Starting phenix.real_space_refine on Fri Mar 6 14:47:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pxm_20521/03_2026/6pxm_20521.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pxm_20521/03_2026/6pxm_20521.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6pxm_20521/03_2026/6pxm_20521.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pxm_20521/03_2026/6pxm_20521.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pxm_20521/03_2026/6pxm_20521.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pxm_20521/03_2026/6pxm_20521.map" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.174 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 120 5.16 5 C 20640 2.51 5 N 5736 2.21 5 O 6240 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 192 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32736 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Restraints were copied for chains: A, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, V, W, X, Y Time building chain proxies: 2.54, per 1000 atoms: 0.08 Number of scatterers: 32736 At special positions: 0 Unit cell: (133.952, 133.952, 133.952, 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 120 16.00 O 6240 8.00 N 5736 7.00 C 20640 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: 2.73 Conformation dependent library (CDL) restraints added in 1.2 seconds 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7632 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 80.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'B' and resid 9 through 37 Processing helix chain 'B' and resid 44 through 72 Processing helix chain 'B' and resid 91 through 120 Processing helix chain 'B' and resid 122 through 133 Processing helix chain 'B' and resid 133 through 155 Processing helix chain 'B' and resid 158 through 170 Processing helix chain 'A' and resid 9 through 37 Processing helix chain 'A' and resid 44 through 72 Processing helix chain 'A' and resid 91 through 120 Processing helix chain 'A' and resid 122 through 133 Processing helix chain 'A' and resid 133 through 155 Processing helix chain 'A' and resid 158 through 170 Processing helix chain 'C' and resid 9 through 37 Processing helix chain 'C' and resid 44 through 72 Processing helix chain 'C' and resid 91 through 120 Processing helix chain 'C' and resid 122 through 133 Processing helix chain 'C' and resid 133 through 155 Processing helix chain 'C' and resid 158 through 170 Processing helix chain 'D' and resid 9 through 37 Processing helix chain 'D' and resid 44 through 72 Processing helix chain 'D' and resid 91 through 120 Processing helix chain 'D' and resid 122 through 133 Processing helix chain 'D' and resid 133 through 155 Processing helix chain 'D' and resid 158 through 170 Processing helix chain 'E' and resid 9 through 37 Processing helix chain 'E' and resid 44 through 72 Processing helix chain 'E' and resid 91 through 120 Processing helix chain 'E' and resid 122 through 133 Processing helix chain 'E' and resid 133 through 155 Processing helix chain 'E' and resid 158 through 170 Processing helix chain 'F' and resid 9 through 37 Processing helix chain 'F' and resid 44 through 72 Processing helix chain 'F' and resid 91 through 120 Processing helix chain 'F' and resid 122 through 133 Processing helix chain 'F' and resid 133 through 155 Processing helix chain 'F' and resid 158 through 170 Processing helix chain 'G' and resid 9 through 37 Processing helix chain 'G' and resid 44 through 72 Processing helix chain 'G' and resid 91 through 120 Processing helix chain 'G' and resid 122 through 133 Processing helix chain 'G' and resid 133 through 155 Processing helix chain 'G' and resid 158 through 170 Processing helix chain 'H' and resid 9 through 37 Processing helix chain 'H' and resid 44 through 72 Processing helix chain 'H' and resid 91 through 120 Processing helix chain 'H' and resid 122 through 133 Processing helix chain 'H' and resid 133 through 155 Processing helix chain 'H' and resid 158 through 170 Processing helix chain 'I' and resid 9 through 37 Processing helix chain 'I' and resid 44 through 72 Processing helix chain 'I' and resid 91 through 120 Processing helix chain 'I' and resid 122 through 133 Processing helix chain 'I' and resid 133 through 155 Processing helix chain 'I' and resid 158 through 170 Processing helix chain 'J' and resid 9 through 37 Processing helix chain 'J' and resid 44 through 72 Processing helix chain 'J' and resid 91 through 120 Processing helix chain 'J' and resid 122 through 133 Processing helix chain 'J' and resid 133 through 155 Processing helix chain 'J' and resid 158 through 170 Processing helix chain 'K' and resid 9 through 37 Processing helix chain 'K' and resid 44 through 72 Processing helix chain 'K' and resid 91 through 120 Processing helix chain 'K' and resid 122 through 133 Processing helix chain 'K' and resid 133 through 155 Processing helix chain 'K' and resid 158 through 170 Processing helix chain 'L' and resid 9 through 37 Processing helix chain 'L' and resid 44 through 72 Processing helix chain 'L' and resid 91 through 120 Processing helix chain 'L' and resid 122 through 133 Processing helix chain 'L' and resid 133 through 155 Processing helix chain 'L' and resid 158 through 170 Processing helix chain 'M' and resid 9 through 37 Processing helix chain 'M' and resid 44 through 72 Processing helix chain 'M' and resid 91 through 120 Processing helix chain 'M' and resid 122 through 133 Processing helix chain 'M' and resid 133 through 155 Processing helix chain 'M' and resid 158 through 170 Processing helix chain 'N' and resid 9 through 37 Processing helix chain 'N' and resid 44 through 72 Processing helix chain 'N' and resid 91 through 120 Processing helix chain 'N' and resid 122 through 133 Processing helix chain 'N' and resid 133 through 155 Processing helix chain 'N' and resid 158 through 170 Processing helix chain 'O' and resid 9 through 37 Processing helix chain 'O' and resid 44 through 72 Processing helix chain 'O' and resid 91 through 120 Processing helix chain 'O' and resid 122 through 133 Processing helix chain 'O' and resid 133 through 155 Processing helix chain 'O' and resid 158 through 170 Processing helix chain 'P' and resid 9 through 37 Processing helix chain 'P' and resid 44 through 72 Processing helix chain 'P' and resid 91 through 120 Processing helix chain 'P' and resid 122 through 133 Processing helix chain 'P' and resid 133 through 155 Processing helix chain 'P' and resid 158 through 170 Processing helix chain 'Q' and resid 9 through 37 Processing helix chain 'Q' and resid 44 through 72 Processing helix chain 'Q' and resid 91 through 120 Processing helix chain 'Q' and resid 122 through 133 Processing helix chain 'Q' and resid 133 through 155 Processing helix chain 'Q' and resid 158 through 170 Processing helix chain 'R' and resid 9 through 37 Processing helix chain 'R' and resid 44 through 72 Processing helix chain 'R' and resid 91 through 120 Processing helix chain 'R' and resid 122 through 133 Processing helix chain 'R' and resid 133 through 155 Processing helix chain 'R' and resid 158 through 170 Processing helix chain 'S' and resid 9 through 37 Processing helix chain 'S' and resid 44 through 72 Processing helix chain 'S' and resid 91 through 120 Processing helix chain 'S' and resid 122 through 133 Processing helix chain 'S' and resid 133 through 155 Processing helix chain 'S' and resid 158 through 170 Processing helix chain 'T' and resid 9 through 37 Processing helix chain 'T' and resid 44 through 72 Processing helix chain 'T' and resid 91 through 120 Processing helix chain 'T' and resid 122 through 133 Processing helix chain 'T' and resid 133 through 155 Processing helix chain 'T' and resid 158 through 170 Processing helix chain 'V' and resid 9 through 37 Processing helix chain 'V' and resid 44 through 72 Processing helix chain 'V' and resid 91 through 120 Processing helix chain 'V' and resid 122 through 133 Processing helix chain 'V' and resid 133 through 155 Processing helix chain 'V' and resid 158 through 170 Processing helix chain 'W' and resid 9 through 37 Processing helix chain 'W' and resid 44 through 72 Processing helix chain 'W' and resid 91 through 120 Processing helix chain 'W' and resid 122 through 133 Processing helix chain 'W' and resid 133 through 155 Processing helix chain 'W' and resid 158 through 170 Processing helix chain 'X' and resid 9 through 37 Processing helix chain 'X' and resid 44 through 72 Processing helix chain 'X' and resid 91 through 120 Processing helix chain 'X' and resid 122 through 133 Processing helix chain 'X' and resid 133 through 155 Processing helix chain 'X' and resid 158 through 170 Processing helix chain 'Y' and resid 9 through 37 Processing helix chain 'Y' and resid 44 through 72 Processing helix chain 'Y' and resid 91 through 120 Processing helix chain 'Y' and resid 122 through 133 Processing helix chain 'Y' and resid 133 through 155 Processing helix chain 'Y' and resid 158 through 170 2688 hydrogen bonds defined for protein. 8064 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: 5.59 Time building geometry restraints manager: 3.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 5736 1.28 - 1.41: 8339 1.41 - 1.55: 18997 1.55 - 1.68: 0 1.68 - 1.81: 192 Bond restraints: 33264 Sorted by residual: bond pdb=" C ALA L 26 " pdb=" O ALA L 26 " ideal model delta sigma weight residual 1.236 1.147 0.089 1.15e-02 7.56e+03 6.06e+01 bond pdb=" C ALA O 26 " pdb=" O ALA O 26 " ideal model delta sigma weight residual 1.236 1.148 0.089 1.15e-02 7.56e+03 5.95e+01 bond pdb=" C ALA B 26 " pdb=" O ALA B 26 " ideal model delta sigma weight residual 1.237 1.146 0.090 1.17e-02 7.31e+03 5.95e+01 bond pdb=" C ALA Y 26 " pdb=" O ALA Y 26 " ideal model delta sigma weight residual 1.237 1.147 0.090 1.17e-02 7.31e+03 5.88e+01 bond pdb=" C ALA T 26 " pdb=" O ALA T 26 " ideal model delta sigma weight residual 1.237 1.147 0.090 1.17e-02 7.31e+03 5.85e+01 ... (remaining 33259 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.78: 37174 0.78 - 1.56: 5516 1.56 - 2.34: 1203 2.34 - 3.12: 639 3.12 - 3.90: 252 Bond angle restraints: 44784 Sorted by residual: angle pdb=" CA ALA D 26 " pdb=" C ALA D 26 " pdb=" O ALA D 26 " ideal model delta sigma weight residual 120.55 116.69 3.86 1.06e+00 8.90e-01 1.33e+01 angle pdb=" CA ALA G 26 " pdb=" C ALA G 26 " pdb=" O ALA G 26 " ideal model delta sigma weight residual 120.82 117.03 3.79 1.05e+00 9.07e-01 1.31e+01 angle pdb=" CA ALA O 26 " pdb=" C ALA O 26 " pdb=" O ALA O 26 " ideal model delta sigma weight residual 120.82 117.03 3.79 1.05e+00 9.07e-01 1.30e+01 angle pdb=" CA ALA L 26 " pdb=" C ALA L 26 " pdb=" O ALA L 26 " ideal model delta sigma weight residual 120.82 117.05 3.77 1.05e+00 9.07e-01 1.29e+01 angle pdb=" CA ALA S 26 " pdb=" C ALA S 26 " pdb=" O ALA S 26 " ideal model delta sigma weight residual 120.55 116.77 3.78 1.06e+00 8.90e-01 1.27e+01 ... (remaining 44779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 17712 17.65 - 35.30: 1806 35.30 - 52.95: 378 52.95 - 70.61: 120 70.61 - 88.26: 48 Dihedral angle restraints: 20064 sinusoidal: 8232 harmonic: 11832 Sorted by residual: dihedral pdb=" CA VAL I 42 " pdb=" C VAL I 42 " pdb=" N ALA I 43 " pdb=" CA ALA I 43 " ideal model delta harmonic sigma weight residual 180.00 161.21 18.79 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA VAL Y 42 " pdb=" C VAL Y 42 " pdb=" N ALA Y 43 " pdb=" CA ALA Y 43 " ideal model delta harmonic sigma weight residual 180.00 161.22 18.78 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA VAL T 42 " pdb=" C VAL T 42 " pdb=" N ALA T 43 " pdb=" CA ALA T 43 " ideal model delta harmonic sigma weight residual 180.00 161.23 18.77 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 20061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2623 0.032 - 0.064: 1656 0.064 - 0.095: 468 0.095 - 0.127: 149 0.127 - 0.159: 24 Chirality restraints: 4920 Sorted by residual: chirality pdb=" CG LEU Q 24 " pdb=" CB LEU Q 24 " pdb=" CD1 LEU Q 24 " pdb=" CD2 LEU Q 24 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.30e-01 chirality pdb=" CG LEU F 24 " pdb=" CB LEU F 24 " pdb=" CD1 LEU F 24 " pdb=" CD2 LEU F 24 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.26e-01 chirality pdb=" CG LEU L 24 " pdb=" CB LEU L 24 " pdb=" CD1 LEU L 24 " pdb=" CD2 LEU L 24 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.26e-01 ... (remaining 4917 not shown) Planarity restraints: 5880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS X 83 " -0.025 5.00e-02 4.00e+02 3.71e-02 2.21e+00 pdb=" N PRO X 84 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO X 84 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO X 84 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS I 83 " -0.025 5.00e-02 4.00e+02 3.71e-02 2.20e+00 pdb=" N PRO I 84 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO I 84 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO I 84 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS T 83 " -0.025 5.00e-02 4.00e+02 3.71e-02 2.20e+00 pdb=" N PRO T 84 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO T 84 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO T 84 " -0.021 5.00e-02 4.00e+02 ... (remaining 5877 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 11474 2.89 - 3.40: 31684 3.40 - 3.90: 61179 3.90 - 4.40: 68991 4.40 - 4.90: 112181 Nonbonded interactions: 285509 Sorted by model distance: nonbonded pdb=" OH TYR V 8 " pdb=" OE1 GLN V 69 " model vdw 2.392 3.040 nonbonded pdb=" OH TYR N 8 " pdb=" OE1 GLN N 69 " model vdw 2.392 3.040 nonbonded pdb=" OH TYR D 8 " pdb=" OE1 GLN D 69 " model vdw 2.392 3.040 nonbonded pdb=" OH TYR Y 8 " pdb=" OE1 GLN Y 69 " model vdw 2.392 3.040 nonbonded pdb=" OH TYR L 8 " pdb=" OE1 GLN L 69 " model vdw 2.392 3.040 ... (remaining 285504 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: 0.10 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } 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: 2.090 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: 0.030 Extract box with map and model: 0.480 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 22.780 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 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:6.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 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 : 0.008 0.090 33264 Z= 0.441 Angle : 0.706 3.904 44784 Z= 0.428 Chirality : 0.044 0.159 4920 Planarity : 0.004 0.037 5880 Dihedral : 16.033 88.256 12432 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % 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: -3.44 (0.09), residues: 4032 helix: -2.24 (0.06), residues: 3312 sheet: None (None), residues: 0 loop : -1.12 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG V 25 TYR 0.012 0.002 TYR B 28 PHE 0.018 0.003 PHE M 37 TRP 0.006 0.001 TRP J 89 HIS 0.005 0.001 HIS O 124 Details of bonding type rmsd covalent geometry : bond 0.00815 (33264) covalent geometry : angle 0.70564 (44784) hydrogen bonds : bond 0.21762 ( 2688) hydrogen bonds : angle 6.46488 ( 8064) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 673 time to evaluate : 1.257 Fit side-chains REVERT: A 135 ASP cc_start: 0.8285 (t70) cc_final: 0.8049 (t0) REVERT: C 135 ASP cc_start: 0.8281 (t70) cc_final: 0.8053 (t0) REVERT: E 135 ASP cc_start: 0.8282 (t70) cc_final: 0.8056 (t0) REVERT: G 135 ASP cc_start: 0.8272 (t70) cc_final: 0.8048 (t0) REVERT: J 135 ASP cc_start: 0.8278 (t70) cc_final: 0.8044 (t0) REVERT: M 135 ASP cc_start: 0.8286 (t70) cc_final: 0.8053 (t0) REVERT: N 135 ASP cc_start: 0.8277 (t70) cc_final: 0.8051 (t0) REVERT: P 135 ASP cc_start: 0.8281 (t70) cc_final: 0.8055 (t0) REVERT: R 135 ASP cc_start: 0.8288 (t70) cc_final: 0.8066 (t0) REVERT: V 135 ASP cc_start: 0.8279 (t70) cc_final: 0.8062 (t0) REVERT: W 135 ASP cc_start: 0.8280 (t70) cc_final: 0.8046 (t0) outliers start: 0 outliers final: 0 residues processed: 673 average time/residue: 1.0121 time to fit residues: 763.6479 Evaluate side-chains 436 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 436 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 0.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 2.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 ASN B 71 GLN B 132 HIS A 7 ASN A 71 GLN A 132 HIS C 7 ASN C 71 GLN C 132 HIS D 71 GLN D 132 HIS E 7 ASN E 71 GLN E 132 HIS F 71 GLN F 132 HIS G 7 ASN G 71 GLN G 132 HIS H 7 ASN H 71 GLN H 132 HIS I 7 ASN I 71 GLN I 132 HIS J 7 ASN J 71 GLN J 132 HIS K 7 ASN K 71 GLN K 132 HIS L 7 ASN L 71 GLN L 132 HIS M 71 GLN M 132 HIS N 7 ASN N 71 GLN N 132 HIS O 71 GLN O 132 HIS P 7 ASN P 71 GLN P 132 HIS Q 7 ASN Q 71 GLN Q 132 HIS R 7 ASN R 71 GLN R 132 HIS S 7 ASN S 71 GLN S 132 HIS T 7 ASN T 71 GLN T 132 HIS V 7 ASN V 71 GLN V 132 HIS W 7 ASN W 71 GLN W 132 HIS X 7 ASN X 71 GLN X 132 HIS Y 7 ASN Y 71 GLN Y 132 HIS Total number of N/Q/H flips: 68 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.125927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.109557 restraints weight = 33576.058| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.31 r_work: 0.3231 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 33264 Z= 0.111 Angle : 0.456 4.925 44784 Z= 0.261 Chirality : 0.033 0.126 4920 Planarity : 0.003 0.028 5880 Dihedral : 4.139 15.712 4464 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.13), residues: 4032 helix: 2.03 (0.08), residues: 3336 sheet: None (None), residues: 0 loop : -0.65 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 52 TYR 0.007 0.001 TYR I 28 PHE 0.012 0.002 PHE S 50 TRP 0.004 0.001 TRP D 89 HIS 0.003 0.001 HIS Y 49 Details of bonding type rmsd covalent geometry : bond 0.00228 (33264) covalent geometry : angle 0.45602 (44784) hydrogen bonds : bond 0.05136 ( 2688) hydrogen bonds : angle 3.06805 ( 8064) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 553 time to evaluate : 1.235 Fit side-chains REVERT: A 59 ARG cc_start: 0.8588 (ttp80) cc_final: 0.8332 (ttp-110) REVERT: C 59 ARG cc_start: 0.8579 (ttp80) cc_final: 0.8365 (ttp-110) REVERT: D 59 ARG cc_start: 0.8576 (ttp80) cc_final: 0.8320 (ttp-110) REVERT: G 80 ASP cc_start: 0.8781 (m-30) cc_final: 0.8546 (m-30) REVERT: I 80 ASP cc_start: 0.8765 (m-30) cc_final: 0.8530 (m-30) REVERT: M 59 ARG cc_start: 0.8584 (ttp80) cc_final: 0.8373 (ttp-110) REVERT: N 59 ARG cc_start: 0.8580 (ttp80) cc_final: 0.8368 (ttp-110) REVERT: O 80 ASP cc_start: 0.8766 (m-30) cc_final: 0.8539 (m-30) REVERT: Q 80 ASP cc_start: 0.8784 (m-30) cc_final: 0.8559 (m-30) REVERT: R 59 ARG cc_start: 0.8584 (ttp80) cc_final: 0.8373 (ttp-110) REVERT: T 59 ARG cc_start: 0.8581 (ttp80) cc_final: 0.8369 (ttp-110) REVERT: V 59 ARG cc_start: 0.8585 (ttp80) cc_final: 0.8375 (ttp-110) REVERT: X 80 ASP cc_start: 0.8776 (m-30) cc_final: 0.8550 (m-30) outliers start: 0 outliers final: 0 residues processed: 553 average time/residue: 0.9747 time to fit residues: 606.5172 Evaluate side-chains 537 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 537 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 313 optimal weight: 3.9990 chunk 363 optimal weight: 8.9990 chunk 196 optimal weight: 0.7980 chunk 140 optimal weight: 4.9990 chunk 274 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 chunk 272 optimal weight: 10.0000 chunk 298 optimal weight: 0.9980 chunk 377 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- 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 = 0.3542 r_free = 0.3542 target = 0.123543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.107258 restraints weight = 33321.873| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.32 r_work: 0.3189 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 33264 Z= 0.173 Angle : 0.519 4.780 44784 Z= 0.288 Chirality : 0.037 0.127 4920 Planarity : 0.003 0.028 5880 Dihedral : 4.336 17.500 4464 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.75 % Allowed : 9.06 % Favored : 90.19 % 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: 3.98 (0.13), residues: 4032 helix: 3.20 (0.09), residues: 3336 sheet: None (None), residues: 0 loop : -0.49 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Q 153 TYR 0.008 0.001 TYR L 28 PHE 0.016 0.003 PHE S 37 TRP 0.005 0.001 TRP H 89 HIS 0.003 0.001 HIS J 124 Details of bonding type rmsd covalent geometry : bond 0.00399 (33264) covalent geometry : angle 0.51943 (44784) hydrogen bonds : bond 0.05826 ( 2688) hydrogen bonds : angle 3.07061 ( 8064) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 612 time to evaluate : 1.276 Fit side-chains REVERT: E 59 ARG cc_start: 0.8613 (ttp80) cc_final: 0.8376 (ttp-110) REVERT: G 59 ARG cc_start: 0.8615 (ttp80) cc_final: 0.8380 (ttp-110) REVERT: I 59 ARG cc_start: 0.8607 (ttp80) cc_final: 0.8363 (ttp-110) REVERT: K 59 ARG cc_start: 0.8611 (ttp80) cc_final: 0.8376 (ttp-110) REVERT: O 59 ARG cc_start: 0.8607 (ttp80) cc_final: 0.8362 (ttp-110) REVERT: P 59 ARG cc_start: 0.8607 (ttp80) cc_final: 0.8372 (ttp-110) REVERT: Q 59 ARG cc_start: 0.8611 (ttp80) cc_final: 0.8366 (ttp-110) REVERT: Y 59 ARG cc_start: 0.8608 (ttp80) cc_final: 0.8364 (ttp-110) outliers start: 26 outliers final: 1 residues processed: 637 average time/residue: 1.0003 time to fit residues: 716.3742 Evaluate side-chains 557 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 556 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 120 optimal weight: 4.9990 chunk 295 optimal weight: 7.9990 chunk 84 optimal weight: 7.9990 chunk 252 optimal weight: 1.9990 chunk 336 optimal weight: 0.9980 chunk 226 optimal weight: 0.9980 chunk 326 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 262 optimal weight: 9.9990 chunk 233 optimal weight: 6.9990 chunk 209 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3585 r_free = 0.3585 target = 0.126725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.110126 restraints weight = 33479.547| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.32 r_work: 0.3234 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 33264 Z= 0.100 Angle : 0.418 4.586 44784 Z= 0.239 Chirality : 0.033 0.114 4920 Planarity : 0.002 0.024 5880 Dihedral : 3.931 14.297 4464 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.72 % Allowed : 8.19 % Favored : 91.09 % 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: 4.79 (0.13), residues: 4032 helix: 3.78 (0.09), residues: 3336 sheet: None (None), residues: 0 loop : -0.35 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG X 59 TYR 0.004 0.001 TYR E 28 PHE 0.014 0.002 PHE L 50 TRP 0.004 0.001 TRP Y 89 HIS 0.002 0.001 HIS P 49 Details of bonding type rmsd covalent geometry : bond 0.00204 (33264) covalent geometry : angle 0.41841 (44784) hydrogen bonds : bond 0.04248 ( 2688) hydrogen bonds : angle 2.94401 ( 8064) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 600 time to evaluate : 1.248 Fit side-chains REVERT: G 80 ASP cc_start: 0.8765 (m-30) cc_final: 0.8559 (m-30) REVERT: Q 80 ASP cc_start: 0.8766 (m-30) cc_final: 0.8564 (m-30) outliers start: 25 outliers final: 0 residues processed: 624 average time/residue: 1.0673 time to fit residues: 742.3218 Evaluate side-chains 578 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 578 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 403 optimal weight: 0.8980 chunk 247 optimal weight: 0.7980 chunk 2 optimal weight: 9.9990 chunk 188 optimal weight: 5.9990 chunk 238 optimal weight: 10.0000 chunk 381 optimal weight: 10.0000 chunk 290 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 16 optimal weight: 7.9990 overall best weight: 2.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 GLN A 69 GLN C 69 GLN D 69 GLN D 71 GLN E 69 GLN F 69 GLN G 69 GLN H 69 GLN I 69 GLN I 71 GLN J 69 GLN K 69 GLN L 69 GLN M 69 GLN N 69 GLN O 69 GLN P 69 GLN Q 69 GLN R 69 GLN S 69 GLN T 69 GLN V 69 GLN W 69 GLN X 69 GLN Y 69 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.124150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.107581 restraints weight = 33441.005| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.33 r_work: 0.3192 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 33264 Z= 0.155 Angle : 0.493 4.455 44784 Z= 0.276 Chirality : 0.036 0.124 4920 Planarity : 0.003 0.027 5880 Dihedral : 4.215 16.931 4464 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.75 % Allowed : 9.11 % Favored : 90.13 % 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: 4.81 (0.13), residues: 4032 helix: 3.79 (0.09), residues: 3336 sheet: None (None), residues: 0 loop : -0.31 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Y 59 TYR 0.006 0.001 TYR E 30 PHE 0.016 0.003 PHE C 37 TRP 0.005 0.001 TRP T 89 HIS 0.003 0.001 HIS O 124 Details of bonding type rmsd covalent geometry : bond 0.00355 (33264) covalent geometry : angle 0.49326 (44784) hydrogen bonds : bond 0.05365 ( 2688) hydrogen bonds : angle 3.03972 ( 8064) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 646 time to evaluate : 1.304 Fit side-chains outliers start: 26 outliers final: 0 residues processed: 670 average time/residue: 1.0702 time to fit residues: 798.8094 Evaluate side-chains 552 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 552 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 43 optimal weight: 3.9990 chunk 212 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 327 optimal weight: 2.9990 chunk 168 optimal weight: 7.9990 chunk 381 optimal weight: 9.9990 chunk 191 optimal weight: 3.9990 chunk 227 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 GLN A 69 GLN C 69 GLN D 69 GLN E 69 GLN F 69 GLN G 69 GLN G 71 GLN H 69 GLN I 69 GLN J 69 GLN K 69 GLN L 69 GLN M 69 GLN N 69 GLN O 69 GLN P 69 GLN Q 69 GLN R 69 GLN S 69 GLN T 69 GLN V 69 GLN W 69 GLN X 69 GLN Y 69 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.124455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.107825 restraints weight = 33299.463| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.33 r_work: 0.3196 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 33264 Z= 0.145 Angle : 0.484 4.437 44784 Z= 0.271 Chirality : 0.036 0.123 4920 Planarity : 0.003 0.026 5880 Dihedral : 4.201 16.717 4464 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.72 % Allowed : 9.49 % Favored : 89.79 % 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: 4.88 (0.13), residues: 4032 helix: 3.84 (0.09), residues: 3336 sheet: None (None), residues: 0 loop : -0.32 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Y 59 TYR 0.005 0.001 TYR H 30 PHE 0.015 0.003 PHE H 37 TRP 0.005 0.001 TRP P 89 HIS 0.003 0.001 HIS P 124 Details of bonding type rmsd covalent geometry : bond 0.00328 (33264) covalent geometry : angle 0.48367 (44784) hydrogen bonds : bond 0.05199 ( 2688) hydrogen bonds : angle 3.02645 ( 8064) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 651 time to evaluate : 1.347 Fit side-chains REVERT: B 53 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8208 (mt-10) REVERT: E 53 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8199 (mt-10) REVERT: G 53 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8219 (mt-10) REVERT: H 53 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8224 (mt-10) REVERT: J 53 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8218 (mt-10) REVERT: L 53 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8220 (mt-10) REVERT: S 53 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8210 (mt-10) REVERT: W 53 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8208 (mt-10) REVERT: X 53 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8204 (mt-10) outliers start: 25 outliers final: 1 residues processed: 675 average time/residue: 1.0680 time to fit residues: 802.9025 Evaluate side-chains 564 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 563 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 130 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 chunk 319 optimal weight: 1.9990 chunk 254 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 358 optimal weight: 0.9990 chunk 125 optimal weight: 0.9980 chunk 348 optimal weight: 2.9990 chunk 333 optimal weight: 4.9990 chunk 296 optimal weight: 9.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 GLN B 71 GLN A 69 GLN A 71 GLN C 69 GLN D 69 GLN E 69 GLN F 69 GLN G 69 GLN H 69 GLN H 71 GLN I 69 GLN J 69 GLN J 71 GLN K 69 GLN K 71 GLN L 69 GLN L 71 GLN M 69 GLN M 71 GLN N 69 GLN N 71 GLN O 69 GLN O 71 GLN P 69 GLN P 71 GLN Q 69 GLN Q 71 GLN R 69 GLN R 71 GLN S 69 GLN T 69 GLN T 71 GLN V 69 GLN V 71 GLN W 69 GLN W 71 GLN X 69 GLN X 71 GLN Y 69 GLN Y 71 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.125863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.109099 restraints weight = 33434.756| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.33 r_work: 0.3216 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 33264 Z= 0.112 Angle : 0.440 4.428 44784 Z= 0.250 Chirality : 0.034 0.115 4920 Planarity : 0.003 0.024 5880 Dihedral : 4.005 15.124 4464 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.64 % Allowed : 9.69 % Favored : 89.67 % 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: 5.06 (0.14), residues: 4032 helix: 3.97 (0.09), residues: 3336 sheet: None (None), residues: 0 loop : -0.24 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 59 TYR 0.005 0.001 TYR I 23 PHE 0.013 0.002 PHE V 37 TRP 0.005 0.001 TRP I 89 HIS 0.002 0.001 HIS A 124 Details of bonding type rmsd covalent geometry : bond 0.00239 (33264) covalent geometry : angle 0.43989 (44784) hydrogen bonds : bond 0.04522 ( 2688) hydrogen bonds : angle 2.97854 ( 8064) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 663 time to evaluate : 1.206 Fit side-chains REVERT: B 53 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8188 (mt-10) REVERT: B 153 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.7317 (ptp90) REVERT: A 53 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8204 (mt-10) REVERT: A 153 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.7320 (ptp90) REVERT: C 53 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8192 (mt-10) REVERT: C 153 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.7322 (ptp90) REVERT: D 53 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8187 (mt-10) REVERT: E 53 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8178 (mt-10) REVERT: F 53 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8192 (mt-10) REVERT: F 153 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.7322 (ptp90) REVERT: G 53 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8185 (mt-10) REVERT: G 80 ASP cc_start: 0.8784 (m-30) cc_final: 0.8575 (m-30) REVERT: H 53 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8203 (mt-10) REVERT: H 153 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.7305 (ptp90) REVERT: I 53 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8188 (mt-10) REVERT: I 153 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.7322 (ptp90) REVERT: J 53 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8191 (mt-10) REVERT: J 153 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.7324 (ptp90) REVERT: K 53 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8202 (mt-10) REVERT: K 153 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.7327 (ptp90) REVERT: L 53 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8184 (mt-10) REVERT: L 153 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.7323 (ptp90) REVERT: M 53 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8186 (mt-10) REVERT: M 153 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.7324 (ptp90) REVERT: N 53 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8181 (mt-10) REVERT: N 153 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.7326 (ptp90) REVERT: O 53 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8184 (mt-10) REVERT: O 153 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.7324 (ptp90) REVERT: P 53 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8210 (mt-10) REVERT: P 153 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.7320 (ptp90) REVERT: Q 53 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8187 (mt-10) REVERT: Q 80 ASP cc_start: 0.8789 (m-30) cc_final: 0.8582 (m-30) REVERT: Q 153 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.7320 (ptp90) REVERT: R 53 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8188 (mt-10) REVERT: R 153 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.7317 (ptp90) REVERT: S 53 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8180 (mt-10) REVERT: S 153 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.7301 (ptp90) REVERT: T 53 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8171 (mt-10) REVERT: T 153 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.7324 (ptp90) REVERT: V 53 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8191 (mt-10) REVERT: V 153 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.7307 (ptp90) REVERT: W 53 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8185 (mt-10) REVERT: W 153 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.7320 (ptp90) REVERT: X 53 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8184 (mt-10) REVERT: X 153 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.7324 (ptp90) REVERT: Y 53 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8186 (mt-10) REVERT: Y 153 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.7313 (ptp90) outliers start: 22 outliers final: 1 residues processed: 684 average time/residue: 1.1322 time to fit residues: 859.1385 Evaluate side-chains 630 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 608 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain C residue 153 ARG Chi-restraints excluded: chain F residue 153 ARG Chi-restraints excluded: chain H residue 153 ARG Chi-restraints excluded: chain I residue 153 ARG Chi-restraints excluded: chain J residue 153 ARG Chi-restraints excluded: chain K residue 153 ARG Chi-restraints excluded: chain L residue 153 ARG Chi-restraints excluded: chain M residue 153 ARG Chi-restraints excluded: chain N residue 153 ARG Chi-restraints excluded: chain O residue 153 ARG Chi-restraints excluded: chain P residue 153 ARG Chi-restraints excluded: chain Q residue 153 ARG Chi-restraints excluded: chain R residue 153 ARG Chi-restraints excluded: chain S residue 153 ARG Chi-restraints excluded: chain T residue 153 ARG Chi-restraints excluded: chain V residue 153 ARG Chi-restraints excluded: chain W residue 153 ARG Chi-restraints excluded: chain X residue 153 ARG Chi-restraints excluded: chain Y residue 153 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 404 optimal weight: 2.9990 chunk 389 optimal weight: 0.9980 chunk 217 optimal weight: 7.9990 chunk 332 optimal weight: 0.9990 chunk 192 optimal weight: 2.9990 chunk 317 optimal weight: 5.9990 chunk 212 optimal weight: 5.9990 chunk 352 optimal weight: 10.0000 chunk 233 optimal weight: 10.0000 chunk 20 optimal weight: 0.3980 chunk 180 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 71 GLN A 71 GLN C 71 GLN H 71 GLN J 71 GLN K 71 GLN L 71 GLN M 71 GLN N 71 GLN O 71 GLN P 71 GLN Q 71 GLN R 71 GLN T 71 GLN V 71 GLN W 71 GLN X 71 GLN Y 71 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.125345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.108646 restraints weight = 33298.456| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.32 r_work: 0.3214 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 33264 Z= 0.115 Angle : 0.445 4.356 44784 Z= 0.251 Chirality : 0.034 0.115 4920 Planarity : 0.003 0.024 5880 Dihedral : 4.019 15.294 4464 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.30 % Allowed : 9.03 % Favored : 89.67 % 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: 5.12 (0.14), residues: 4032 helix: 4.01 (0.09), residues: 3336 sheet: None (None), residues: 0 loop : -0.21 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Y 59 TYR 0.005 0.001 TYR I 23 PHE 0.014 0.002 PHE V 37 TRP 0.005 0.001 TRP D 89 HIS 0.002 0.001 HIS K 124 Details of bonding type rmsd covalent geometry : bond 0.00246 (33264) covalent geometry : angle 0.44461 (44784) hydrogen bonds : bond 0.04605 ( 2688) hydrogen bonds : angle 2.96761 ( 8064) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 614 time to evaluate : 1.303 Fit side-chains REVERT: B 53 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8180 (mt-10) REVERT: B 69 GLN cc_start: 0.9242 (OUTLIER) cc_final: 0.8656 (tp-100) REVERT: B 153 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.7291 (ptp90) REVERT: A 53 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8178 (mt-10) REVERT: A 69 GLN cc_start: 0.9239 (OUTLIER) cc_final: 0.8649 (tp-100) REVERT: A 153 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.7282 (ptp90) REVERT: C 53 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8179 (mt-10) REVERT: C 69 GLN cc_start: 0.9226 (OUTLIER) cc_final: 0.8622 (tp-100) REVERT: D 53 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8179 (mt-10) REVERT: D 69 GLN cc_start: 0.9232 (OUTLIER) cc_final: 0.8688 (tp-100) REVERT: D 153 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.7283 (ptp90) REVERT: E 53 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8175 (mt-10) REVERT: E 69 GLN cc_start: 0.9236 (OUTLIER) cc_final: 0.8637 (tp-100) REVERT: E 153 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.7282 (ptp90) REVERT: F 53 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8189 (mt-10) REVERT: F 69 GLN cc_start: 0.9234 (OUTLIER) cc_final: 0.8632 (tp-100) REVERT: G 53 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8181 (mt-10) REVERT: G 69 GLN cc_start: 0.9234 (OUTLIER) cc_final: 0.8688 (tp-100) REVERT: G 80 ASP cc_start: 0.8788 (m-30) cc_final: 0.8574 (m-30) REVERT: G 153 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.7337 (ptp90) REVERT: H 53 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8189 (mt-10) REVERT: H 69 GLN cc_start: 0.9237 (OUTLIER) cc_final: 0.8650 (tp-100) REVERT: I 53 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8174 (mt-10) REVERT: I 69 GLN cc_start: 0.9229 (OUTLIER) cc_final: 0.8680 (tp-100) REVERT: J 53 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8184 (mt-10) REVERT: J 69 GLN cc_start: 0.9239 (OUTLIER) cc_final: 0.8652 (tp-100) REVERT: J 153 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.7286 (ptp90) REVERT: K 53 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8189 (mt-10) REVERT: K 69 GLN cc_start: 0.9239 (OUTLIER) cc_final: 0.8651 (tp-100) REVERT: K 153 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.7289 (ptp90) REVERT: L 53 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8181 (mt-10) REVERT: L 69 GLN cc_start: 0.9241 (OUTLIER) cc_final: 0.8654 (tp-100) REVERT: L 153 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.7283 (ptp90) REVERT: M 53 GLU cc_start: 0.8406 (mt-10) cc_final: 0.8177 (mt-10) REVERT: M 69 GLN cc_start: 0.9238 (OUTLIER) cc_final: 0.8650 (tp-100) REVERT: M 153 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.7286 (ptp90) REVERT: N 53 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8180 (mt-10) REVERT: N 69 GLN cc_start: 0.9242 (OUTLIER) cc_final: 0.8650 (tp-100) REVERT: N 153 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.7286 (ptp90) REVERT: O 53 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8182 (mt-10) REVERT: O 69 GLN cc_start: 0.9240 (OUTLIER) cc_final: 0.8654 (tp-100) REVERT: O 153 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.7284 (ptp90) REVERT: P 53 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8181 (mt-10) REVERT: P 69 GLN cc_start: 0.9238 (OUTLIER) cc_final: 0.8647 (tp-100) REVERT: P 153 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.7281 (ptp90) REVERT: Q 53 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8177 (mt-10) REVERT: Q 69 GLN cc_start: 0.9240 (OUTLIER) cc_final: 0.8649 (tp-100) REVERT: Q 80 ASP cc_start: 0.8794 (m-30) cc_final: 0.8581 (m-30) REVERT: Q 153 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.7281 (ptp90) REVERT: R 53 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8182 (mt-10) REVERT: R 69 GLN cc_start: 0.9238 (OUTLIER) cc_final: 0.8650 (tp-100) REVERT: R 153 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.7279 (ptp90) REVERT: S 53 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8183 (mt-10) REVERT: S 69 GLN cc_start: 0.9234 (OUTLIER) cc_final: 0.8635 (tp-100) REVERT: S 153 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.7307 (ptp90) REVERT: T 53 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8167 (mt-10) REVERT: T 69 GLN cc_start: 0.9241 (OUTLIER) cc_final: 0.8651 (tp-100) REVERT: T 153 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.7299 (ptp90) REVERT: V 53 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8185 (mt-10) REVERT: V 69 GLN cc_start: 0.9238 (OUTLIER) cc_final: 0.8650 (tp-100) REVERT: V 153 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.7312 (ptp90) REVERT: W 53 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8177 (mt-10) REVERT: W 69 GLN cc_start: 0.9240 (OUTLIER) cc_final: 0.8654 (tp-100) REVERT: W 153 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.7277 (ptp90) REVERT: X 53 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8172 (mt-10) REVERT: X 69 GLN cc_start: 0.9240 (OUTLIER) cc_final: 0.8652 (tp-100) REVERT: X 153 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.7281 (ptp90) REVERT: Y 53 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8184 (mt-10) REVERT: Y 69 GLN cc_start: 0.9237 (OUTLIER) cc_final: 0.8647 (tp-100) REVERT: Y 153 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.7290 (ptp90) outliers start: 45 outliers final: 1 residues processed: 659 average time/residue: 1.0955 time to fit residues: 802.1088 Evaluate side-chains 666 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 621 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain D residue 69 GLN Chi-restraints excluded: chain D residue 153 ARG Chi-restraints excluded: chain E residue 69 GLN Chi-restraints excluded: chain E residue 153 ARG Chi-restraints excluded: chain F residue 69 GLN Chi-restraints excluded: chain G residue 69 GLN Chi-restraints excluded: chain G residue 153 ARG Chi-restraints excluded: chain H residue 69 GLN Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain J residue 69 GLN Chi-restraints excluded: chain J residue 153 ARG Chi-restraints excluded: chain K residue 69 GLN Chi-restraints excluded: chain K residue 153 ARG Chi-restraints excluded: chain L residue 69 GLN Chi-restraints excluded: chain L residue 153 ARG Chi-restraints excluded: chain M residue 69 GLN Chi-restraints excluded: chain M residue 153 ARG Chi-restraints excluded: chain N residue 69 GLN Chi-restraints excluded: chain N residue 153 ARG Chi-restraints excluded: chain O residue 69 GLN Chi-restraints excluded: chain O residue 153 ARG Chi-restraints excluded: chain P residue 69 GLN Chi-restraints excluded: chain P residue 153 ARG Chi-restraints excluded: chain Q residue 69 GLN Chi-restraints excluded: chain Q residue 153 ARG Chi-restraints excluded: chain R residue 69 GLN Chi-restraints excluded: chain R residue 153 ARG Chi-restraints excluded: chain S residue 69 GLN Chi-restraints excluded: chain S residue 153 ARG Chi-restraints excluded: chain T residue 69 GLN Chi-restraints excluded: chain T residue 153 ARG Chi-restraints excluded: chain V residue 69 GLN Chi-restraints excluded: chain V residue 153 ARG Chi-restraints excluded: chain W residue 69 GLN Chi-restraints excluded: chain W residue 153 ARG Chi-restraints excluded: chain X residue 69 GLN Chi-restraints excluded: chain X residue 153 ARG Chi-restraints excluded: chain Y residue 69 GLN Chi-restraints excluded: chain Y residue 153 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 211 optimal weight: 7.9990 chunk 312 optimal weight: 9.9990 chunk 243 optimal weight: 10.0000 chunk 257 optimal weight: 6.9990 chunk 352 optimal weight: 6.9990 chunk 402 optimal weight: 8.9990 chunk 18 optimal weight: 0.9990 chunk 347 optimal weight: 7.9990 chunk 141 optimal weight: 1.9990 chunk 287 optimal weight: 10.0000 chunk 301 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 71 GLN F 71 GLN J 71 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.122309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.105976 restraints weight = 33157.907| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.32 r_work: 0.3176 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 33264 Z= 0.227 Angle : 0.562 4.756 44784 Z= 0.311 Chirality : 0.040 0.133 4920 Planarity : 0.004 0.029 5880 Dihedral : 4.423 17.061 4464 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.81 % Allowed : 9.55 % Favored : 89.64 % 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: 4.77 (0.13), residues: 4032 helix: 3.76 (0.09), residues: 3336 sheet: None (None), residues: 0 loop : -0.31 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 153 TYR 0.009 0.002 TYR O 30 PHE 0.017 0.003 PHE B 37 TRP 0.004 0.002 TRP O 89 HIS 0.004 0.002 HIS W 124 Details of bonding type rmsd covalent geometry : bond 0.00533 (33264) covalent geometry : angle 0.56168 (44784) hydrogen bonds : bond 0.06076 ( 2688) hydrogen bonds : angle 3.08585 ( 8064) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 598 time to evaluate : 1.230 Fit side-chains REVERT: B 69 GLN cc_start: 0.9311 (OUTLIER) cc_final: 0.8765 (tp-100) REVERT: A 69 GLN cc_start: 0.9309 (OUTLIER) cc_final: 0.8760 (tp-100) REVERT: C 69 GLN cc_start: 0.9308 (OUTLIER) cc_final: 0.8759 (tp-100) REVERT: C 153 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.7204 (ptp90) REVERT: D 69 GLN cc_start: 0.9300 (OUTLIER) cc_final: 0.8745 (tp-100) REVERT: E 69 GLN cc_start: 0.9312 (OUTLIER) cc_final: 0.8764 (tp-100) REVERT: E 153 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.7212 (ptp90) REVERT: F 69 GLN cc_start: 0.9309 (OUTLIER) cc_final: 0.8763 (tp-100) REVERT: F 153 ARG cc_start: 0.8901 (OUTLIER) cc_final: 0.7217 (ptp90) REVERT: G 69 GLN cc_start: 0.9301 (OUTLIER) cc_final: 0.8742 (tp-100) REVERT: H 69 GLN cc_start: 0.9312 (OUTLIER) cc_final: 0.8768 (tp-100) REVERT: I 69 GLN cc_start: 0.9300 (OUTLIER) cc_final: 0.8738 (tp-100) REVERT: J 69 GLN cc_start: 0.9311 (OUTLIER) cc_final: 0.8767 (tp-100) REVERT: K 69 GLN cc_start: 0.9311 (OUTLIER) cc_final: 0.8766 (tp-100) REVERT: L 69 GLN cc_start: 0.9313 (OUTLIER) cc_final: 0.8765 (tp-100) REVERT: M 69 GLN cc_start: 0.9310 (OUTLIER) cc_final: 0.8764 (tp-100) REVERT: N 69 GLN cc_start: 0.9308 (OUTLIER) cc_final: 0.8759 (tp-100) REVERT: O 69 GLN cc_start: 0.9310 (OUTLIER) cc_final: 0.8764 (tp-100) REVERT: P 69 GLN cc_start: 0.9311 (OUTLIER) cc_final: 0.8765 (tp-100) REVERT: Q 69 GLN cc_start: 0.9309 (OUTLIER) cc_final: 0.8762 (tp-100) REVERT: R 69 GLN cc_start: 0.9310 (OUTLIER) cc_final: 0.8766 (tp-100) REVERT: S 69 GLN cc_start: 0.9310 (OUTLIER) cc_final: 0.8764 (tp-100) REVERT: T 69 GLN cc_start: 0.9309 (OUTLIER) cc_final: 0.8760 (tp-100) REVERT: V 69 GLN cc_start: 0.9309 (OUTLIER) cc_final: 0.8763 (tp-100) REVERT: W 69 GLN cc_start: 0.9312 (OUTLIER) cc_final: 0.8766 (tp-100) REVERT: X 69 GLN cc_start: 0.9309 (OUTLIER) cc_final: 0.8760 (tp-100) REVERT: Y 69 GLN cc_start: 0.9310 (OUTLIER) cc_final: 0.8767 (tp-100) outliers start: 28 outliers final: 1 residues processed: 625 average time/residue: 1.0075 time to fit residues: 705.6615 Evaluate side-chains 594 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 566 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 153 ARG Chi-restraints excluded: chain D residue 69 GLN Chi-restraints excluded: chain E residue 69 GLN Chi-restraints excluded: chain E residue 153 ARG Chi-restraints excluded: chain F residue 69 GLN Chi-restraints excluded: chain F residue 153 ARG Chi-restraints excluded: chain G residue 69 GLN Chi-restraints excluded: chain H residue 69 GLN Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain J residue 69 GLN Chi-restraints excluded: chain K residue 69 GLN Chi-restraints excluded: chain L residue 69 GLN Chi-restraints excluded: chain M residue 69 GLN Chi-restraints excluded: chain N residue 69 GLN Chi-restraints excluded: chain O residue 69 GLN Chi-restraints excluded: chain P residue 69 GLN Chi-restraints excluded: chain Q residue 69 GLN Chi-restraints excluded: chain R residue 69 GLN Chi-restraints excluded: chain S residue 69 GLN Chi-restraints excluded: chain T residue 69 GLN Chi-restraints excluded: chain V residue 69 GLN Chi-restraints excluded: chain W residue 69 GLN Chi-restraints excluded: chain X residue 69 GLN Chi-restraints excluded: chain Y residue 69 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 319 optimal weight: 4.9990 chunk 272 optimal weight: 10.0000 chunk 375 optimal weight: 1.9990 chunk 286 optimal weight: 1.9990 chunk 343 optimal weight: 1.9990 chunk 208 optimal weight: 2.9990 chunk 261 optimal weight: 8.9990 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 274 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.3559 r_free = 0.3559 target = 0.124818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.108220 restraints weight = 33216.829| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.32 r_work: 0.3208 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 33264 Z= 0.125 Angle : 0.462 4.477 44784 Z= 0.261 Chirality : 0.035 0.119 4920 Planarity : 0.003 0.025 5880 Dihedral : 4.119 15.956 4464 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.90 % Allowed : 9.46 % Favored : 89.64 % 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: 5.04 (0.14), residues: 4032 helix: 3.96 (0.09), residues: 3336 sheet: None (None), residues: 0 loop : -0.26 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 72 TYR 0.005 0.001 TYR O 23 PHE 0.015 0.002 PHE S 37 TRP 0.005 0.001 TRP O 89 HIS 0.003 0.001 HIS I 124 Details of bonding type rmsd covalent geometry : bond 0.00276 (33264) covalent geometry : angle 0.46232 (44784) hydrogen bonds : bond 0.04825 ( 2688) hydrogen bonds : angle 2.98326 ( 8064) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 614 time to evaluate : 1.324 Fit side-chains REVERT: B 53 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8208 (mt-10) REVERT: B 69 GLN cc_start: 0.9253 (OUTLIER) cc_final: 0.8651 (tp-100) REVERT: A 53 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8211 (mt-10) REVERT: A 69 GLN cc_start: 0.9253 (OUTLIER) cc_final: 0.8649 (tp-100) REVERT: C 53 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8217 (mt-10) REVERT: C 69 GLN cc_start: 0.9247 (OUTLIER) cc_final: 0.8641 (tp-100) REVERT: C 153 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.7280 (ptp90) REVERT: D 53 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8217 (mt-10) REVERT: D 69 GLN cc_start: 0.9253 (OUTLIER) cc_final: 0.8706 (tp-100) REVERT: D 153 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.7239 (ptp90) REVERT: E 69 GLN cc_start: 0.9254 (OUTLIER) cc_final: 0.8655 (tp-100) REVERT: E 153 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.7291 (ptp90) REVERT: F 69 GLN cc_start: 0.9254 (OUTLIER) cc_final: 0.8654 (tp-100) REVERT: F 153 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.7288 (ptp90) REVERT: G 69 GLN cc_start: 0.9256 (OUTLIER) cc_final: 0.8710 (tp-100) REVERT: H 69 GLN cc_start: 0.9253 (OUTLIER) cc_final: 0.8653 (tp-100) REVERT: H 153 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.7251 (ptp90) REVERT: I 53 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8213 (mt-10) REVERT: I 69 GLN cc_start: 0.9253 (OUTLIER) cc_final: 0.8703 (tp-100) REVERT: I 153 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.7285 (ptp90) REVERT: J 53 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8225 (mt-10) REVERT: J 69 GLN cc_start: 0.9259 (OUTLIER) cc_final: 0.8679 (tp-100) REVERT: K 53 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8227 (mt-10) REVERT: K 69 GLN cc_start: 0.9253 (OUTLIER) cc_final: 0.8653 (tp-100) REVERT: L 69 GLN cc_start: 0.9253 (OUTLIER) cc_final: 0.8652 (tp-100) REVERT: M 53 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8220 (mt-10) REVERT: M 69 GLN cc_start: 0.9252 (OUTLIER) cc_final: 0.8652 (tp-100) REVERT: N 53 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8215 (mt-10) REVERT: N 69 GLN cc_start: 0.9252 (OUTLIER) cc_final: 0.8647 (tp-100) REVERT: O 53 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8223 (mt-10) REVERT: O 69 GLN cc_start: 0.9252 (OUTLIER) cc_final: 0.8652 (tp-100) REVERT: P 53 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8217 (mt-10) REVERT: P 69 GLN cc_start: 0.9252 (OUTLIER) cc_final: 0.8649 (tp-100) REVERT: Q 53 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8211 (mt-10) REVERT: Q 69 GLN cc_start: 0.9254 (OUTLIER) cc_final: 0.8652 (tp-100) REVERT: R 53 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8223 (mt-10) REVERT: R 69 GLN cc_start: 0.9253 (OUTLIER) cc_final: 0.8651 (tp-100) REVERT: S 53 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8220 (mt-10) REVERT: S 69 GLN cc_start: 0.9259 (OUTLIER) cc_final: 0.8678 (tp-100) REVERT: T 53 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8209 (mt-10) REVERT: T 69 GLN cc_start: 0.9254 (OUTLIER) cc_final: 0.8653 (tp-100) REVERT: V 53 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8220 (mt-10) REVERT: V 69 GLN cc_start: 0.9253 (OUTLIER) cc_final: 0.8651 (tp-100) REVERT: W 53 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8218 (mt-10) REVERT: W 69 GLN cc_start: 0.9255 (OUTLIER) cc_final: 0.8657 (tp-100) REVERT: X 53 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8212 (mt-10) REVERT: X 69 GLN cc_start: 0.9254 (OUTLIER) cc_final: 0.8652 (tp-100) REVERT: Y 53 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8218 (mt-10) REVERT: Y 69 GLN cc_start: 0.9253 (OUTLIER) cc_final: 0.8652 (tp-100) outliers start: 31 outliers final: 1 residues processed: 644 average time/residue: 1.0517 time to fit residues: 756.1971 Evaluate side-chains 646 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 615 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 153 ARG Chi-restraints excluded: chain D residue 69 GLN Chi-restraints excluded: chain D residue 153 ARG Chi-restraints excluded: chain E residue 69 GLN Chi-restraints excluded: chain E residue 153 ARG Chi-restraints excluded: chain F residue 69 GLN Chi-restraints excluded: chain F residue 153 ARG Chi-restraints excluded: chain G residue 69 GLN Chi-restraints excluded: chain H residue 69 GLN Chi-restraints excluded: chain H residue 153 ARG Chi-restraints excluded: chain I residue 69 GLN Chi-restraints excluded: chain I residue 153 ARG Chi-restraints excluded: chain J residue 69 GLN Chi-restraints excluded: chain K residue 69 GLN Chi-restraints excluded: chain L residue 69 GLN Chi-restraints excluded: chain M residue 69 GLN Chi-restraints excluded: chain N residue 69 GLN Chi-restraints excluded: chain O residue 69 GLN Chi-restraints excluded: chain P residue 69 GLN Chi-restraints excluded: chain Q residue 69 GLN Chi-restraints excluded: chain R residue 69 GLN Chi-restraints excluded: chain S residue 69 GLN Chi-restraints excluded: chain T residue 69 GLN Chi-restraints excluded: chain V residue 69 GLN Chi-restraints excluded: chain W residue 69 GLN Chi-restraints excluded: chain X residue 69 GLN Chi-restraints excluded: chain Y residue 69 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 311 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 323 optimal weight: 5.9990 chunk 178 optimal weight: 2.9990 chunk 271 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 309 optimal weight: 2.9990 chunk 66 optimal weight: 0.4980 chunk 173 optimal weight: 6.9990 chunk 246 optimal weight: 5.9990 chunk 226 optimal weight: 0.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 71 GLN S 71 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.125807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.109008 restraints weight = 33319.545| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.33 r_work: 0.3214 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 33264 Z= 0.115 Angle : 0.448 4.406 44784 Z= 0.253 Chirality : 0.034 0.115 4920 Planarity : 0.003 0.024 5880 Dihedral : 4.025 15.122 4464 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.27 % Allowed : 9.06 % Favored : 89.67 % 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: 5.16 (0.13), residues: 4032 helix: 4.03 (0.09), residues: 3336 sheet: None (None), residues: 0 loop : -0.18 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 59 TYR 0.005 0.001 TYR I 23 PHE 0.014 0.002 PHE F 37 TRP 0.005 0.001 TRP I 89 HIS 0.002 0.001 HIS C 124 Details of bonding type rmsd covalent geometry : bond 0.00249 (33264) covalent geometry : angle 0.44778 (44784) hydrogen bonds : bond 0.04587 ( 2688) hydrogen bonds : angle 2.95666 ( 8064) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15226.53 seconds wall clock time: 258 minutes 30.91 seconds (15510.91 seconds total)