Starting phenix.real_space_refine on Tue Aug 4 18:42:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8pds_17620/08_2026/8pds_17620.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pds_17620/08_2026/8pds_17620.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pds_17620/08_2026/8pds_17620.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pds_17620/08_2026/8pds_17620.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8pds_17620/08_2026/8pds_17620.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8pds_17620/08_2026/8pds_17620.cif" model { file = "/net/cci-nas-00/data/ceres_data/8pds_17620/08_2026/8pds_17620.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pds_17620/08_2026/8pds_17620.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.025 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 14 5.49 5 S 26 5.16 5 C 3776 2.51 5 N 1044 2.21 5 O 1196 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 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: 6056 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2827 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 11, 'TRANS': 353} Chain: "E" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 280 Classifications: {'RNAv2': 14} Modifications used: {'rna2p_pyr': 2, 'rna3p_pyr': 12} Link IDs: {'rna2p': 2, 'rna3p': 11} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 61 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "C" Number of atoms: 2827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2827 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 11, 'TRANS': 353} Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 61 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Time building chain proxies: 1.24, per 1000 atoms: 0.20 Number of scatterers: 6056 At special positions: 0 Unit cell: (110.25, 90.3, 89.25, 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 26 16.00 P 14 15.00 O 1196 8.00 N 1044 7.00 C 3776 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.35 Conformation dependent library (CDL) restraints added in 254.5 milliseconds 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1380 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 4 sheets defined 67.1% alpha, 5.1% beta 0 base pairs and 10 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 9 through 20 Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 40 through 51 removed outlier: 3.636A pdb=" N LEU A 47 " --> pdb=" O GLU A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 75 Processing helix chain 'A' and resid 75 through 86 Processing helix chain 'A' and resid 120 through 142 removed outlier: 3.628A pdb=" N VAL A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 151 removed outlier: 3.646A pdb=" N GLN A 150 " --> pdb=" O PRO A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 171 removed outlier: 3.883A pdb=" N LYS A 171 " --> pdb=" O LEU A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 191 removed outlier: 3.795A pdb=" N ARG A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 198 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 217 through 233 removed outlier: 3.894A pdb=" N ARG A 221 " --> pdb=" O LYS A 217 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 251 Processing helix chain 'A' and resid 256 through 268 removed outlier: 3.719A pdb=" N ARG A 260 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 274 Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 281 through 296 Processing helix chain 'A' and resid 297 through 300 removed outlier: 3.527A pdb=" N GLY A 300 " --> pdb=" O PRO A 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 297 through 300' Processing helix chain 'A' and resid 318 through 332 Processing helix chain 'A' and resid 344 through 361 Processing helix chain 'B' and resid 10 through 14 removed outlier: 3.549A pdb=" N GLN B 13 " --> pdb=" O ASP B 10 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU B 14 " --> pdb=" O ILE B 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 10 through 14' Processing helix chain 'C' and resid 9 through 20 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 51 removed outlier: 3.613A pdb=" N LEU C 47 " --> pdb=" O GLU C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 75 Processing helix chain 'C' and resid 75 through 86 Processing helix chain 'C' and resid 120 through 142 removed outlier: 3.570A pdb=" N VAL C 124 " --> pdb=" O GLU C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 151 Processing helix chain 'C' and resid 156 through 171 removed outlier: 3.910A pdb=" N LYS C 171 " --> pdb=" O LEU C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 191 removed outlier: 3.884A pdb=" N ARG C 189 " --> pdb=" O ARG C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 198 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 217 through 233 removed outlier: 3.902A pdb=" N ARG C 221 " --> pdb=" O LYS C 217 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER C 222 " --> pdb=" O VAL C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 251 Processing helix chain 'C' and resid 256 through 268 removed outlier: 3.651A pdb=" N ARG C 260 " --> pdb=" O GLN C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 274 Processing helix chain 'C' and resid 275 through 280 Processing helix chain 'C' and resid 281 through 296 Processing helix chain 'C' and resid 297 through 300 removed outlier: 3.762A pdb=" N GLY C 300 " --> pdb=" O PRO C 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 297 through 300' Processing helix chain 'C' and resid 318 through 332 Processing helix chain 'C' and resid 344 through 361 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 35 removed outlier: 6.193A pdb=" N THR A 33 " --> pdb=" O VAL A 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 104 removed outlier: 7.803A pdb=" N LEU A 111 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 32 through 35 Processing sheet with id=AA4, first strand: chain 'C' and resid 96 through 104 removed outlier: 7.875A pdb=" N LEU C 111 " --> pdb=" O LEU C 100 " (cutoff:3.500A) 338 hydrogen bonds defined for protein. 987 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 10 stacking parallelities Total time for adding SS restraints: 1.26 Time building geometry restraints manager: 0.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1949 1.34 - 1.46: 815 1.46 - 1.57: 3334 1.57 - 1.69: 27 1.69 - 1.81: 46 Bond restraints: 6171 Sorted by residual: bond pdb=" N ILE B 11 " pdb=" CA ILE B 11 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.30e-02 5.92e+03 7.53e+00 bond pdb=" CB VAL C 92 " pdb=" CG1 VAL C 92 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.74e+00 bond pdb=" CB VAL A 92 " pdb=" CG1 VAL A 92 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.45e+00 bond pdb=" CB VAL C 190 " pdb=" CG1 VAL C 190 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.89e+00 bond pdb=" CG LEU C 282 " pdb=" CD2 LEU C 282 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.07e+00 ... (remaining 6166 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 7908 1.17 - 2.35: 375 2.35 - 3.52: 74 3.52 - 4.69: 22 4.69 - 5.87: 5 Bond angle restraints: 8384 Sorted by residual: angle pdb=" CA ILE B 11 " pdb=" C ILE B 11 " pdb=" O ILE B 11 " ideal model delta sigma weight residual 120.47 117.86 2.61 1.08e+00 8.57e-01 5.86e+00 angle pdb=" C LEU C 52 " pdb=" N TYR C 53 " pdb=" CA TYR C 53 " ideal model delta sigma weight residual 122.60 118.83 3.77 1.56e+00 4.11e-01 5.83e+00 angle pdb=" C LEU A 52 " pdb=" N TYR A 53 " pdb=" CA TYR A 53 " ideal model delta sigma weight residual 122.65 119.02 3.63 1.60e+00 3.91e-01 5.14e+00 angle pdb=" N ILE C 51 " pdb=" CA ILE C 51 " pdb=" C ILE C 51 " ideal model delta sigma weight residual 113.00 110.37 2.63 1.30e+00 5.92e-01 4.10e+00 angle pdb=" N GLN C 216 " pdb=" CA GLN C 216 " pdb=" CB GLN C 216 " ideal model delta sigma weight residual 110.07 112.91 -2.84 1.45e+00 4.76e-01 3.83e+00 ... (remaining 8379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 3419 17.57 - 35.15: 291 35.15 - 52.72: 51 52.72 - 70.29: 23 70.29 - 87.87: 25 Dihedral angle restraints: 3809 sinusoidal: 1657 harmonic: 2152 Sorted by residual: dihedral pdb=" C4' C E 67 " pdb=" C3' C E 67 " pdb=" C2' C E 67 " pdb=" C1' C E 67 " ideal model delta sinusoidal sigma weight residual 36.34 -33.79 70.14 1 3.10e+00 1.04e-01 6.60e+02 dihedral pdb=" C4' C E 74 " pdb=" C3' C E 74 " pdb=" C2' C E 74 " pdb=" C1' C E 74 " ideal model delta sinusoidal sigma weight residual 36.35 -33.21 69.55 1 3.10e+00 1.04e-01 6.50e+02 dihedral pdb=" O4' C E 67 " pdb=" C4' C E 67 " pdb=" C3' C E 67 " pdb=" C2' C E 67 " ideal model delta sinusoidal sigma weight residual -35.15 21.25 -56.40 1 4.00e+00 6.25e-02 2.68e+02 ... (remaining 3806 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 817 0.059 - 0.118: 140 0.118 - 0.177: 12 0.177 - 0.235: 13 0.235 - 0.294: 4 Chirality restraints: 986 Sorted by residual: chirality pdb=" C2' C E 67 " pdb=" C3' C E 67 " pdb=" O2' C E 67 " pdb=" C1' C E 67 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" C2' C E 74 " pdb=" C3' C E 74 " pdb=" O2' C E 74 " pdb=" C1' C E 74 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" P C E 64 " pdb=" OP1 C E 64 " pdb=" OP2 C E 64 " pdb=" O5' C E 64 " both_signs ideal model delta sigma weight residual True 2.17 -2.42 -0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 983 not shown) Planarity restraints: 1018 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C E 66 " -0.021 2.00e-02 2.50e+03 1.11e-02 2.76e+00 pdb=" N1 C E 66 " 0.024 2.00e-02 2.50e+03 pdb=" C2 C E 66 " 0.001 2.00e-02 2.50e+03 pdb=" O2 C E 66 " 0.003 2.00e-02 2.50e+03 pdb=" N3 C E 66 " -0.002 2.00e-02 2.50e+03 pdb=" C4 C E 66 " -0.001 2.00e-02 2.50e+03 pdb=" N4 C E 66 " -0.007 2.00e-02 2.50e+03 pdb=" C5 C E 66 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C E 66 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 53 " -0.006 2.00e-02 2.50e+03 1.11e-02 2.46e+00 pdb=" CG TYR C 53 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR C 53 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR C 53 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR C 53 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR C 53 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 53 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 53 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C E 73 " -0.020 2.00e-02 2.50e+03 1.02e-02 2.33e+00 pdb=" N1 C E 73 " 0.021 2.00e-02 2.50e+03 pdb=" C2 C E 73 " 0.002 2.00e-02 2.50e+03 pdb=" O2 C E 73 " 0.003 2.00e-02 2.50e+03 pdb=" N3 C E 73 " -0.003 2.00e-02 2.50e+03 pdb=" C4 C E 73 " -0.001 2.00e-02 2.50e+03 pdb=" N4 C E 73 " -0.007 2.00e-02 2.50e+03 pdb=" C5 C E 73 " 0.002 2.00e-02 2.50e+03 pdb=" C6 C E 73 " 0.002 2.00e-02 2.50e+03 ... (remaining 1015 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1066 2.76 - 3.30: 5996 3.30 - 3.83: 10436 3.83 - 4.37: 12651 4.37 - 4.90: 20723 Nonbonded interactions: 50872 Sorted by model distance: nonbonded pdb=" OH TYR A 338 " pdb=" OP2 C E 74 " model vdw 2.230 3.040 nonbonded pdb=" O LEU A 18 " pdb=" OG SER C 233 " model vdw 2.262 3.040 nonbonded pdb=" OG SER A 307 " pdb=" O SER C 235 " model vdw 2.262 3.040 nonbonded pdb=" OP2 C E 67 " pdb=" OH TYR C 338 " model vdw 2.266 3.040 nonbonded pdb=" O2 C E 71 " pdb=" ND2 ASN C 246 " model vdw 2.315 3.120 ... (remaining 50867 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 5.440 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 6.780 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 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 : 0.004 0.055 6171 Z= 0.194 Angle : 0.615 5.865 8384 Z= 0.333 Chirality : 0.052 0.294 986 Planarity : 0.004 0.028 1018 Dihedral : 15.761 87.867 2429 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.16 % Allowed : 0.00 % Favored : 99.84 % 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: -0.16 (0.30), residues: 736 helix: 0.32 (0.24), residues: 474 sheet: -1.22 (0.64), residues: 42 loop : -0.54 (0.39), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 78 TYR 0.025 0.002 TYR C 53 PHE 0.016 0.002 PHE C 169 TRP 0.007 0.001 TRP C 123 HIS 0.004 0.001 HIS C 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 ( 6171) covalent geometry : angle 0.61483 / 0.33 ( 8384) hydrogen bonds : bond 0.12069 / 8.05 ( 338) hydrogen bonds : angle 6.23451 / 4.59 ( 987) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 0.146 Fit side-chains REVERT: C 135 MET cc_start: 0.8191 (ttm) cc_final: 0.7928 (ttm) outliers start: 1 outliers final: 0 residues processed: 98 average time/residue: 0.6592 time to fit residues: 66.9021 Evaluate side-chains 82 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.0970 chunk 38 optimal weight: 0.3980 chunk 61 optimal weight: 0.2980 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 81 GLN C 150 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.144816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.118383 restraints weight = 6992.983| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.54 r_work: 0.3084 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6171 Z= 0.168 Angle : 0.643 8.893 8384 Z= 0.307 Chirality : 0.050 0.449 986 Planarity : 0.004 0.036 1018 Dihedral : 12.665 81.179 1031 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.58 % Allowed : 8.36 % Favored : 90.06 % 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: 0.49 (0.30), residues: 736 helix: 0.87 (0.24), residues: 478 sheet: -1.03 (0.63), residues: 42 loop : -0.43 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 96 TYR 0.015 0.002 TYR C 69 PHE 0.014 0.002 PHE C 169 TRP 0.005 0.001 TRP C 123 HIS 0.003 0.001 HIS C 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 ( 6171) covalent geometry : angle 0.64263 / 0.31 ( 8384) hydrogen bonds : bond 0.04465 / 2.98 ( 338) hydrogen bonds : angle 4.53304 / 3.32 ( 987) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.204 Fit side-chains REVERT: A 26 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7884 (mtmm) REVERT: A 105 ASN cc_start: 0.7639 (OUTLIER) cc_final: 0.7057 (p0) REVERT: A 208 ARG cc_start: 0.8304 (tpt-90) cc_final: 0.7544 (tpm-80) REVERT: A 339 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7785 (mmt180) REVERT: C 283 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7455 (mmpt) REVERT: C 341 ARG cc_start: 0.8146 (ptt-90) cc_final: 0.7708 (ptm-80) outliers start: 10 outliers final: 6 residues processed: 92 average time/residue: 0.6245 time to fit residues: 59.6617 Evaluate side-chains 90 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 105 ASN Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 283 LYS Chi-restraints excluded: chain C residue 358 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 36 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 47 optimal weight: 0.0370 chunk 13 optimal weight: 1.9990 chunk 52 optimal weight: 0.0670 chunk 33 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 GLN A 284 GLN C 81 GLN C 150 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.144455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.118396 restraints weight = 6950.849| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.60 r_work: 0.3083 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6171 Z= 0.167 Angle : 0.579 6.737 8384 Z= 0.284 Chirality : 0.046 0.252 986 Planarity : 0.004 0.031 1018 Dihedral : 12.909 117.236 1031 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.68 % Allowed : 9.46 % Favored : 87.85 % 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: 0.64 (0.30), residues: 736 helix: 1.01 (0.24), residues: 478 sheet: -0.93 (0.66), residues: 42 loop : -0.42 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 96 TYR 0.015 0.002 TYR C 69 PHE 0.014 0.002 PHE C 169 TRP 0.005 0.001 TRP C 123 HIS 0.003 0.001 HIS C 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 ( 6171) covalent geometry : angle 0.57936 / 0.28 ( 8384) hydrogen bonds : bond 0.04377 / 2.93 ( 338) hydrogen bonds : angle 4.41598 / 3.23 ( 987) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.175 Fit side-chains REVERT: A 26 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7894 (mtmm) REVERT: A 208 ARG cc_start: 0.8292 (tpt-90) cc_final: 0.7542 (tpm-80) REVERT: A 339 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7822 (mmt180) REVERT: C 272 MET cc_start: 0.8491 (mmm) cc_final: 0.8264 (mmm) REVERT: C 283 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7398 (mmpt) REVERT: C 341 ARG cc_start: 0.8127 (ptt-90) cc_final: 0.7703 (ptm-80) outliers start: 17 outliers final: 11 residues processed: 91 average time/residue: 0.5605 time to fit residues: 53.0181 Evaluate side-chains 93 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 216 GLN Chi-restraints excluded: chain C residue 283 LYS Chi-restraints excluded: chain C residue 358 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 20 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 41 optimal weight: 0.3980 chunk 61 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 14 optimal weight: 0.4980 chunk 13 optimal weight: 0.5980 chunk 53 optimal weight: 0.0980 chunk 48 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 81 GLN C 150 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.143910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.117713 restraints weight = 6944.884| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.41 r_work: 0.3104 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6171 Z= 0.171 Angle : 0.582 6.652 8384 Z= 0.286 Chirality : 0.047 0.252 986 Planarity : 0.004 0.031 1018 Dihedral : 13.036 136.146 1031 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 3.00 % Allowed : 11.67 % Favored : 85.33 % 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: 0.67 (0.30), residues: 736 helix: 1.04 (0.24), residues: 478 sheet: -1.04 (0.65), residues: 42 loop : -0.41 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 96 TYR 0.015 0.002 TYR C 69 PHE 0.014 0.002 PHE C 169 TRP 0.008 0.001 TRP C 123 HIS 0.003 0.001 HIS C 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 ( 6171) covalent geometry : angle 0.58195 / 0.29 ( 8384) hydrogen bonds : bond 0.04325 / 2.90 ( 338) hydrogen bonds : angle 4.36982 / 3.20 ( 987) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: A 26 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7907 (mtmm) REVERT: A 208 ARG cc_start: 0.8265 (tpt-90) cc_final: 0.7528 (tpm-80) REVERT: A 339 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7801 (mmt180) REVERT: C 341 ARG cc_start: 0.8059 (ptt-90) cc_final: 0.7665 (ptm-80) REVERT: C 342 VAL cc_start: 0.8812 (p) cc_final: 0.8610 (t) outliers start: 19 outliers final: 12 residues processed: 89 average time/residue: 0.5680 time to fit residues: 52.6058 Evaluate side-chains 93 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 358 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 37 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 69 optimal weight: 0.0870 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 = 0.3512 r_free = 0.3512 target = 0.143618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.118203 restraints weight = 7022.233| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.30 r_work: 0.3094 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6171 Z= 0.185 Angle : 0.599 6.912 8384 Z= 0.293 Chirality : 0.048 0.255 986 Planarity : 0.004 0.038 1018 Dihedral : 13.056 138.330 1031 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.31 % Allowed : 12.15 % Favored : 84.54 % 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: 0.64 (0.30), residues: 736 helix: 1.02 (0.24), residues: 478 sheet: -1.03 (0.66), residues: 42 loop : -0.43 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 96 TYR 0.016 0.002 TYR C 69 PHE 0.015 0.002 PHE C 169 TRP 0.006 0.001 TRP C 123 HIS 0.003 0.001 HIS C 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.18 ( 6171) covalent geometry : angle 0.59942 / 0.29 ( 8384) hydrogen bonds : bond 0.04418 / 2.97 ( 338) hydrogen bonds : angle 4.37181 / 3.20 ( 987) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.134 Fit side-chains revert: symmetry clash REVERT: A 208 ARG cc_start: 0.8244 (tpt-90) cc_final: 0.7495 (tpm-80) REVERT: A 339 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7757 (mmt180) REVERT: C 341 ARG cc_start: 0.8061 (ptt-90) cc_final: 0.7654 (ptm-80) REVERT: C 363 LYS cc_start: 0.7671 (mmtt) cc_final: 0.6982 (mtpm) outliers start: 21 outliers final: 13 residues processed: 95 average time/residue: 0.5378 time to fit residues: 53.2108 Evaluate side-chains 96 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 358 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 70 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 29 optimal weight: 0.3980 chunk 19 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3499 r_free = 0.3499 target = 0.142479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.116909 restraints weight = 6954.966| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.28 r_work: 0.3066 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6171 Z= 0.220 Angle : 0.641 6.986 8384 Z= 0.313 Chirality : 0.051 0.269 986 Planarity : 0.004 0.041 1018 Dihedral : 13.108 139.726 1031 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.15 % Allowed : 12.93 % Favored : 83.91 % 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: 0.46 (0.30), residues: 736 helix: 0.89 (0.24), residues: 478 sheet: -1.11 (0.67), residues: 42 loop : -0.52 (0.39), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 96 TYR 0.017 0.002 TYR C 69 PHE 0.017 0.002 PHE C 169 TRP 0.008 0.001 TRP C 123 HIS 0.002 0.001 HIS C 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.22 ( 6171) covalent geometry : angle 0.64143 / 0.31 ( 8384) hydrogen bonds : bond 0.04688 / 3.15 ( 338) hydrogen bonds : angle 4.46240 / 3.27 ( 987) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.177 Fit side-chains revert: symmetry clash REVERT: A 53 TYR cc_start: 0.6703 (OUTLIER) cc_final: 0.5107 (p90) REVERT: A 105 ASN cc_start: 0.8493 (t0) cc_final: 0.8282 (t0) REVERT: A 208 ARG cc_start: 0.8241 (tpt-90) cc_final: 0.7489 (tpm-80) REVERT: A 339 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7762 (mmt180) REVERT: C 283 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7831 (pptt) REVERT: C 341 ARG cc_start: 0.8085 (ptt-90) cc_final: 0.7672 (ptm-80) REVERT: C 363 LYS cc_start: 0.7703 (mmtt) cc_final: 0.7077 (mtpt) outliers start: 20 outliers final: 13 residues processed: 91 average time/residue: 0.4908 time to fit residues: 46.6388 Evaluate side-chains 94 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 283 LYS Chi-restraints excluded: chain C residue 358 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 2 optimal weight: 0.0270 chunk 26 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 150 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.143347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.117959 restraints weight = 6959.478| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.38 r_work: 0.3083 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6171 Z= 0.182 Angle : 0.608 7.060 8384 Z= 0.297 Chirality : 0.048 0.259 986 Planarity : 0.004 0.045 1018 Dihedral : 13.050 138.216 1031 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.47 % Allowed : 12.93 % Favored : 83.60 % 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: 0.61 (0.30), residues: 736 helix: 0.99 (0.24), residues: 480 sheet: -1.07 (0.67), residues: 42 loop : -0.44 (0.40), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 96 TYR 0.015 0.002 TYR C 69 PHE 0.015 0.002 PHE C 169 TRP 0.007 0.001 TRP C 123 HIS 0.002 0.001 HIS C 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.18 ( 6171) covalent geometry : angle 0.60843 / 0.30 ( 8384) hydrogen bonds : bond 0.04387 / 2.94 ( 338) hydrogen bonds : angle 4.36180 / 3.20 ( 987) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 0.191 Fit side-chains revert: symmetry clash REVERT: A 53 TYR cc_start: 0.6698 (OUTLIER) cc_final: 0.5317 (p90) REVERT: A 105 ASN cc_start: 0.8452 (t0) cc_final: 0.8180 (t0) REVERT: A 208 ARG cc_start: 0.8223 (tpt-90) cc_final: 0.7470 (tpm-80) REVERT: A 339 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7748 (mmt180) REVERT: C 283 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7871 (pptt) REVERT: C 341 ARG cc_start: 0.8040 (ptt-90) cc_final: 0.7631 (ptm-80) REVERT: C 363 LYS cc_start: 0.7691 (mmtt) cc_final: 0.7013 (mtpt) outliers start: 22 outliers final: 15 residues processed: 90 average time/residue: 0.5189 time to fit residues: 48.7176 Evaluate side-chains 96 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 283 LYS Chi-restraints excluded: chain C residue 358 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 0 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 8 optimal weight: 0.0970 chunk 21 optimal weight: 0.9990 chunk 6 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 = 0.3504 r_free = 0.3504 target = 0.142848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.116809 restraints weight = 6986.276| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.40 r_work: 0.3066 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6171 Z= 0.206 Angle : 0.630 6.994 8384 Z= 0.307 Chirality : 0.050 0.268 986 Planarity : 0.004 0.051 1018 Dihedral : 13.085 139.218 1031 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.47 % Allowed : 14.20 % Favored : 82.33 % 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: 0.51 (0.30), residues: 736 helix: 0.91 (0.24), residues: 480 sheet: -1.05 (0.68), residues: 42 loop : -0.46 (0.40), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 96 TYR 0.017 0.002 TYR C 69 PHE 0.016 0.002 PHE C 169 TRP 0.007 0.001 TRP C 123 HIS 0.002 0.001 HIS A 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.21 ( 6171) covalent geometry : angle 0.62975 / 0.31 ( 8384) hydrogen bonds : bond 0.04582 / 3.07 ( 338) hydrogen bonds : angle 4.41966 / 3.24 ( 987) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: A 53 TYR cc_start: 0.6788 (OUTLIER) cc_final: 0.5180 (p90) REVERT: A 105 ASN cc_start: 0.8399 (t0) cc_final: 0.8113 (t0) REVERT: A 208 ARG cc_start: 0.8266 (tpt-90) cc_final: 0.7505 (tpm-80) REVERT: A 339 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7776 (mmt180) REVERT: C 283 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7872 (pptt) REVERT: C 341 ARG cc_start: 0.8096 (ptt-90) cc_final: 0.7664 (ptm-80) REVERT: C 363 LYS cc_start: 0.7722 (mmtt) cc_final: 0.7057 (mtpm) outliers start: 22 outliers final: 15 residues processed: 97 average time/residue: 0.5986 time to fit residues: 60.5584 Evaluate side-chains 98 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 283 LYS Chi-restraints excluded: chain C residue 358 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 68 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 56 optimal weight: 0.4980 chunk 20 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 365 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.142534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.116983 restraints weight = 6996.136| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.34 r_work: 0.3049 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6171 Z= 0.212 Angle : 0.645 7.825 8384 Z= 0.314 Chirality : 0.050 0.269 986 Planarity : 0.004 0.054 1018 Dihedral : 13.091 139.401 1031 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.00 % Allowed : 15.14 % Favored : 81.86 % 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: 0.51 (0.30), residues: 736 helix: 0.92 (0.24), residues: 478 sheet: -1.05 (0.68), residues: 42 loop : -0.48 (0.39), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 96 TYR 0.017 0.002 TYR C 69 PHE 0.016 0.002 PHE C 169 TRP 0.007 0.001 TRP C 123 HIS 0.002 0.001 HIS A 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.21 ( 6171) covalent geometry : angle 0.64546 / 0.31 ( 8384) hydrogen bonds : bond 0.04611 / 3.09 ( 338) hydrogen bonds : angle 4.43053 / 3.25 ( 987) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: A 53 TYR cc_start: 0.6938 (OUTLIER) cc_final: 0.5346 (p90) REVERT: A 105 ASN cc_start: 0.8456 (t0) cc_final: 0.8165 (t0) REVERT: A 208 ARG cc_start: 0.8281 (tpt-90) cc_final: 0.7520 (tpm-80) REVERT: A 339 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7775 (mmt180) REVERT: C 283 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7924 (pptt) REVERT: C 341 ARG cc_start: 0.8076 (ptt-90) cc_final: 0.7662 (ptm-80) REVERT: C 363 LYS cc_start: 0.7733 (mmtt) cc_final: 0.7100 (mtpt) outliers start: 19 outliers final: 14 residues processed: 89 average time/residue: 0.4819 time to fit residues: 44.7602 Evaluate side-chains 97 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 283 LYS Chi-restraints excluded: chain C residue 358 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 6 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 57 optimal weight: 0.4980 chunk 33 optimal weight: 0.2980 chunk 54 optimal weight: 0.6980 chunk 20 optimal weight: 0.1980 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 0.0770 chunk 61 optimal weight: 0.5980 chunk 5 optimal weight: 0.2980 chunk 49 optimal weight: 0.6980 overall best weight: 0.2738 ------------------------------------------------------------------------------- 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 = 0.3539 r_free = 0.3539 target = 0.146103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.120023 restraints weight = 6958.761| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.54 r_work: 0.3123 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6171 Z= 0.128 Angle : 0.566 8.014 8384 Z= 0.274 Chirality : 0.046 0.265 986 Planarity : 0.004 0.056 1018 Dihedral : 12.924 134.244 1031 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.21 % Allowed : 15.93 % Favored : 81.86 % 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: 0.99 (0.31), residues: 736 helix: 1.29 (0.24), residues: 480 sheet: -0.94 (0.68), residues: 42 loop : -0.31 (0.41), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 96 TYR 0.013 0.001 TYR A 354 PHE 0.011 0.001 PHE C 169 TRP 0.006 0.001 TRP C 123 HIS 0.002 0.001 HIS A 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 6171) covalent geometry : angle 0.56605 / 0.27 ( 8384) hydrogen bonds : bond 0.03827 / 2.54 ( 338) hydrogen bonds : angle 4.17357 / 3.06 ( 987) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: A 208 ARG cc_start: 0.8224 (tpt-90) cc_final: 0.7472 (tpm-80) REVERT: A 339 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7729 (mmt180) REVERT: C 341 ARG cc_start: 0.7970 (ptt-90) cc_final: 0.7573 (ptm-80) REVERT: C 363 LYS cc_start: 0.7702 (mmtt) cc_final: 0.7100 (mtpt) outliers start: 14 outliers final: 10 residues processed: 84 average time/residue: 0.5458 time to fit residues: 47.6908 Evaluate side-chains 86 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain C residue 358 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 13 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 66 optimal weight: 0.4980 chunk 1 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 67 optimal weight: 0.4980 chunk 20 optimal weight: 0.1980 chunk 57 optimal weight: 0.1980 chunk 47 optimal weight: 2.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.144996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.119933 restraints weight = 7000.681| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.34 r_work: 0.3093 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6171 Z= 0.155 Angle : 0.594 8.717 8384 Z= 0.290 Chirality : 0.047 0.257 986 Planarity : 0.004 0.059 1018 Dihedral : 12.961 135.804 1031 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.05 % Allowed : 15.62 % Favored : 82.33 % 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: 0.97 (0.30), residues: 736 helix: 1.26 (0.24), residues: 480 sheet: -0.76 (0.70), residues: 42 loop : -0.32 (0.41), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 96 TYR 0.015 0.002 TYR A 354 PHE 0.013 0.002 PHE C 169 TRP 0.007 0.001 TRP C 123 HIS 0.002 0.001 HIS C 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 ( 6171) covalent geometry : angle 0.59387 / 0.29 ( 8384) hydrogen bonds : bond 0.04100 / 2.73 ( 338) hydrogen bonds : angle 4.20309 / 3.08 ( 987) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1996.80 seconds wall clock time: 34 minutes 38.85 seconds (2078.85 seconds total)