005 0.037 1137 Dihedral : 17.610 142.801 1276 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.91 % Allowed : 9.39 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.29), residues: 771 helix: 2.18 (0.21), residues: 522 sheet: None (None), residues: 0 loop : 0.51 (0.41), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 46 TYR 0.013 0.002 TYR B 81 PHE 0.015 0.002 PHE A 134 TRP 0.012 0.002 TRP C 42 HIS 0.003 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 ( 7128) covalent geometry : angle 0.56626 / 0.28 ( 9501) hydrogen bonds : bond 0.05474 / 3.70 ( 414) hydrogen bonds : angle 4.22312 / 2.96 ( 1233) Misc. bond : bond 0.00012 / 0.01 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1903.94 seconds wall clock time: 33 minutes 13.26 seconds (1993.26 seconds total)