Starting phenix.real_space_refine on Wed Feb 4 06:33:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e03_47347/02_2026/9e03_47347.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e03_47347/02_2026/9e03_47347.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9e03_47347/02_2026/9e03_47347.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e03_47347/02_2026/9e03_47347.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e03_47347/02_2026/9e03_47347.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e03_47347/02_2026/9e03_47347.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 5889 2.51 5 N 1545 2.21 5 O 1596 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9072 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2900 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 15, 'TRANS': 361} Chain breaks: 1 Chain: "B" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 124 Classifications: {'peptide': 18} Link IDs: {'PTRANS': 1, 'TRANS': 16} Restraints were copied for chains: E, C, F, D Time building chain proxies: 1.50, per 1000 atoms: 0.17 Number of scatterers: 9072 At special positions: 0 Unit cell: (98.176, 106.496, 112.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 1596 8.00 N 1545 7.00 C 5889 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: 0.62 Conformation dependent library (CDL) restraints added in 286.9 milliseconds 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2196 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 3 sheets defined 89.9% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 7 through 29 Processing helix chain 'A' and resid 31 through 47 Proline residue: A 42 - end of helix Processing helix chain 'A' and resid 48 through 52 removed outlier: 3.639A pdb=" N ARG A 52 " --> pdb=" O PRO A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 78 Processing helix chain 'A' and resid 78 through 90 Processing helix chain 'A' and resid 102 through 133 Proline residue: A 126 - end of helix Processing helix chain 'A' and resid 137 through 161 Processing helix chain 'A' and resid 163 through 181 Processing helix chain 'A' and resid 194 through 218 Processing helix chain 'A' and resid 221 through 241 removed outlier: 3.540A pdb=" N LEU A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG A 226 " --> pdb=" O ARG A 222 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN A 227 " --> pdb=" O GLY A 223 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 241 " --> pdb=" O THR A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 259 Processing helix chain 'A' and resid 260 through 264 Proline residue: A 263 - end of helix No H-bonds generated for 'chain 'A' and resid 260 through 264' Processing helix chain 'A' and resid 265 through 290 Processing helix chain 'A' and resid 297 through 329 Proline residue: A 319 - end of helix removed outlier: 3.670A pdb=" N VAL A 328 " --> pdb=" O LEU A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 339 Processing helix chain 'A' and resid 339 through 355 Processing helix chain 'A' and resid 359 through 392 Proline residue: A 369 - end of helix Processing helix chain 'B' and resid 6 through 21 removed outlier: 3.873A pdb=" N LEU B 20 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 21 removed outlier: 3.872A pdb=" N LEU F 20 " --> pdb=" O ALA F 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 21 removed outlier: 3.873A pdb=" N LEU D 20 " --> pdb=" O ALA D 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 29 Processing helix chain 'E' and resid 31 through 47 Proline residue: E 42 - end of helix Processing helix chain 'E' and resid 48 through 52 removed outlier: 3.639A pdb=" N ARG E 52 " --> pdb=" O PRO E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 78 Processing helix chain 'E' and resid 78 through 90 Processing helix chain 'E' and resid 102 through 133 Proline residue: E 126 - end of helix Processing helix chain 'E' and resid 137 through 161 Processing helix chain 'E' and resid 163 through 181 Processing helix chain 'E' and resid 194 through 218 Processing helix chain 'E' and resid 221 through 241 removed outlier: 3.539A pdb=" N LEU E 225 " --> pdb=" O SER E 221 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG E 226 " --> pdb=" O ARG E 222 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN E 227 " --> pdb=" O GLY E 223 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS E 241 " --> pdb=" O THR E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 259 Processing helix chain 'E' and resid 260 through 264 Proline residue: E 263 - end of helix No H-bonds generated for 'chain 'E' and resid 260 through 264' Processing helix chain 'E' and resid 265 through 290 Processing helix chain 'E' and resid 297 through 329 Proline residue: E 319 - end of helix removed outlier: 3.670A pdb=" N VAL E 328 " --> pdb=" O LEU E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 339 Processing helix chain 'E' and resid 339 through 355 Processing helix chain 'E' and resid 359 through 392 Proline residue: E 369 - end of helix Processing helix chain 'C' and resid 7 through 29 Processing helix chain 'C' and resid 31 through 47 Proline residue: C 42 - end of helix Processing helix chain 'C' and resid 48 through 52 removed outlier: 3.639A pdb=" N ARG C 52 " --> pdb=" O PRO C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 78 Processing helix chain 'C' and resid 78 through 90 Processing helix chain 'C' and resid 102 through 133 Proline residue: C 126 - end of helix Processing helix chain 'C' and resid 137 through 161 Processing helix chain 'C' and resid 163 through 181 Processing helix chain 'C' and resid 194 through 218 Processing helix chain 'C' and resid 221 through 241 removed outlier: 3.539A pdb=" N LEU C 225 " --> pdb=" O SER C 221 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG C 226 " --> pdb=" O ARG C 222 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN C 227 " --> pdb=" O GLY C 223 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS C 241 " --> pdb=" O THR C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 259 Processing helix chain 'C' and resid 260 through 264 Proline residue: C 263 - end of helix No H-bonds generated for 'chain 'C' and resid 260 through 264' Processing helix chain 'C' and resid 265 through 290 Processing helix chain 'C' and resid 297 through 329 Proline residue: C 319 - end of helix removed outlier: 3.670A pdb=" N VAL C 328 " --> pdb=" O LEU C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 339 Processing helix chain 'C' and resid 339 through 355 Processing helix chain 'C' and resid 359 through 392 Proline residue: C 369 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 56 removed outlier: 6.366A pdb=" N LEU A 54 " --> pdb=" O ARG C 293 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 292 through 294 Processing sheet with id=AA3, first strand: chain 'E' and resid 292 through 294 796 hydrogen bonds defined for protein. 2379 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: 1.13 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2948 1.34 - 1.46: 1602 1.46 - 1.57: 4603 1.57 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 9237 Sorted by residual: bond pdb=" CG LEU C 308 " pdb=" CD1 LEU C 308 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.17e+00 bond pdb=" CG LEU A 308 " pdb=" CD1 LEU A 308 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.17e+00 bond pdb=" CG LEU E 308 " pdb=" CD1 LEU E 308 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.17e+00 bond pdb=" CB LEU E 308 " pdb=" CG LEU E 308 " ideal model delta sigma weight residual 1.530 1.514 0.016 2.00e-02 2.50e+03 6.02e-01 bond pdb=" CB LEU C 308 " pdb=" CG LEU C 308 " ideal model delta sigma weight residual 1.530 1.515 0.015 2.00e-02 2.50e+03 5.75e-01 ... (remaining 9232 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.06: 11978 1.06 - 2.12: 411 2.12 - 3.19: 82 3.19 - 4.25: 38 4.25 - 5.31: 19 Bond angle restraints: 12528 Sorted by residual: angle pdb=" N PRO E 92 " pdb=" CA PRO E 92 " pdb=" C PRO E 92 " ideal model delta sigma weight residual 114.68 111.53 3.15 1.04e+00 9.25e-01 9.17e+00 angle pdb=" N PRO C 92 " pdb=" CA PRO C 92 " pdb=" C PRO C 92 " ideal model delta sigma weight residual 114.68 111.55 3.13 1.04e+00 9.25e-01 9.06e+00 angle pdb=" N PRO A 92 " pdb=" CA PRO A 92 " pdb=" C PRO A 92 " ideal model delta sigma weight residual 114.68 111.56 3.12 1.04e+00 9.25e-01 8.98e+00 angle pdb=" CA PRO A 92 " pdb=" C PRO A 92 " pdb=" O PRO A 92 " ideal model delta sigma weight residual 118.92 121.15 -2.23 1.14e+00 7.69e-01 3.84e+00 angle pdb=" CA TYR E 56 " pdb=" CB TYR E 56 " pdb=" CG TYR E 56 " ideal model delta sigma weight residual 113.90 117.38 -3.48 1.80e+00 3.09e-01 3.73e+00 ... (remaining 12523 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 4648 17.72 - 35.45: 632 35.45 - 53.17: 210 53.17 - 70.89: 36 70.89 - 88.62: 12 Dihedral angle restraints: 5538 sinusoidal: 2142 harmonic: 3396 Sorted by residual: dihedral pdb=" CA TYR C 95 " pdb=" C TYR C 95 " pdb=" N PRO C 96 " pdb=" CA PRO C 96 " ideal model delta harmonic sigma weight residual -180.00 -156.95 -23.05 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA TYR A 95 " pdb=" C TYR A 95 " pdb=" N PRO A 96 " pdb=" CA PRO A 96 " ideal model delta harmonic sigma weight residual 180.00 -156.96 -23.04 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA TYR E 95 " pdb=" C TYR E 95 " pdb=" N PRO E 96 " pdb=" CA PRO E 96 " ideal model delta harmonic sigma weight residual -180.00 -156.99 -23.01 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 5535 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1022 0.030 - 0.060: 359 0.060 - 0.090: 71 0.090 - 0.120: 41 0.120 - 0.150: 7 Chirality restraints: 1500 Sorted by residual: chirality pdb=" CB ILE D 19 " pdb=" CA ILE D 19 " pdb=" CG1 ILE D 19 " pdb=" CG2 ILE D 19 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.65e-01 chirality pdb=" CB ILE B 19 " pdb=" CA ILE B 19 " pdb=" CG1 ILE B 19 " pdb=" CG2 ILE B 19 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" CA PRO E 96 " pdb=" N PRO E 96 " pdb=" C PRO E 96 " pdb=" CB PRO E 96 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.38e-01 ... (remaining 1497 not shown) Planarity restraints: 1572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR C 121 " -0.014 2.00e-02 2.50e+03 2.83e-02 7.99e+00 pdb=" C TYR C 121 " 0.049 2.00e-02 2.50e+03 pdb=" O TYR C 121 " -0.018 2.00e-02 2.50e+03 pdb=" N PHE C 122 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR E 121 " -0.014 2.00e-02 2.50e+03 2.82e-02 7.96e+00 pdb=" C TYR E 121 " 0.049 2.00e-02 2.50e+03 pdb=" O TYR E 121 " -0.018 2.00e-02 2.50e+03 pdb=" N PHE E 122 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 121 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.92e+00 pdb=" C TYR A 121 " -0.049 2.00e-02 2.50e+03 pdb=" O TYR A 121 " 0.018 2.00e-02 2.50e+03 pdb=" N PHE A 122 " 0.016 2.00e-02 2.50e+03 ... (remaining 1569 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1955 2.78 - 3.31: 9298 3.31 - 3.84: 15587 3.84 - 4.37: 16652 4.37 - 4.90: 29861 Nonbonded interactions: 73353 Sorted by model distance: nonbonded pdb=" OE2 GLU E 61 " pdb=" ND1 HIS E 299 " model vdw 2.250 3.120 nonbonded pdb=" OE2 GLU A 61 " pdb=" ND1 HIS A 299 " model vdw 2.250 3.120 nonbonded pdb=" OE2 GLU C 61 " pdb=" ND1 HIS C 299 " model vdw 2.250 3.120 nonbonded pdb=" O LEU E 24 " pdb=" OG SER E 28 " model vdw 2.281 3.040 nonbonded pdb=" O LEU C 24 " pdb=" OG SER C 28 " model vdw 2.281 3.040 ... (remaining 73348 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'F' 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: 2.340 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: 0.020 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.820 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9237 Z= 0.141 Angle : 0.527 5.312 12528 Z= 0.282 Chirality : 0.035 0.150 1500 Planarity : 0.006 0.064 1572 Dihedral : 18.436 88.617 3342 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.30 % Allowed : 27.92 % Favored : 70.78 % 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: 2.30 (0.26), residues: 1167 helix: 2.21 (0.17), residues: 1020 sheet: None (None), residues: 0 loop : -3.70 (0.34), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 169 TYR 0.019 0.002 TYR A 56 PHE 0.010 0.001 PHE A 36 TRP 0.007 0.001 TRP C 87 HIS 0.002 0.001 HIS A 6 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 9237) covalent geometry : angle 0.52691 (12528) hydrogen bonds : bond 0.10861 ( 796) hydrogen bonds : angle 5.43147 ( 2379) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 228 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 MET cc_start: 0.7750 (ttp) cc_final: 0.7521 (ttp) REVERT: A 100 ARG cc_start: 0.7298 (mtm110) cc_final: 0.6926 (mtt90) REVERT: A 287 GLU cc_start: 0.7194 (pp20) cc_final: 0.6882 (pp20) REVERT: E 84 MET cc_start: 0.8039 (mtp) cc_final: 0.7811 (mtp) REVERT: E 97 GLU cc_start: 0.7527 (tp30) cc_final: 0.7291 (tp30) REVERT: E 265 ARG cc_start: 0.8033 (mmt-90) cc_final: 0.7522 (mmt-90) REVERT: E 268 GLU cc_start: 0.7034 (mp0) cc_final: 0.6224 (mp0) REVERT: E 383 MET cc_start: 0.4843 (ttp) cc_final: 0.4596 (ttp) REVERT: C 15 MET cc_start: 0.7680 (ttp) cc_final: 0.7427 (ttp) REVERT: C 40 MET cc_start: 0.8331 (mmp) cc_final: 0.8093 (mmt) REVERT: C 50 GLU cc_start: 0.7607 (tm-30) cc_final: 0.6977 (tm-30) REVERT: C 84 MET cc_start: 0.8003 (mtp) cc_final: 0.7785 (mtp) REVERT: C 287 GLU cc_start: 0.7064 (pp20) cc_final: 0.6702 (pp20) REVERT: C 378 VAL cc_start: 0.7973 (p) cc_final: 0.7704 (t) outliers start: 12 outliers final: 7 residues processed: 236 average time/residue: 0.1337 time to fit residues: 39.9252 Evaluate side-chains 220 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 213 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 295 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 0.3980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.0040 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 ASN E 362 ASN C 362 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.145201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.124642 restraints weight = 12240.638| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.67 r_work: 0.3415 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.0869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9237 Z= 0.147 Angle : 0.529 5.771 12528 Z= 0.272 Chirality : 0.036 0.179 1500 Planarity : 0.005 0.066 1572 Dihedral : 4.409 39.075 1293 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.22 % Allowed : 24.68 % Favored : 71.10 % 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: 2.95 (0.25), residues: 1167 helix: 2.67 (0.16), residues: 1020 sheet: None (None), residues: 0 loop : -3.80 (0.34), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 265 TYR 0.017 0.002 TYR A 56 PHE 0.007 0.001 PHE C 119 TRP 0.008 0.001 TRP A 291 HIS 0.004 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 9237) covalent geometry : angle 0.52950 (12528) hydrogen bonds : bond 0.03916 ( 796) hydrogen bonds : angle 4.17325 ( 2379) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 228 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 15 MET cc_start: 0.7705 (ttp) cc_final: 0.7459 (ttp) REVERT: A 75 ILE cc_start: 0.8420 (tt) cc_final: 0.7923 (pt) REVERT: A 84 MET cc_start: 0.8205 (mtp) cc_final: 0.7984 (mtm) REVERT: A 100 ARG cc_start: 0.7288 (mtm110) cc_final: 0.6843 (mtt90) REVERT: A 128 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7670 (tmm) REVERT: A 220 GLN cc_start: 0.7585 (OUTLIER) cc_final: 0.7277 (pm20) REVERT: A 287 GLU cc_start: 0.7495 (pp20) cc_final: 0.7143 (pp20) REVERT: F 9 MET cc_start: 0.6124 (tpp) cc_final: 0.5795 (tpp) REVERT: E 220 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.7115 (pm20) REVERT: E 378 VAL cc_start: 0.8135 (p) cc_final: 0.7922 (t) REVERT: E 383 MET cc_start: 0.4978 (ttp) cc_final: 0.4717 (ttp) REVERT: C 15 MET cc_start: 0.7737 (ttp) cc_final: 0.7493 (ttp) REVERT: C 40 MET cc_start: 0.8371 (mmp) cc_final: 0.8165 (mmt) REVERT: C 50 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7260 (tm-30) REVERT: C 75 ILE cc_start: 0.8477 (tt) cc_final: 0.8104 (pt) REVERT: C 84 MET cc_start: 0.8051 (mtp) cc_final: 0.7704 (mtp) REVERT: C 220 GLN cc_start: 0.7426 (OUTLIER) cc_final: 0.7160 (pm20) REVERT: C 265 ARG cc_start: 0.8048 (mmt-90) cc_final: 0.7848 (mmt-90) REVERT: C 287 GLU cc_start: 0.7441 (pp20) cc_final: 0.7048 (pp20) REVERT: C 374 TYR cc_start: 0.7260 (t80) cc_final: 0.6941 (t80) REVERT: C 378 VAL cc_start: 0.8073 (p) cc_final: 0.7808 (t) outliers start: 39 outliers final: 18 residues processed: 251 average time/residue: 0.1276 time to fit residues: 41.1341 Evaluate side-chains 244 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 221 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 128 MET Chi-restraints excluded: chain A residue 220 GLN Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 220 GLN Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 295 MET Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 220 GLN Chi-restraints excluded: chain C residue 307 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 26 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 99 optimal weight: 0.0980 chunk 51 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.143288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.123070 restraints weight = 12238.770| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.61 r_work: 0.3391 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9237 Z= 0.169 Angle : 0.550 6.124 12528 Z= 0.282 Chirality : 0.037 0.186 1500 Planarity : 0.005 0.068 1572 Dihedral : 4.138 28.901 1288 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.11 % Allowed : 25.22 % Favored : 70.67 % 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: 2.91 (0.25), residues: 1167 helix: 2.58 (0.16), residues: 1029 sheet: None (None), residues: 0 loop : -3.67 (0.35), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 100 TYR 0.026 0.002 TYR C 56 PHE 0.010 0.001 PHE C 119 TRP 0.008 0.001 TRP E 87 HIS 0.004 0.001 HIS E 283 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 9237) covalent geometry : angle 0.55009 (12528) hydrogen bonds : bond 0.03857 ( 796) hydrogen bonds : angle 4.21219 ( 2379) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 221 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 15 MET cc_start: 0.7825 (ttp) cc_final: 0.7590 (ttp) REVERT: A 61 GLU cc_start: 0.7199 (tt0) cc_final: 0.6868 (tt0) REVERT: A 84 MET cc_start: 0.8238 (mtp) cc_final: 0.8007 (mtm) REVERT: A 100 ARG cc_start: 0.7324 (mtm110) cc_final: 0.6909 (mtt90) REVERT: A 165 GLU cc_start: 0.7098 (mt-10) cc_final: 0.6768 (mt-10) REVERT: A 220 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.7278 (pm20) REVERT: A 265 ARG cc_start: 0.8189 (mmt-90) cc_final: 0.7796 (mpt180) REVERT: A 287 GLU cc_start: 0.7542 (pp20) cc_final: 0.7200 (pp20) REVERT: A 376 LEU cc_start: 0.7006 (OUTLIER) cc_final: 0.6771 (mm) REVERT: F 9 MET cc_start: 0.6130 (tpp) cc_final: 0.5799 (tpp) REVERT: E 75 ILE cc_start: 0.8341 (tt) cc_final: 0.8033 (pt) REVERT: E 97 GLU cc_start: 0.7523 (tp30) cc_final: 0.7266 (tp30) REVERT: E 220 GLN cc_start: 0.7432 (OUTLIER) cc_final: 0.7097 (pm20) REVERT: E 242 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7632 (mtpp) REVERT: E 287 GLU cc_start: 0.7285 (pp20) cc_final: 0.6871 (pp20) REVERT: E 374 TYR cc_start: 0.7251 (t80) cc_final: 0.6977 (t80) REVERT: E 383 MET cc_start: 0.5001 (ttp) cc_final: 0.4776 (ttp) REVERT: C 15 MET cc_start: 0.7780 (ttp) cc_final: 0.7530 (ttp) REVERT: C 50 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7210 (tm-30) REVERT: C 61 GLU cc_start: 0.7342 (tt0) cc_final: 0.7035 (tt0) REVERT: C 75 ILE cc_start: 0.8454 (tt) cc_final: 0.8136 (pt) REVERT: C 84 MET cc_start: 0.8099 (mtp) cc_final: 0.7803 (mtp) REVERT: C 106 VAL cc_start: 0.8216 (t) cc_final: 0.7996 (m) REVERT: C 220 GLN cc_start: 0.7378 (OUTLIER) cc_final: 0.7092 (pm20) REVERT: C 265 ARG cc_start: 0.8137 (mmt-90) cc_final: 0.7782 (mpt180) REVERT: C 287 GLU cc_start: 0.7538 (pp20) cc_final: 0.7132 (pp20) REVERT: C 374 TYR cc_start: 0.7381 (t80) cc_final: 0.7050 (t80) REVERT: C 378 VAL cc_start: 0.8163 (p) cc_final: 0.7903 (t) outliers start: 38 outliers final: 22 residues processed: 239 average time/residue: 0.1357 time to fit residues: 41.1295 Evaluate side-chains 243 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 216 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 220 GLN Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 220 GLN Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 295 MET Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 220 GLN Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 307 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 82 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 17 optimal weight: 0.0000 chunk 91 optimal weight: 0.7980 chunk 31 optimal weight: 0.0770 chunk 90 optimal weight: 1.9990 overall best weight: 0.5142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.143541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.123265 restraints weight = 12308.848| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.62 r_work: 0.3397 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9237 Z= 0.140 Angle : 0.534 8.487 12528 Z= 0.270 Chirality : 0.036 0.185 1500 Planarity : 0.005 0.067 1572 Dihedral : 4.150 28.704 1288 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.33 % Allowed : 24.78 % Favored : 70.89 % 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: 2.95 (0.25), residues: 1167 helix: 2.61 (0.16), residues: 1029 sheet: None (None), residues: 0 loop : -3.65 (0.35), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 11 TYR 0.024 0.002 TYR C 56 PHE 0.010 0.001 PHE A 119 TRP 0.007 0.001 TRP E 87 HIS 0.004 0.001 HIS C 299 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 9237) covalent geometry : angle 0.53366 (12528) hydrogen bonds : bond 0.03582 ( 796) hydrogen bonds : angle 4.14802 ( 2379) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 217 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: A 15 MET cc_start: 0.7837 (ttp) cc_final: 0.7619 (ttp) REVERT: A 61 GLU cc_start: 0.7195 (tt0) cc_final: 0.6863 (tt0) REVERT: A 75 ILE cc_start: 0.8396 (tt) cc_final: 0.8020 (pt) REVERT: A 84 MET cc_start: 0.8217 (mtp) cc_final: 0.7995 (mtm) REVERT: A 165 GLU cc_start: 0.7119 (mt-10) cc_final: 0.6772 (mt-10) REVERT: A 220 GLN cc_start: 0.7566 (OUTLIER) cc_final: 0.7290 (pm20) REVERT: A 265 ARG cc_start: 0.8175 (mmt-90) cc_final: 0.7742 (mpt180) REVERT: A 287 GLU cc_start: 0.7529 (pp20) cc_final: 0.7191 (pp20) REVERT: A 376 LEU cc_start: 0.6955 (OUTLIER) cc_final: 0.6711 (mm) REVERT: F 9 MET cc_start: 0.6107 (tpp) cc_final: 0.5800 (tpp) REVERT: E 75 ILE cc_start: 0.8352 (tt) cc_final: 0.7987 (pt) REVERT: E 135 GLU cc_start: 0.6563 (OUTLIER) cc_final: 0.6301 (mt-10) REVERT: E 220 GLN cc_start: 0.7452 (OUTLIER) cc_final: 0.7115 (pm20) REVERT: E 242 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7597 (mtpp) REVERT: E 287 GLU cc_start: 0.7306 (pp20) cc_final: 0.6892 (pp20) REVERT: E 374 TYR cc_start: 0.7254 (t80) cc_final: 0.6961 (t80) REVERT: C 15 MET cc_start: 0.7839 (ttp) cc_final: 0.7609 (ttp) REVERT: C 50 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7211 (tm-30) REVERT: C 75 ILE cc_start: 0.8495 (tt) cc_final: 0.8115 (pt) REVERT: C 84 MET cc_start: 0.8084 (mtp) cc_final: 0.7776 (mtp) REVERT: C 106 VAL cc_start: 0.8221 (t) cc_final: 0.7997 (m) REVERT: C 142 GLU cc_start: 0.7496 (tt0) cc_final: 0.7269 (tt0) REVERT: C 220 GLN cc_start: 0.7404 (OUTLIER) cc_final: 0.7112 (pm20) REVERT: C 265 ARG cc_start: 0.8149 (mmt-90) cc_final: 0.7860 (mmt-90) REVERT: C 287 GLU cc_start: 0.7550 (pp20) cc_final: 0.7131 (pp20) REVERT: C 374 TYR cc_start: 0.7355 (t80) cc_final: 0.7048 (t80) REVERT: C 378 VAL cc_start: 0.8094 (p) cc_final: 0.7837 (t) outliers start: 40 outliers final: 28 residues processed: 237 average time/residue: 0.1258 time to fit residues: 38.2789 Evaluate side-chains 250 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 215 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 220 GLN Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 135 GLU Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 220 GLN Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 295 MET Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 220 GLN Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 376 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 26 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 67 optimal weight: 0.0010 chunk 104 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.142985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.122718 restraints weight = 12259.724| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.62 r_work: 0.3394 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9237 Z= 0.158 Angle : 0.531 6.697 12528 Z= 0.271 Chirality : 0.037 0.185 1500 Planarity : 0.005 0.067 1572 Dihedral : 4.168 28.687 1288 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.76 % Allowed : 25.43 % Favored : 69.81 % 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: 2.93 (0.25), residues: 1167 helix: 2.60 (0.16), residues: 1023 sheet: None (None), residues: 0 loop : -3.41 (0.36), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 265 TYR 0.023 0.002 TYR C 56 PHE 0.010 0.001 PHE A 129 TRP 0.007 0.001 TRP E 87 HIS 0.003 0.001 HIS E 299 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 9237) covalent geometry : angle 0.53103 (12528) hydrogen bonds : bond 0.03630 ( 796) hydrogen bonds : angle 4.16051 ( 2379) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 220 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 15 MET cc_start: 0.7809 (ttp) cc_final: 0.7575 (ttp) REVERT: A 61 GLU cc_start: 0.7177 (tt0) cc_final: 0.6842 (tt0) REVERT: A 75 ILE cc_start: 0.8376 (tt) cc_final: 0.8007 (pt) REVERT: A 165 GLU cc_start: 0.7084 (mt-10) cc_final: 0.6693 (mt-10) REVERT: A 220 GLN cc_start: 0.7535 (OUTLIER) cc_final: 0.7259 (pm20) REVERT: A 265 ARG cc_start: 0.8198 (mmt-90) cc_final: 0.7769 (mpt180) REVERT: A 287 GLU cc_start: 0.7538 (pp20) cc_final: 0.7242 (pp20) REVERT: A 293 ARG cc_start: 0.8273 (mmt90) cc_final: 0.7999 (mpt180) REVERT: F 9 MET cc_start: 0.6123 (tpp) cc_final: 0.5815 (tpp) REVERT: E 132 LEU cc_start: 0.8372 (mt) cc_final: 0.8078 (mt) REVERT: E 135 GLU cc_start: 0.6545 (OUTLIER) cc_final: 0.6315 (mt-10) REVERT: E 220 GLN cc_start: 0.7353 (OUTLIER) cc_final: 0.7015 (pm20) REVERT: E 242 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7608 (mtpp) REVERT: E 287 GLU cc_start: 0.7352 (pp20) cc_final: 0.6944 (pp20) REVERT: E 374 TYR cc_start: 0.7311 (t80) cc_final: 0.7024 (t80) REVERT: C 15 MET cc_start: 0.7815 (ttp) cc_final: 0.7562 (ttp) REVERT: C 50 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7219 (tm-30) REVERT: C 106 VAL cc_start: 0.8184 (t) cc_final: 0.7959 (m) REVERT: C 128 MET cc_start: 0.8090 (ppp) cc_final: 0.7806 (ttp) REVERT: C 142 GLU cc_start: 0.7456 (tt0) cc_final: 0.7237 (tt0) REVERT: C 220 GLN cc_start: 0.7409 (OUTLIER) cc_final: 0.7107 (pm20) REVERT: C 226 ARG cc_start: 0.7881 (ttm-80) cc_final: 0.7614 (ttt90) REVERT: C 265 ARG cc_start: 0.8173 (mmt-90) cc_final: 0.7760 (mmt-90) REVERT: C 287 GLU cc_start: 0.7565 (pp20) cc_final: 0.7145 (pp20) REVERT: C 374 TYR cc_start: 0.7356 (t80) cc_final: 0.7066 (t80) REVERT: C 378 VAL cc_start: 0.8111 (p) cc_final: 0.7858 (t) outliers start: 44 outliers final: 30 residues processed: 241 average time/residue: 0.1302 time to fit residues: 40.1837 Evaluate side-chains 251 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 215 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 220 GLN Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 135 GLU Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 220 GLN Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 295 MET Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain E residue 370 MET Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 220 GLN Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 376 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 92 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 47 optimal weight: 0.0060 chunk 6 optimal weight: 0.5980 chunk 39 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 56 optimal weight: 0.7980 chunk 97 optimal weight: 0.1980 chunk 8 optimal weight: 1.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.144034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.123866 restraints weight = 12270.489| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.61 r_work: 0.3408 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9237 Z= 0.128 Angle : 0.509 7.093 12528 Z= 0.259 Chirality : 0.035 0.186 1500 Planarity : 0.005 0.066 1572 Dihedral : 4.132 28.192 1288 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.22 % Allowed : 26.08 % Favored : 69.70 % 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: 3.06 (0.25), residues: 1167 helix: 2.68 (0.16), residues: 1023 sheet: None (None), residues: 0 loop : -3.31 (0.37), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 265 TYR 0.020 0.002 TYR C 56 PHE 0.012 0.001 PHE E 119 TRP 0.006 0.001 TRP A 87 HIS 0.003 0.001 HIS E 299 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 9237) covalent geometry : angle 0.50864 (12528) hydrogen bonds : bond 0.03336 ( 796) hydrogen bonds : angle 4.10087 ( 2379) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 215 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 MET cc_start: 0.7746 (ttp) cc_final: 0.7502 (ttp) REVERT: A 61 GLU cc_start: 0.7172 (tt0) cc_final: 0.6832 (tt0) REVERT: A 75 ILE cc_start: 0.8365 (tt) cc_final: 0.7963 (pt) REVERT: A 84 MET cc_start: 0.8169 (mtm) cc_final: 0.7920 (mtm) REVERT: A 91 SER cc_start: 0.7690 (OUTLIER) cc_final: 0.7132 (m) REVERT: A 100 ARG cc_start: 0.7284 (mtm110) cc_final: 0.6822 (mtt90) REVERT: A 151 ARG cc_start: 0.8121 (mmm160) cc_final: 0.7803 (mmt180) REVERT: A 165 GLU cc_start: 0.7034 (mt-10) cc_final: 0.6670 (mt-10) REVERT: A 220 GLN cc_start: 0.7532 (OUTLIER) cc_final: 0.7258 (pm20) REVERT: A 265 ARG cc_start: 0.8152 (mmt-90) cc_final: 0.7722 (mpt180) REVERT: A 287 GLU cc_start: 0.7507 (pp20) cc_final: 0.7238 (pp20) REVERT: A 376 LEU cc_start: 0.6963 (mm) cc_final: 0.6724 (mm) REVERT: F 9 MET cc_start: 0.6080 (tpp) cc_final: 0.5782 (tpp) REVERT: E 135 GLU cc_start: 0.6527 (OUTLIER) cc_final: 0.6293 (mt-10) REVERT: E 220 GLN cc_start: 0.7362 (OUTLIER) cc_final: 0.7019 (pm20) REVERT: E 242 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7546 (mtpp) REVERT: E 374 TYR cc_start: 0.7266 (t80) cc_final: 0.7023 (t80) REVERT: C 15 MET cc_start: 0.7781 (ttp) cc_final: 0.7532 (ttp) REVERT: C 50 GLU cc_start: 0.7832 (tm-30) cc_final: 0.7161 (tm-30) REVERT: C 75 ILE cc_start: 0.8374 (tt) cc_final: 0.8149 (pt) REVERT: C 84 MET cc_start: 0.8002 (mtp) cc_final: 0.7682 (mtp) REVERT: C 106 VAL cc_start: 0.8176 (t) cc_final: 0.7941 (m) REVERT: C 128 MET cc_start: 0.8071 (ppp) cc_final: 0.7807 (ttp) REVERT: C 142 GLU cc_start: 0.7420 (tt0) cc_final: 0.7200 (tt0) REVERT: C 220 GLN cc_start: 0.7368 (OUTLIER) cc_final: 0.7080 (pm20) REVERT: C 265 ARG cc_start: 0.8089 (mmt-90) cc_final: 0.7718 (mpt180) REVERT: C 287 GLU cc_start: 0.7581 (pp20) cc_final: 0.7157 (pp20) REVERT: C 374 TYR cc_start: 0.7401 (t80) cc_final: 0.7133 (t80) REVERT: C 378 VAL cc_start: 0.8037 (p) cc_final: 0.7776 (t) outliers start: 39 outliers final: 27 residues processed: 237 average time/residue: 0.1372 time to fit residues: 41.3047 Evaluate side-chains 247 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 214 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 220 GLN Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain E residue 11 ARG Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 135 GLU Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 220 GLN Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 295 MET Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain E residue 370 MET Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 220 GLN Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 376 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 42 optimal weight: 0.3980 chunk 20 optimal weight: 0.0980 chunk 50 optimal weight: 0.0870 chunk 3 optimal weight: 0.2980 chunk 106 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 overall best weight: 0.2958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.144484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.124777 restraints weight = 12335.166| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.57 r_work: 0.3425 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9237 Z= 0.113 Angle : 0.508 8.312 12528 Z= 0.256 Chirality : 0.035 0.188 1500 Planarity : 0.005 0.065 1572 Dihedral : 4.075 27.814 1288 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.22 % Allowed : 26.52 % Favored : 69.26 % 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: 3.09 (0.25), residues: 1167 helix: 2.75 (0.16), residues: 1020 sheet: None (None), residues: 0 loop : -3.57 (0.35), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 226 TYR 0.025 0.002 TYR C 56 PHE 0.010 0.001 PHE C 119 TRP 0.006 0.001 TRP A 87 HIS 0.003 0.001 HIS C 299 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 9237) covalent geometry : angle 0.50825 (12528) hydrogen bonds : bond 0.03158 ( 796) hydrogen bonds : angle 4.03794 ( 2379) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 219 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 MET cc_start: 0.7702 (ttp) cc_final: 0.7476 (ttp) REVERT: A 61 GLU cc_start: 0.7144 (tt0) cc_final: 0.6824 (tt0) REVERT: A 75 ILE cc_start: 0.8379 (tt) cc_final: 0.7979 (pt) REVERT: A 84 MET cc_start: 0.8129 (mtm) cc_final: 0.7903 (mtm) REVERT: A 91 SER cc_start: 0.7723 (OUTLIER) cc_final: 0.7074 (m) REVERT: A 100 ARG cc_start: 0.7255 (mtm110) cc_final: 0.6806 (mtt90) REVERT: A 165 GLU cc_start: 0.6990 (mt-10) cc_final: 0.6628 (mt-10) REVERT: A 220 GLN cc_start: 0.7494 (OUTLIER) cc_final: 0.7235 (pm20) REVERT: A 265 ARG cc_start: 0.8150 (mmt-90) cc_final: 0.7716 (mpt180) REVERT: A 287 GLU cc_start: 0.7491 (pp20) cc_final: 0.7223 (pp20) REVERT: A 296 LEU cc_start: 0.8396 (mt) cc_final: 0.8135 (mt) REVERT: A 376 LEU cc_start: 0.6915 (mm) cc_final: 0.6673 (mm) REVERT: F 9 MET cc_start: 0.6046 (tpp) cc_final: 0.5742 (tpp) REVERT: E 132 LEU cc_start: 0.8224 (mt) cc_final: 0.7979 (mt) REVERT: E 135 GLU cc_start: 0.6503 (OUTLIER) cc_final: 0.6256 (mt-10) REVERT: E 200 THR cc_start: 0.8475 (m) cc_final: 0.8212 (p) REVERT: E 220 GLN cc_start: 0.7335 (OUTLIER) cc_final: 0.7009 (pm20) REVERT: E 242 LYS cc_start: 0.7695 (OUTLIER) cc_final: 0.7409 (mtpp) REVERT: C 15 MET cc_start: 0.7745 (ttp) cc_final: 0.7501 (ttp) REVERT: C 50 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7167 (tm-30) REVERT: C 75 ILE cc_start: 0.8423 (tt) cc_final: 0.8178 (pt) REVERT: C 84 MET cc_start: 0.7943 (mtp) cc_final: 0.7614 (mtp) REVERT: C 106 VAL cc_start: 0.8206 (t) cc_final: 0.7962 (m) REVERT: C 142 GLU cc_start: 0.7407 (tt0) cc_final: 0.7188 (tt0) REVERT: C 208 ARG cc_start: 0.7827 (mtm-85) cc_final: 0.7609 (mtt-85) REVERT: C 220 GLN cc_start: 0.7330 (OUTLIER) cc_final: 0.7047 (pm20) REVERT: C 265 ARG cc_start: 0.8098 (mmt-90) cc_final: 0.7801 (mpt180) REVERT: C 287 GLU cc_start: 0.7565 (pp20) cc_final: 0.7147 (pp20) REVERT: C 374 TYR cc_start: 0.7335 (t80) cc_final: 0.7097 (t80) outliers start: 39 outliers final: 29 residues processed: 239 average time/residue: 0.1246 time to fit residues: 37.9807 Evaluate side-chains 250 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 215 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 220 GLN Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain E residue 11 ARG Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 135 GLU Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 220 GLN Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 295 MET Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain E residue 370 MET Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 220 GLN Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 376 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 31 optimal weight: 0.7980 chunk 85 optimal weight: 0.4980 chunk 22 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.143136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.123018 restraints weight = 12245.592| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.61 r_work: 0.3395 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 9237 Z= 0.164 Angle : 0.545 8.057 12528 Z= 0.276 Chirality : 0.037 0.185 1500 Planarity : 0.005 0.066 1572 Dihedral : 4.140 27.670 1288 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.87 % Allowed : 25.65 % Favored : 69.48 % 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 (0.25), residues: 1167 helix: 2.53 (0.16), residues: 1026 sheet: None (None), residues: 0 loop : -3.48 (0.38), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 16 TYR 0.026 0.002 TYR C 56 PHE 0.011 0.001 PHE A 119 TRP 0.007 0.001 TRP A 87 HIS 0.004 0.001 HIS C 299 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 9237) covalent geometry : angle 0.54457 (12528) hydrogen bonds : bond 0.03544 ( 796) hydrogen bonds : angle 4.15551 ( 2379) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 215 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7152 (tt0) cc_final: 0.6834 (tt0) REVERT: A 75 ILE cc_start: 0.8376 (tt) cc_final: 0.7963 (pt) REVERT: A 84 MET cc_start: 0.8204 (mtm) cc_final: 0.7958 (mtm) REVERT: A 91 SER cc_start: 0.7742 (OUTLIER) cc_final: 0.6093 (p) REVERT: A 100 ARG cc_start: 0.7316 (mtm110) cc_final: 0.6869 (mtt90) REVERT: A 151 ARG cc_start: 0.8126 (mmm160) cc_final: 0.7811 (mmt180) REVERT: A 165 GLU cc_start: 0.7128 (mt-10) cc_final: 0.6719 (mt-10) REVERT: A 220 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.7246 (pm20) REVERT: A 265 ARG cc_start: 0.8180 (mmt-90) cc_final: 0.7708 (mpt180) REVERT: A 287 GLU cc_start: 0.7551 (pp20) cc_final: 0.7257 (pp20) REVERT: F 9 MET cc_start: 0.6087 (tpp) cc_final: 0.5780 (tpp) REVERT: E 75 ILE cc_start: 0.8352 (tt) cc_final: 0.7981 (pt) REVERT: E 91 SER cc_start: 0.7964 (OUTLIER) cc_final: 0.7288 (m) REVERT: E 132 LEU cc_start: 0.8428 (mt) cc_final: 0.8182 (mt) REVERT: E 135 GLU cc_start: 0.6551 (OUTLIER) cc_final: 0.6294 (mt-10) REVERT: E 220 GLN cc_start: 0.7324 (OUTLIER) cc_final: 0.6995 (pm20) REVERT: E 242 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7486 (mtpp) REVERT: E 374 TYR cc_start: 0.7352 (t80) cc_final: 0.7106 (t80) REVERT: C 15 MET cc_start: 0.7799 (ttp) cc_final: 0.7548 (ttp) REVERT: C 50 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7184 (tm-30) REVERT: C 75 ILE cc_start: 0.8366 (tt) cc_final: 0.8130 (pt) REVERT: C 84 MET cc_start: 0.8011 (mtp) cc_final: 0.7698 (mtp) REVERT: C 142 GLU cc_start: 0.7458 (tt0) cc_final: 0.7242 (tt0) REVERT: C 265 ARG cc_start: 0.8148 (mmt-90) cc_final: 0.7826 (mpt180) REVERT: C 287 GLU cc_start: 0.7510 (pp20) cc_final: 0.7132 (pp20) REVERT: C 374 TYR cc_start: 0.7402 (t80) cc_final: 0.7146 (t80) outliers start: 45 outliers final: 33 residues processed: 242 average time/residue: 0.1246 time to fit residues: 38.5681 Evaluate side-chains 253 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 214 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 220 GLN Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain E residue 11 ARG Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 135 GLU Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 220 GLN Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 295 MET Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain E residue 370 MET Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 220 GLN Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 307 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 14 optimal weight: 0.7980 chunk 105 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 27 optimal weight: 0.3980 chunk 44 optimal weight: 0.3980 chunk 50 optimal weight: 0.0050 chunk 10 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 0.0770 chunk 95 optimal weight: 0.0980 overall best weight: 0.1952 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.145033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.124911 restraints weight = 12276.642| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.63 r_work: 0.3424 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9237 Z= 0.111 Angle : 0.517 8.498 12528 Z= 0.261 Chirality : 0.035 0.191 1500 Planarity : 0.005 0.065 1572 Dihedral : 4.080 27.707 1288 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.22 % Allowed : 26.62 % Favored : 69.16 % 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: 3.08 (0.25), residues: 1167 helix: 2.71 (0.16), residues: 1023 sheet: None (None), residues: 0 loop : -3.45 (0.38), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 16 TYR 0.026 0.002 TYR C 56 PHE 0.024 0.001 PHE E 105 TRP 0.007 0.001 TRP E 87 HIS 0.006 0.001 HIS C 299 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 9237) covalent geometry : angle 0.51728 (12528) hydrogen bonds : bond 0.03109 ( 796) hydrogen bonds : angle 4.06626 ( 2379) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 216 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 MET cc_start: 0.7700 (ttp) cc_final: 0.7456 (ttp) REVERT: A 75 ILE cc_start: 0.8378 (tt) cc_final: 0.7962 (pt) REVERT: A 84 MET cc_start: 0.8176 (mtm) cc_final: 0.7940 (mtm) REVERT: A 91 SER cc_start: 0.7653 (OUTLIER) cc_final: 0.6956 (m) REVERT: A 100 ARG cc_start: 0.7261 (mtm110) cc_final: 0.6811 (mtt90) REVERT: A 165 GLU cc_start: 0.6979 (mt-10) cc_final: 0.6617 (mt-10) REVERT: A 220 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.7263 (pm20) REVERT: A 265 ARG cc_start: 0.8143 (mmt-90) cc_final: 0.7696 (mpt180) REVERT: A 287 GLU cc_start: 0.7509 (pp20) cc_final: 0.7207 (pp20) REVERT: A 293 ARG cc_start: 0.8126 (mmt90) cc_final: 0.7885 (mmt180) REVERT: A 376 LEU cc_start: 0.6927 (mm) cc_final: 0.6683 (mm) REVERT: F 9 MET cc_start: 0.6058 (tpp) cc_final: 0.5741 (tpp) REVERT: E 75 ILE cc_start: 0.8333 (tt) cc_final: 0.7953 (pt) REVERT: E 91 SER cc_start: 0.7870 (OUTLIER) cc_final: 0.6510 (p) REVERT: E 132 LEU cc_start: 0.8390 (mt) cc_final: 0.8141 (mt) REVERT: E 135 GLU cc_start: 0.6461 (OUTLIER) cc_final: 0.6201 (mt-10) REVERT: E 220 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.6988 (pm20) REVERT: E 242 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.7337 (mtpp) REVERT: C 15 MET cc_start: 0.7770 (ttp) cc_final: 0.7524 (ttp) REVERT: C 50 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7174 (tm-30) REVERT: C 75 ILE cc_start: 0.8381 (tt) cc_final: 0.8125 (pt) REVERT: C 84 MET cc_start: 0.7934 (mtp) cc_final: 0.7631 (mtp) REVERT: C 91 SER cc_start: 0.7848 (OUTLIER) cc_final: 0.6343 (p) REVERT: C 142 GLU cc_start: 0.7457 (tt0) cc_final: 0.7244 (tt0) REVERT: C 265 ARG cc_start: 0.8080 (mmt-90) cc_final: 0.7765 (mpt180) REVERT: C 287 GLU cc_start: 0.7493 (pp20) cc_final: 0.7113 (pp20) REVERT: C 374 TYR cc_start: 0.7324 (t80) cc_final: 0.7075 (t80) outliers start: 39 outliers final: 29 residues processed: 238 average time/residue: 0.1091 time to fit residues: 33.3209 Evaluate side-chains 250 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 214 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 220 GLN Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain E residue 11 ARG Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 135 GLU Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 220 GLN Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 267 GLU Chi-restraints excluded: chain E residue 295 MET Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 370 MET Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 307 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 94 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 36 optimal weight: 0.0970 chunk 76 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 113 optimal weight: 0.4980 chunk 62 optimal weight: 0.3980 chunk 68 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 80 optimal weight: 0.3980 chunk 105 optimal weight: 0.9980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.144329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.124245 restraints weight = 12222.224| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.63 r_work: 0.3414 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9237 Z= 0.129 Angle : 0.535 8.537 12528 Z= 0.270 Chirality : 0.036 0.195 1500 Planarity : 0.005 0.065 1572 Dihedral : 4.074 27.347 1288 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.90 % Allowed : 26.73 % Favored : 69.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.02 (0.25), residues: 1167 helix: 2.66 (0.16), residues: 1023 sheet: None (None), residues: 0 loop : -3.35 (0.38), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 16 TYR 0.027 0.002 TYR C 56 PHE 0.019 0.001 PHE E 105 TRP 0.007 0.001 TRP E 87 HIS 0.007 0.001 HIS C 299 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 9237) covalent geometry : angle 0.53504 (12528) hydrogen bonds : bond 0.03263 ( 796) hydrogen bonds : angle 4.08283 ( 2379) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 216 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ILE cc_start: 0.8381 (tt) cc_final: 0.7954 (pt) REVERT: A 84 MET cc_start: 0.8161 (mtm) cc_final: 0.7925 (mtm) REVERT: A 91 SER cc_start: 0.7672 (OUTLIER) cc_final: 0.6993 (m) REVERT: A 100 ARG cc_start: 0.7282 (mtm110) cc_final: 0.6833 (mtt90) REVERT: A 165 GLU cc_start: 0.7042 (mt-10) cc_final: 0.6644 (mt-10) REVERT: A 220 GLN cc_start: 0.7514 (OUTLIER) cc_final: 0.7240 (pm20) REVERT: A 265 ARG cc_start: 0.8129 (mmt-90) cc_final: 0.7666 (mpt180) REVERT: A 287 GLU cc_start: 0.7515 (pp20) cc_final: 0.7203 (pp20) REVERT: A 293 ARG cc_start: 0.8137 (mmt90) cc_final: 0.7894 (mmt180) REVERT: F 9 MET cc_start: 0.6097 (tpp) cc_final: 0.5792 (tpp) REVERT: E 91 SER cc_start: 0.7903 (OUTLIER) cc_final: 0.6485 (p) REVERT: E 132 LEU cc_start: 0.8411 (mt) cc_final: 0.8171 (mt) REVERT: E 135 GLU cc_start: 0.6500 (OUTLIER) cc_final: 0.6228 (mt-10) REVERT: E 220 GLN cc_start: 0.7303 (OUTLIER) cc_final: 0.6987 (pm20) REVERT: E 242 LYS cc_start: 0.7666 (OUTLIER) cc_final: 0.7403 (mtpp) REVERT: E 374 TYR cc_start: 0.7290 (t80) cc_final: 0.7063 (t80) REVERT: C 15 MET cc_start: 0.7765 (ttp) cc_final: 0.7519 (ttp) REVERT: C 50 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7161 (tm-30) REVERT: C 75 ILE cc_start: 0.8422 (tt) cc_final: 0.8169 (pt) REVERT: C 84 MET cc_start: 0.7958 (mtp) cc_final: 0.7608 (mtp) REVERT: C 91 SER cc_start: 0.7851 (OUTLIER) cc_final: 0.6345 (p) REVERT: C 106 VAL cc_start: 0.8229 (t) cc_final: 0.7987 (m) REVERT: C 142 GLU cc_start: 0.7433 (tt0) cc_final: 0.7228 (tt0) REVERT: C 265 ARG cc_start: 0.8150 (mmt-90) cc_final: 0.7820 (mpt180) REVERT: C 287 GLU cc_start: 0.7473 (pp20) cc_final: 0.7100 (pp20) REVERT: C 374 TYR cc_start: 0.7359 (t80) cc_final: 0.7108 (t80) outliers start: 36 outliers final: 27 residues processed: 236 average time/residue: 0.1208 time to fit residues: 36.2717 Evaluate side-chains 249 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 215 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 220 GLN Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain E residue 11 ARG Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 135 GLU Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 220 GLN Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain E residue 264 THR Chi-restraints excluded: chain E residue 295 MET Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 370 MET Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 307 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 72 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 85 optimal weight: 0.4980 chunk 14 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 62 optimal weight: 0.3980 chunk 111 optimal weight: 0.0870 chunk 92 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.144568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.124428 restraints weight = 12218.511| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.63 r_work: 0.3416 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9237 Z= 0.128 Angle : 0.536 8.822 12528 Z= 0.270 Chirality : 0.036 0.197 1500 Planarity : 0.005 0.065 1572 Dihedral : 4.066 27.381 1288 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.90 % Allowed : 26.95 % Favored : 69.16 % 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: 3.05 (0.25), residues: 1167 helix: 2.68 (0.16), residues: 1020 sheet: None (None), residues: 0 loop : -3.25 (0.39), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 16 TYR 0.026 0.002 TYR C 56 PHE 0.019 0.001 PHE E 105 TRP 0.007 0.001 TRP E 87 HIS 0.007 0.001 HIS C 299 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 9237) covalent geometry : angle 0.53553 (12528) hydrogen bonds : bond 0.03255 ( 796) hydrogen bonds : angle 4.07416 ( 2379) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2381.48 seconds wall clock time: 41 minutes 20.26 seconds (2480.26 seconds total)