Starting phenix.real_space_refine on Thu Sep 18 01:26:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c1i_45120/09_2025/9c1i_45120.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c1i_45120/09_2025/9c1i_45120.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c1i_45120/09_2025/9c1i_45120.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c1i_45120/09_2025/9c1i_45120.map" model { file = "/net/cci-nas-00/data/ceres_data/9c1i_45120/09_2025/9c1i_45120.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c1i_45120/09_2025/9c1i_45120.cif" } resolution = 3.52 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 ------------------------------------------------------------------------------- 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 22 5.16 5 C 4228 2.51 5 N 1092 2.21 5 O 1306 1.98 5 H 6348 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12996 Number of models: 1 Model: "" Number of chains: 2 Chain: "2" Number of atoms: 6498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 6498 Classifications: {'peptide': 420} Link IDs: {'PCIS': 3, 'PTRANS': 20, 'TRANS': 396} Chain breaks: 1 Chain: "3" Number of atoms: 6498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 6498 Classifications: {'peptide': 420} Link IDs: {'PCIS': 3, 'PTRANS': 20, 'TRANS': 396} Chain breaks: 1 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N GLY 2 156 " occ=0.50 ... (5 atoms not shown) pdb=" HA3 GLY 2 156 " occ=0.50 residue: pdb=" N GLY 3 156 " occ=0.50 ... (5 atoms not shown) pdb=" HA3 GLY 3 156 " occ=0.50 Time building chain proxies: 3.14, per 1000 atoms: 0.24 Number of scatterers: 12996 At special positions: 0 Unit cell: (92.4, 117.15, 94.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 22 16.00 O 1306 8.00 N 1092 7.00 C 4228 6.00 H 6348 1.00 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: 1.22 Conformation dependent library (CDL) restraints added in 430.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1568 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 13 sheets defined 5.2% alpha, 41.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain '2' and resid 193 through 197 Processing helix chain '2' and resid 212 through 222 Processing helix chain '2' and resid 359 through 364 removed outlier: 3.859A pdb=" N ARG 2 363 " --> pdb=" O SER 2 359 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN 2 364 " --> pdb=" O GLN 2 360 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 359 through 364' Processing helix chain '3' and resid 193 through 197 Processing helix chain '3' and resid 212 through 222 Processing helix chain '3' and resid 359 through 364 removed outlier: 3.566A pdb=" N ARG 3 363 " --> pdb=" O SER 3 359 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '2' and resid 48 through 50 WARNING: can't find start of bonding for strands! previous: chain '2' and resid 48 through 50 current: chain '2' and resid 310 through 321 WARNING: can't find start of bonding for strands! previous: chain '2' and resid 350 through 357 current: chain '2' and resid 396 through 415 removed outlier: 9.146A pdb=" N MET 2 397 " --> pdb=" O PHE 2 437 " (cutoff:3.500A) removed outlier: 9.080A pdb=" N PHE 2 437 " --> pdb=" O MET 2 397 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLY 2 399 " --> pdb=" O PRO 2 435 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA 2 401 " --> pdb=" O GLU 2 433 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ARG 2 427 " --> pdb=" O ALA 2 407 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N VAL 2 409 " --> pdb=" O ARG 2 425 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG 2 425 " --> pdb=" O VAL 2 409 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU 2 411 " --> pdb=" O SER 2 423 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N SER 2 423 " --> pdb=" O LEU 2 411 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N THR 2 413 " --> pdb=" O LEU 2 421 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU 2 421 " --> pdb=" O THR 2 413 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '2' and resid 420 through 439 current: chain '3' and resid 310 through 321 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 350 through 357 current: chain '3' and resid 401 through 416 removed outlier: 5.580A pdb=" N LEU 3 404 " --> pdb=" O THR 3 431 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR 3 431 " --> pdb=" O LEU 3 404 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N SER 3 406 " --> pdb=" O ARG 3 429 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ARG 3 429 " --> pdb=" O SER 3 406 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLY 3 408 " --> pdb=" O ARG 3 427 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG 3 427 " --> pdb=" O GLY 3 408 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '2' and resid 58 through 60 WARNING: can't find start of bonding for strands! previous: chain '2' and resid 58 through 60 current: chain '3' and resid 290 through 297 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 290 through 297 current: chain '3' and resid 338 through 345 removed outlier: 3.696A pdb=" N ILE 3 345 " --> pdb=" O LEU 3 450 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU 3 450 " --> pdb=" O ILE 3 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain '2' and resid 185 through 190 removed outlier: 5.125A pdb=" N ALA 2 166 " --> pdb=" O TYR 2 177 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N LYS 2 169 " --> pdb=" O TYR 2 80 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N TYR 2 80 " --> pdb=" O LYS 2 169 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '2' and resid 153 through 160 removed outlier: 6.382A pdb=" N PHE 2 140 " --> pdb=" O PRO 2 157 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLN 2 159 " --> pdb=" O TRP 2 138 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N TRP 2 138 " --> pdb=" O GLN 2 159 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU 2 103 " --> pdb=" O GLU 2 94 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N GLU 2 94 " --> pdb=" O LEU 2 103 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N THR 2 105 " --> pdb=" O VAL 2 92 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '2' and resid 115 through 121 Processing sheet with id=AA6, first strand: chain '2' and resid 252 through 257 removed outlier: 7.182A pdb=" N GLU 3 264 " --> pdb=" O VAL 2 256 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU 3 473 " --> pdb=" O VAL 3 368 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N VAL 3 368 " --> pdb=" O LEU 3 473 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '2' and resid 368 through 375 removed outlier: 5.913A pdb=" N VAL 2 368 " --> pdb=" O LEU 2 473 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU 2 473 " --> pdb=" O VAL 2 368 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N GLU 2 264 " --> pdb=" O VAL 3 256 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU 3 252 " --> pdb=" O ASN 2 268 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '2' and resid 278 through 283 removed outlier: 4.138A pdb=" N ALA 2 278 " --> pdb=" O LYS 2 297 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '2' and resid 450 through 451 Processing sheet with id=AB1, first strand: chain '3' and resid 185 through 190 removed outlier: 5.753A pdb=" N ALA 3 166 " --> pdb=" O TYR 3 177 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LYS 3 169 " --> pdb=" O TYR 3 80 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N TYR 3 80 " --> pdb=" O LYS 3 169 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '3' and resid 154 through 160 removed outlier: 6.266A pdb=" N GLN 3 154 " --> pdb=" O VAL 3 144 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL 3 144 " --> pdb=" O GLN 3 154 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N GLY 3 156 " --> pdb=" O ASP 3 142 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ASP 3 142 " --> pdb=" O GLY 3 156 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU 3 103 " --> pdb=" O GLU 3 94 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLU 3 94 " --> pdb=" O LEU 3 103 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N THR 3 105 " --> pdb=" O VAL 3 92 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '3' and resid 112 through 121 removed outlier: 3.682A pdb=" N SER 3 114 " --> pdb=" O ILE 3 130 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ILE 3 130 " --> pdb=" O SER 3 114 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N THR 3 116 " --> pdb=" O ILE 3 128 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE 3 128 " --> pdb=" O THR 3 116 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N SER 3 118 " --> pdb=" O GLU 3 126 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N GLU 3 126 " --> pdb=" O SER 3 118 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N THR 3 120 " --> pdb=" O THR 3 124 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N THR 3 124 " --> pdb=" O THR 3 120 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '3' and resid 385 through 386 195 hydrogen bonds defined for protein. 486 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: 3.08 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6340 1.03 - 1.23: 11 1.23 - 1.42: 2994 1.42 - 1.61: 3791 1.61 - 1.81: 36 Bond restraints: 13172 Sorted by residual: bond pdb=" C GLU 3 180 " pdb=" N THR 3 181 " ideal model delta sigma weight residual 1.331 1.377 -0.046 2.83e-02 1.25e+03 2.59e+00 bond pdb=" C GLY 3 330 " pdb=" N GLY 3 331 " ideal model delta sigma weight residual 1.321 1.331 -0.009 1.24e-02 6.50e+03 5.77e-01 bond pdb=" CB THR 3 316 " pdb=" CG2 THR 3 316 " ideal model delta sigma weight residual 1.521 1.496 0.025 3.30e-02 9.18e+02 5.64e-01 bond pdb=" CB VAL 3 353 " pdb=" CG1 VAL 3 353 " ideal model delta sigma weight residual 1.521 1.497 0.024 3.30e-02 9.18e+02 5.46e-01 bond pdb=" CG PRO 2 162 " pdb=" CD PRO 2 162 " ideal model delta sigma weight residual 1.503 1.479 0.024 3.40e-02 8.65e+02 4.95e-01 ... (remaining 13167 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 22715 1.21 - 2.43: 822 2.43 - 3.64: 71 3.64 - 4.85: 19 4.85 - 6.07: 3 Bond angle restraints: 23630 Sorted by residual: angle pdb=" C GLY 2 156 " pdb=" N PRO 2 157 " pdb=" CA PRO 2 157 " ideal model delta sigma weight residual 127.00 131.94 -4.94 2.40e+00 1.74e-01 4.24e+00 angle pdb=" N ARG 3 363 " pdb=" CA ARG 3 363 " pdb=" C ARG 3 363 " ideal model delta sigma weight residual 111.71 109.59 2.12 1.15e+00 7.56e-01 3.39e+00 angle pdb=" CA PRO 3 162 " pdb=" N PRO 3 162 " pdb=" CD PRO 3 162 " ideal model delta sigma weight residual 112.00 109.47 2.53 1.40e+00 5.10e-01 3.26e+00 angle pdb=" N VAL 3 92 " pdb=" CA VAL 3 92 " pdb=" C VAL 3 92 " ideal model delta sigma weight residual 111.62 110.20 1.42 7.90e-01 1.60e+00 3.25e+00 angle pdb=" CA THR 3 161 " pdb=" C THR 3 161 " pdb=" N PRO 3 162 " ideal model delta sigma weight residual 118.44 121.04 -2.60 1.59e+00 3.96e-01 2.67e+00 ... (remaining 23625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.88: 5663 16.88 - 33.75: 521 33.75 - 50.63: 126 50.63 - 67.51: 37 67.51 - 84.38: 7 Dihedral angle restraints: 6354 sinusoidal: 3356 harmonic: 2998 Sorted by residual: dihedral pdb=" CA ASN 2 229 " pdb=" C ASN 2 229 " pdb=" N THR 2 230 " pdb=" CA THR 2 230 " ideal model delta harmonic sigma weight residual -180.00 -163.15 -16.85 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA ARG 3 429 " pdb=" C ARG 3 429 " pdb=" N LEU 3 430 " pdb=" CA LEU 3 430 " ideal model delta harmonic sigma weight residual -180.00 -164.03 -15.97 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CA LEU 3 450 " pdb=" CB LEU 3 450 " pdb=" CG LEU 3 450 " pdb=" CD1 LEU 3 450 " ideal model delta sinusoidal sigma weight residual 180.00 121.62 58.38 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 6351 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 570 0.031 - 0.062: 318 0.062 - 0.092: 70 0.092 - 0.123: 61 0.123 - 0.154: 11 Chirality restraints: 1030 Sorted by residual: chirality pdb=" CA ILE 3 294 " pdb=" N ILE 3 294 " pdb=" C ILE 3 294 " pdb=" CB ILE 3 294 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CA ILE 2 294 " pdb=" N ILE 2 294 " pdb=" C ILE 2 294 " pdb=" CB ILE 2 294 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.91e-01 chirality pdb=" CA VAL 3 143 " pdb=" N VAL 3 143 " pdb=" C VAL 3 143 " pdb=" CB VAL 3 143 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.12e-01 ... (remaining 1027 not shown) Planarity restraints: 1996 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE 3 208 " 0.021 5.00e-02 4.00e+02 3.11e-02 1.54e+00 pdb=" N PRO 3 209 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO 3 209 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO 3 209 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR 2 161 " 0.018 5.00e-02 4.00e+02 2.72e-02 1.19e+00 pdb=" N PRO 2 162 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO 2 162 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO 2 162 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR 3 161 " 0.018 5.00e-02 4.00e+02 2.70e-02 1.17e+00 pdb=" N PRO 3 162 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO 3 162 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO 3 162 " 0.015 5.00e-02 4.00e+02 ... (remaining 1993 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 1238 2.22 - 2.81: 27443 2.81 - 3.41: 33001 3.41 - 4.00: 46412 4.00 - 4.60: 69181 Nonbonded interactions: 177275 Sorted by model distance: nonbonded pdb=" O GLU 3 212 " pdb=" HG1 THR 3 215 " model vdw 1.624 2.450 nonbonded pdb=" H SER 2 260 " pdb=" O TRP 3 262 " model vdw 1.630 2.450 nonbonded pdb=" H THR 2 96 " pdb=" OD1 ASN 2 198 " model vdw 1.656 2.450 nonbonded pdb=" OE1 GLN 2 228 " pdb=" HG SER 3 438 " model vdw 1.660 2.450 nonbonded pdb="HD21 ASN 3 97 " pdb=" OD1 ASP 3 100 " model vdw 1.660 2.450 ... (remaining 177270 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain '2' selection = chain '3' } 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=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.140 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: 0.090 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.140 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6824 Z= 0.157 Angle : 0.552 6.069 9324 Z= 0.297 Chirality : 0.045 0.154 1030 Planarity : 0.004 0.031 1206 Dihedral : 13.697 84.383 2420 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.14 % Allowed : 15.08 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % 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 aren not related in a simple way. whole: -1.88 (0.28), residues: 832 helix: -2.82 (0.78), residues: 36 sheet: -0.92 (0.25), residues: 374 loop : -1.32 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 3 210 TYR 0.012 0.001 TYR 3 342 PHE 0.016 0.001 PHE 2 468 TRP 0.012 0.001 TRP 3 81 HIS 0.002 0.001 HIS 2 315 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 6824) covalent geometry : angle 0.55200 ( 9324) hydrogen bonds : bond 0.12483 ( 195) hydrogen bonds : angle 6.90504 ( 486) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 228 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 109 GLU cc_start: 0.7008 (mt-10) cc_final: 0.6033 (pm20) REVERT: 2 138 TRP cc_start: 0.5325 (m100) cc_final: 0.4976 (m100) REVERT: 2 175 TYR cc_start: 0.4496 (m-80) cc_final: 0.4143 (m-80) REVERT: 2 199 MET cc_start: 0.4971 (mmt) cc_final: 0.4699 (mtt) REVERT: 2 323 MET cc_start: 0.8201 (ptp) cc_final: 0.7919 (ptp) REVERT: 2 337 PHE cc_start: 0.8609 (t80) cc_final: 0.8315 (t80) REVERT: 2 374 ASN cc_start: 0.7634 (m-40) cc_final: 0.7233 (p0) REVERT: 3 154 GLN cc_start: 0.4470 (mt0) cc_final: 0.2822 (pm20) REVERT: 3 213 GLU cc_start: 0.7344 (pt0) cc_final: 0.6881 (tm-30) REVERT: 3 253 ASP cc_start: 0.7448 (p0) cc_final: 0.7074 (p0) REVERT: 3 292 SER cc_start: 0.8901 (t) cc_final: 0.8386 (p) REVERT: 3 297 LYS cc_start: 0.8839 (tttt) cc_final: 0.8469 (ttmt) REVERT: 3 339 ILE cc_start: 0.8371 (mm) cc_final: 0.8151 (mm) outliers start: 1 outliers final: 1 residues processed: 229 average time/residue: 0.1646 time to fit residues: 52.5237 Evaluate side-chains 168 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 167 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 81 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 7.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 329 ASN 3 393 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.207039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.179726 restraints weight = 30269.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.184410 restraints weight = 9513.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.186755 restraints weight = 4549.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.187929 restraints weight = 3089.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.188126 restraints weight = 2592.270| |-----------------------------------------------------------------------------| r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4128 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4128 r_free = 0.4128 target_work(ls_wunit_k1) = 0.184 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4101 r_free = 0.4101 target_work(ls_wunit_k1) = 0.182 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.4101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6824 Z= 0.158 Angle : 0.536 4.986 9324 Z= 0.288 Chirality : 0.044 0.173 1030 Planarity : 0.005 0.063 1206 Dihedral : 5.001 51.002 928 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 1.77 % Allowed : 18.07 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % 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 aren not related in a simple way. whole: -1.90 (0.28), residues: 832 helix: -2.46 (0.78), residues: 36 sheet: -1.06 (0.25), residues: 394 loop : -1.22 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 2 441 TYR 0.009 0.001 TYR 2 355 PHE 0.014 0.001 PHE 2 468 TRP 0.008 0.001 TRP 2 356 HIS 0.002 0.001 HIS 2 170 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 6824) covalent geometry : angle 0.53622 ( 9324) hydrogen bonds : bond 0.04018 ( 195) hydrogen bonds : angle 5.92953 ( 486) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 168 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 109 GLU cc_start: 0.7062 (mt-10) cc_final: 0.6069 (pm20) REVERT: 2 138 TRP cc_start: 0.5458 (m100) cc_final: 0.5127 (m100) REVERT: 2 168 MET cc_start: 0.6403 (ttp) cc_final: 0.5810 (ttp) REVERT: 2 175 TYR cc_start: 0.4503 (m-80) cc_final: 0.4152 (m-80) REVERT: 2 199 MET cc_start: 0.4750 (mmt) cc_final: 0.4540 (mtt) REVERT: 2 200 THR cc_start: 0.8331 (t) cc_final: 0.8043 (m) REVERT: 2 337 PHE cc_start: 0.8578 (t80) cc_final: 0.8302 (t80) REVERT: 2 374 ASN cc_start: 0.7652 (m-40) cc_final: 0.7188 (p0) REVERT: 2 396 VAL cc_start: 0.6539 (OUTLIER) cc_final: 0.6247 (m) REVERT: 3 187 LYS cc_start: 0.6431 (mttt) cc_final: 0.6212 (tptt) REVERT: 3 213 GLU cc_start: 0.7279 (pt0) cc_final: 0.6858 (tm-30) REVERT: 3 292 SER cc_start: 0.8819 (t) cc_final: 0.8454 (p) REVERT: 3 297 LYS cc_start: 0.8857 (tttt) cc_final: 0.8454 (ttmt) outliers start: 13 outliers final: 9 residues processed: 176 average time/residue: 0.1592 time to fit residues: 39.3248 Evaluate side-chains 157 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 147 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 81 TRP Chi-restraints excluded: chain 2 residue 105 THR Chi-restraints excluded: chain 2 residue 134 SER Chi-restraints excluded: chain 2 residue 292 SER Chi-restraints excluded: chain 2 residue 304 THR Chi-restraints excluded: chain 2 residue 306 THR Chi-restraints excluded: chain 2 residue 396 VAL Chi-restraints excluded: chain 3 residue 143 VAL Chi-restraints excluded: chain 3 residue 176 THR Chi-restraints excluded: chain 3 residue 338 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 76 optimal weight: 5.9990 chunk 49 optimal weight: 0.0020 chunk 55 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 overall best weight: 3.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.203471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.176048 restraints weight = 30314.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.180686 restraints weight = 9512.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.183065 restraints weight = 4554.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.184023 restraints weight = 3070.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.184639 restraints weight = 2612.619| |-----------------------------------------------------------------------------| r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4079 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4079 r_free = 0.4079 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4073 r_free = 0.4073 target_work(ls_wunit_k1) = 0.179 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| r_final: 0.4073 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6824 Z= 0.154 Angle : 0.520 4.954 9324 Z= 0.279 Chirality : 0.044 0.187 1030 Planarity : 0.004 0.061 1206 Dihedral : 4.950 50.821 928 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 2.58 % Allowed : 19.43 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % 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 aren not related in a simple way. whole: -1.98 (0.28), residues: 832 helix: -2.14 (0.83), residues: 34 sheet: -1.13 (0.25), residues: 386 loop : -1.30 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 3 441 TYR 0.010 0.001 TYR 2 355 PHE 0.014 0.001 PHE 2 468 TRP 0.007 0.001 TRP 2 356 HIS 0.003 0.001 HIS 3 170 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 6824) covalent geometry : angle 0.52039 ( 9324) hydrogen bonds : bond 0.03664 ( 195) hydrogen bonds : angle 5.71866 ( 486) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 155 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 109 GLU cc_start: 0.7137 (mt-10) cc_final: 0.6106 (pm20) REVERT: 2 138 TRP cc_start: 0.5473 (m100) cc_final: 0.5179 (m100) REVERT: 2 168 MET cc_start: 0.6792 (ttp) cc_final: 0.6237 (ttp) REVERT: 2 175 TYR cc_start: 0.4497 (m-80) cc_final: 0.4266 (m-80) REVERT: 2 200 THR cc_start: 0.8304 (t) cc_final: 0.7997 (m) REVERT: 2 337 PHE cc_start: 0.8589 (t80) cc_final: 0.8280 (t80) REVERT: 2 374 ASN cc_start: 0.7685 (m-40) cc_final: 0.7122 (p0) REVERT: 2 396 VAL cc_start: 0.6534 (OUTLIER) cc_final: 0.6250 (m) REVERT: 3 187 LYS cc_start: 0.6578 (mttt) cc_final: 0.6319 (tptt) REVERT: 3 213 GLU cc_start: 0.7233 (pt0) cc_final: 0.6714 (tm-30) REVERT: 3 253 ASP cc_start: 0.7521 (p0) cc_final: 0.7112 (p0) REVERT: 3 267 TYR cc_start: 0.8459 (m-80) cc_final: 0.8256 (m-80) REVERT: 3 292 SER cc_start: 0.8849 (t) cc_final: 0.8452 (p) REVERT: 3 297 LYS cc_start: 0.8846 (tttt) cc_final: 0.8466 (ttmt) outliers start: 19 outliers final: 12 residues processed: 168 average time/residue: 0.1621 time to fit residues: 38.3961 Evaluate side-chains 161 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 81 TRP Chi-restraints excluded: chain 2 residue 100 ASP Chi-restraints excluded: chain 2 residue 134 SER Chi-restraints excluded: chain 2 residue 292 SER Chi-restraints excluded: chain 2 residue 304 THR Chi-restraints excluded: chain 2 residue 306 THR Chi-restraints excluded: chain 2 residue 396 VAL Chi-restraints excluded: chain 3 residue 141 ILE Chi-restraints excluded: chain 3 residue 143 VAL Chi-restraints excluded: chain 3 residue 176 THR Chi-restraints excluded: chain 3 residue 300 ASN Chi-restraints excluded: chain 3 residue 318 CYS Chi-restraints excluded: chain 3 residue 338 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 76 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 74 optimal weight: 9.9990 chunk 36 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 178 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.199805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.171890 restraints weight = 30181.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.176488 restraints weight = 9427.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.178864 restraints weight = 4505.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.179814 restraints weight = 3033.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.180492 restraints weight = 2590.999| |-----------------------------------------------------------------------------| r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4110 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4110 r_free = 0.4110 target_work(ls_wunit_k1) = 0.182 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4109 r_free = 0.4109 target_work(ls_wunit_k1) = 0.182 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| r_final: 0.4109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6824 Z= 0.155 Angle : 0.526 5.082 9324 Z= 0.279 Chirality : 0.044 0.168 1030 Planarity : 0.004 0.059 1206 Dihedral : 4.948 51.240 928 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 2.99 % Allowed : 19.84 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % 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 aren not related in a simple way. whole: -2.08 (0.27), residues: 832 helix: -2.05 (0.82), residues: 34 sheet: -1.23 (0.24), residues: 392 loop : -1.35 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 3 441 TYR 0.012 0.001 TYR 2 119 PHE 0.014 0.001 PHE 2 468 TRP 0.007 0.001 TRP 2 356 HIS 0.001 0.001 HIS 2 170 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 6824) covalent geometry : angle 0.52578 ( 9324) hydrogen bonds : bond 0.03407 ( 195) hydrogen bonds : angle 5.63633 ( 486) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 109 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6119 (pm20) REVERT: 2 138 TRP cc_start: 0.5465 (m100) cc_final: 0.5206 (m100) REVERT: 2 168 MET cc_start: 0.7098 (ttp) cc_final: 0.6427 (ttp) REVERT: 2 175 TYR cc_start: 0.4480 (m-80) cc_final: 0.4144 (m-80) REVERT: 2 200 THR cc_start: 0.8396 (t) cc_final: 0.8051 (m) REVERT: 2 374 ASN cc_start: 0.7616 (m-40) cc_final: 0.7113 (p0) REVERT: 2 396 VAL cc_start: 0.6536 (OUTLIER) cc_final: 0.6264 (m) REVERT: 3 177 TYR cc_start: 0.7416 (m-80) cc_final: 0.7105 (m-80) REVERT: 3 187 LYS cc_start: 0.6525 (mttt) cc_final: 0.6270 (tptt) REVERT: 3 212 GLU cc_start: 0.8327 (mt-10) cc_final: 0.8115 (mt-10) REVERT: 3 213 GLU cc_start: 0.7248 (pt0) cc_final: 0.6777 (tm-30) REVERT: 3 267 TYR cc_start: 0.8445 (m-80) cc_final: 0.8190 (m-80) REVERT: 3 292 SER cc_start: 0.8894 (t) cc_final: 0.8470 (p) REVERT: 3 297 LYS cc_start: 0.8851 (tttt) cc_final: 0.8447 (ttmt) outliers start: 22 outliers final: 17 residues processed: 162 average time/residue: 0.1649 time to fit residues: 37.3043 Evaluate side-chains 162 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 81 TRP Chi-restraints excluded: chain 2 residue 100 ASP Chi-restraints excluded: chain 2 residue 134 SER Chi-restraints excluded: chain 2 residue 199 MET Chi-restraints excluded: chain 2 residue 292 SER Chi-restraints excluded: chain 2 residue 304 THR Chi-restraints excluded: chain 2 residue 306 THR Chi-restraints excluded: chain 2 residue 391 VAL Chi-restraints excluded: chain 2 residue 396 VAL Chi-restraints excluded: chain 3 residue 141 ILE Chi-restraints excluded: chain 3 residue 143 VAL Chi-restraints excluded: chain 3 residue 176 THR Chi-restraints excluded: chain 3 residue 186 THR Chi-restraints excluded: chain 3 residue 287 LEU Chi-restraints excluded: chain 3 residue 318 CYS Chi-restraints excluded: chain 3 residue 338 VAL Chi-restraints excluded: chain 3 residue 391 VAL Chi-restraints excluded: chain 3 residue 431 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 77 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 39 optimal weight: 0.7980 chunk 63 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.199918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.172193 restraints weight = 30669.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.176660 restraints weight = 9565.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.178947 restraints weight = 4581.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.180117 restraints weight = 3102.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.180548 restraints weight = 2601.358| |-----------------------------------------------------------------------------| r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4049 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4049 r_free = 0.4049 target_work(ls_wunit_k1) = 0.177 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4049 r_free = 0.4049 target_work(ls_wunit_k1) = 0.177 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 41 | |-----------------------------------------------------------------------------| r_final: 0.4049 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6824 Z= 0.209 Angle : 0.547 4.854 9324 Z= 0.294 Chirality : 0.044 0.160 1030 Planarity : 0.005 0.061 1206 Dihedral : 5.056 51.552 928 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 3.40 % Allowed : 20.38 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % 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 aren not related in a simple way. whole: -2.30 (0.27), residues: 832 helix: -2.14 (0.78), residues: 34 sheet: -1.37 (0.24), residues: 402 loop : -1.50 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 3 441 TYR 0.013 0.001 TYR 2 355 PHE 0.020 0.002 PHE 2 140 TRP 0.008 0.001 TRP 2 356 HIS 0.002 0.001 HIS 3 170 Details of bonding type rmsd covalent geometry : bond 0.00479 ( 6824) covalent geometry : angle 0.54660 ( 9324) hydrogen bonds : bond 0.03474 ( 195) hydrogen bonds : angle 5.66131 ( 486) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 109 GLU cc_start: 0.7199 (mt-10) cc_final: 0.6069 (pm20) REVERT: 2 138 TRP cc_start: 0.5433 (m100) cc_final: 0.5151 (m100) REVERT: 2 168 MET cc_start: 0.7251 (ttp) cc_final: 0.6624 (ttp) REVERT: 2 175 TYR cc_start: 0.4593 (m-80) cc_final: 0.4256 (m-80) REVERT: 2 200 THR cc_start: 0.8346 (t) cc_final: 0.7983 (m) REVERT: 2 374 ASN cc_start: 0.7639 (m-40) cc_final: 0.7141 (p0) REVERT: 2 396 VAL cc_start: 0.6580 (OUTLIER) cc_final: 0.6291 (m) REVERT: 2 456 ASN cc_start: 0.8286 (m-40) cc_final: 0.8082 (t0) REVERT: 3 177 TYR cc_start: 0.7582 (m-80) cc_final: 0.7345 (m-80) REVERT: 3 199 MET cc_start: 0.7539 (mmt) cc_final: 0.6622 (mmt) REVERT: 3 213 GLU cc_start: 0.7350 (pt0) cc_final: 0.6859 (tm-30) REVERT: 3 292 SER cc_start: 0.8907 (t) cc_final: 0.8487 (p) REVERT: 3 297 LYS cc_start: 0.8817 (tttt) cc_final: 0.8424 (ttmt) REVERT: 3 443 ARG cc_start: 0.8424 (ptp-170) cc_final: 0.8195 (ptp-170) outliers start: 25 outliers final: 20 residues processed: 163 average time/residue: 0.1622 time to fit residues: 37.1258 Evaluate side-chains 161 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 81 TRP Chi-restraints excluded: chain 2 residue 100 ASP Chi-restraints excluded: chain 2 residue 105 THR Chi-restraints excluded: chain 2 residue 134 SER Chi-restraints excluded: chain 2 residue 280 SER Chi-restraints excluded: chain 2 residue 292 SER Chi-restraints excluded: chain 2 residue 304 THR Chi-restraints excluded: chain 2 residue 306 THR Chi-restraints excluded: chain 2 residue 391 VAL Chi-restraints excluded: chain 2 residue 396 VAL Chi-restraints excluded: chain 3 residue 141 ILE Chi-restraints excluded: chain 3 residue 143 VAL Chi-restraints excluded: chain 3 residue 176 THR Chi-restraints excluded: chain 3 residue 186 THR Chi-restraints excluded: chain 3 residue 257 SER Chi-restraints excluded: chain 3 residue 287 LEU Chi-restraints excluded: chain 3 residue 300 ASN Chi-restraints excluded: chain 3 residue 318 CYS Chi-restraints excluded: chain 3 residue 338 VAL Chi-restraints excluded: chain 3 residue 391 VAL Chi-restraints excluded: chain 3 residue 431 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 20.0000 chunk 54 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 17 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 chunk 9 optimal weight: 20.0000 chunk 43 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 300 ASN ** 3 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.198284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.170766 restraints weight = 30693.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.175214 restraints weight = 9574.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.177403 restraints weight = 4583.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.178560 restraints weight = 3131.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.178969 restraints weight = 2634.867| |-----------------------------------------------------------------------------| r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4056 r_free = 0.4056 target_work(ls_wunit_k1) = 0.177 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 41 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4055 r_free = 0.4055 target_work(ls_wunit_k1) = 0.177 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 47 | |-----------------------------------------------------------------------------| r_final: 0.4055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 6824 Z= 0.225 Angle : 0.564 4.730 9324 Z= 0.304 Chirality : 0.045 0.154 1030 Planarity : 0.005 0.055 1206 Dihedral : 5.178 51.636 928 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 3.94 % Allowed : 20.65 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % 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 aren not related in a simple way. whole: -2.41 (0.27), residues: 832 helix: -1.17 (0.93), residues: 22 sheet: -1.41 (0.25), residues: 382 loop : -1.73 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 3 441 TYR 0.017 0.002 TYR 2 119 PHE 0.023 0.002 PHE 2 140 TRP 0.009 0.001 TRP 2 356 HIS 0.002 0.001 HIS 2 170 Details of bonding type rmsd covalent geometry : bond 0.00514 ( 6824) covalent geometry : angle 0.56410 ( 9324) hydrogen bonds : bond 0.03557 ( 195) hydrogen bonds : angle 5.75257 ( 486) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 109 GLU cc_start: 0.7176 (mt-10) cc_final: 0.6077 (pm20) REVERT: 2 138 TRP cc_start: 0.5510 (m100) cc_final: 0.5265 (m100) REVERT: 2 175 TYR cc_start: 0.4604 (m-80) cc_final: 0.4246 (m-80) REVERT: 2 200 THR cc_start: 0.8317 (t) cc_final: 0.7942 (m) REVERT: 2 374 ASN cc_start: 0.7637 (m-40) cc_final: 0.7132 (p0) REVERT: 2 396 VAL cc_start: 0.6553 (OUTLIER) cc_final: 0.6249 (m) REVERT: 2 456 ASN cc_start: 0.8264 (m-40) cc_final: 0.8060 (t0) REVERT: 3 70 GLN cc_start: 0.7256 (pt0) cc_final: 0.6908 (pp30) REVERT: 3 154 GLN cc_start: 0.5276 (mt0) cc_final: 0.3360 (pm20) REVERT: 3 177 TYR cc_start: 0.7547 (m-80) cc_final: 0.7339 (m-80) REVERT: 3 213 GLU cc_start: 0.7388 (pt0) cc_final: 0.6917 (tm-30) REVERT: 3 267 TYR cc_start: 0.8505 (m-80) cc_final: 0.8279 (m-80) REVERT: 3 292 SER cc_start: 0.8946 (t) cc_final: 0.8523 (p) REVERT: 3 297 LYS cc_start: 0.8823 (tttt) cc_final: 0.8434 (ttmt) outliers start: 29 outliers final: 25 residues processed: 159 average time/residue: 0.1646 time to fit residues: 36.5761 Evaluate side-chains 163 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 81 TRP Chi-restraints excluded: chain 2 residue 100 ASP Chi-restraints excluded: chain 2 residue 105 THR Chi-restraints excluded: chain 2 residue 134 SER Chi-restraints excluded: chain 2 residue 147 THR Chi-restraints excluded: chain 2 residue 199 MET Chi-restraints excluded: chain 2 residue 280 SER Chi-restraints excluded: chain 2 residue 292 SER Chi-restraints excluded: chain 2 residue 304 THR Chi-restraints excluded: chain 2 residue 306 THR Chi-restraints excluded: chain 2 residue 327 ASN Chi-restraints excluded: chain 2 residue 391 VAL Chi-restraints excluded: chain 2 residue 396 VAL Chi-restraints excluded: chain 2 residue 423 SER Chi-restraints excluded: chain 3 residue 62 GLU Chi-restraints excluded: chain 3 residue 141 ILE Chi-restraints excluded: chain 3 residue 143 VAL Chi-restraints excluded: chain 3 residue 176 THR Chi-restraints excluded: chain 3 residue 186 THR Chi-restraints excluded: chain 3 residue 257 SER Chi-restraints excluded: chain 3 residue 300 ASN Chi-restraints excluded: chain 3 residue 318 CYS Chi-restraints excluded: chain 3 residue 338 VAL Chi-restraints excluded: chain 3 residue 391 VAL Chi-restraints excluded: chain 3 residue 416 THR Chi-restraints excluded: chain 3 residue 431 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.199086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.171752 restraints weight = 30144.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.176208 restraints weight = 9244.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.178449 restraints weight = 4380.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.179403 restraints weight = 2972.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.179711 restraints weight = 2533.697| |-----------------------------------------------------------------------------| r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4056 r_free = 0.4056 target_work(ls_wunit_k1) = 0.178 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 47 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4056 r_free = 0.4056 target_work(ls_wunit_k1) = 0.178 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 58 | |-----------------------------------------------------------------------------| r_final: 0.4056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6824 Z= 0.166 Angle : 0.532 4.664 9324 Z= 0.284 Chirality : 0.044 0.160 1030 Planarity : 0.004 0.054 1206 Dihedral : 5.046 52.112 928 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 3.40 % Allowed : 21.74 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % 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 aren not related in a simple way. whole: -2.33 (0.27), residues: 832 helix: -0.84 (0.97), residues: 22 sheet: -1.32 (0.25), residues: 382 loop : -1.74 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 3 443 TYR 0.016 0.001 TYR 2 119 PHE 0.017 0.002 PHE 2 468 TRP 0.006 0.001 TRP 2 356 HIS 0.002 0.001 HIS 3 170 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 6824) covalent geometry : angle 0.53221 ( 9324) hydrogen bonds : bond 0.03277 ( 195) hydrogen bonds : angle 5.65209 ( 486) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 109 GLU cc_start: 0.7167 (mt-10) cc_final: 0.6036 (pm20) REVERT: 2 138 TRP cc_start: 0.5434 (m100) cc_final: 0.5218 (m100) REVERT: 2 152 TYR cc_start: 0.4674 (OUTLIER) cc_final: 0.3266 (m-80) REVERT: 2 175 TYR cc_start: 0.4585 (m-80) cc_final: 0.4193 (m-80) REVERT: 2 200 THR cc_start: 0.8253 (t) cc_final: 0.7877 (m) REVERT: 2 374 ASN cc_start: 0.7609 (m-40) cc_final: 0.7098 (p0) REVERT: 2 396 VAL cc_start: 0.6501 (OUTLIER) cc_final: 0.6224 (m) REVERT: 2 456 ASN cc_start: 0.8282 (m-40) cc_final: 0.8039 (t0) REVERT: 3 70 GLN cc_start: 0.7242 (pt0) cc_final: 0.6880 (pp30) REVERT: 3 154 GLN cc_start: 0.5203 (mt0) cc_final: 0.3240 (pm20) REVERT: 3 177 TYR cc_start: 0.7524 (m-80) cc_final: 0.7304 (m-80) REVERT: 3 199 MET cc_start: 0.7489 (mmt) cc_final: 0.6521 (mmt) REVERT: 3 213 GLU cc_start: 0.7462 (pt0) cc_final: 0.6941 (tm-30) REVERT: 3 267 TYR cc_start: 0.8482 (m-80) cc_final: 0.8233 (m-80) REVERT: 3 292 SER cc_start: 0.8945 (t) cc_final: 0.8483 (p) REVERT: 3 297 LYS cc_start: 0.8794 (tttt) cc_final: 0.8404 (ttmt) outliers start: 25 outliers final: 22 residues processed: 160 average time/residue: 0.1595 time to fit residues: 36.1325 Evaluate side-chains 162 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 81 TRP Chi-restraints excluded: chain 2 residue 100 ASP Chi-restraints excluded: chain 2 residue 105 THR Chi-restraints excluded: chain 2 residue 134 SER Chi-restraints excluded: chain 2 residue 147 THR Chi-restraints excluded: chain 2 residue 152 TYR Chi-restraints excluded: chain 2 residue 221 ASN Chi-restraints excluded: chain 2 residue 292 SER Chi-restraints excluded: chain 2 residue 304 THR Chi-restraints excluded: chain 2 residue 306 THR Chi-restraints excluded: chain 2 residue 327 ASN Chi-restraints excluded: chain 2 residue 391 VAL Chi-restraints excluded: chain 2 residue 396 VAL Chi-restraints excluded: chain 2 residue 423 SER Chi-restraints excluded: chain 3 residue 141 ILE Chi-restraints excluded: chain 3 residue 143 VAL Chi-restraints excluded: chain 3 residue 176 THR Chi-restraints excluded: chain 3 residue 186 THR Chi-restraints excluded: chain 3 residue 265 MET Chi-restraints excluded: chain 3 residue 300 ASN Chi-restraints excluded: chain 3 residue 318 CYS Chi-restraints excluded: chain 3 residue 338 VAL Chi-restraints excluded: chain 3 residue 391 VAL Chi-restraints excluded: chain 3 residue 430 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 69 optimal weight: 9.9990 chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 74 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.196307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.168998 restraints weight = 30401.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.173354 restraints weight = 9558.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.175583 restraints weight = 4621.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.176606 restraints weight = 3153.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.176942 restraints weight = 2680.372| |-----------------------------------------------------------------------------| r_work (final): 0.4020 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4020 r_free = 0.4020 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 58 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4020 r_free = 0.4020 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 69 | |-----------------------------------------------------------------------------| r_final: 0.4020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 6824 Z= 0.218 Angle : 0.558 4.552 9324 Z= 0.299 Chirality : 0.045 0.155 1030 Planarity : 0.005 0.053 1206 Dihedral : 5.175 51.711 928 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 4.35 % Allowed : 21.60 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % 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 aren not related in a simple way. whole: -2.45 (0.27), residues: 832 helix: -0.90 (0.93), residues: 22 sheet: -1.37 (0.25), residues: 382 loop : -1.86 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 3 441 TYR 0.014 0.002 TYR 2 355 PHE 0.020 0.002 PHE 2 468 TRP 0.009 0.001 TRP 2 356 HIS 0.002 0.001 HIS 2 170 Details of bonding type rmsd covalent geometry : bond 0.00501 ( 6824) covalent geometry : angle 0.55797 ( 9324) hydrogen bonds : bond 0.03486 ( 195) hydrogen bonds : angle 5.75261 ( 486) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 144 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 109 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6051 (pm20) REVERT: 2 152 TYR cc_start: 0.4908 (OUTLIER) cc_final: 0.3561 (m-80) REVERT: 2 175 TYR cc_start: 0.4562 (m-80) cc_final: 0.4152 (m-80) REVERT: 2 200 THR cc_start: 0.8254 (t) cc_final: 0.7870 (m) REVERT: 2 374 ASN cc_start: 0.7644 (m-40) cc_final: 0.7124 (p0) REVERT: 2 396 VAL cc_start: 0.6500 (OUTLIER) cc_final: 0.6212 (m) REVERT: 2 456 ASN cc_start: 0.8266 (m-40) cc_final: 0.8026 (t0) REVERT: 3 70 GLN cc_start: 0.7250 (pt0) cc_final: 0.6820 (pp30) REVERT: 3 154 GLN cc_start: 0.5385 (mt0) cc_final: 0.3360 (pm20) REVERT: 3 213 GLU cc_start: 0.7451 (pt0) cc_final: 0.7021 (tm-30) REVERT: 3 267 TYR cc_start: 0.8504 (m-80) cc_final: 0.8231 (m-80) REVERT: 3 292 SER cc_start: 0.8941 (t) cc_final: 0.8493 (p) REVERT: 3 297 LYS cc_start: 0.8803 (tttt) cc_final: 0.8435 (ttmt) outliers start: 32 outliers final: 26 residues processed: 166 average time/residue: 0.1567 time to fit residues: 36.8115 Evaluate side-chains 168 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 81 TRP Chi-restraints excluded: chain 2 residue 100 ASP Chi-restraints excluded: chain 2 residue 105 THR Chi-restraints excluded: chain 2 residue 134 SER Chi-restraints excluded: chain 2 residue 147 THR Chi-restraints excluded: chain 2 residue 152 TYR Chi-restraints excluded: chain 2 residue 191 THR Chi-restraints excluded: chain 2 residue 221 ASN Chi-restraints excluded: chain 2 residue 280 SER Chi-restraints excluded: chain 2 residue 292 SER Chi-restraints excluded: chain 2 residue 304 THR Chi-restraints excluded: chain 2 residue 306 THR Chi-restraints excluded: chain 2 residue 327 ASN Chi-restraints excluded: chain 2 residue 391 VAL Chi-restraints excluded: chain 2 residue 396 VAL Chi-restraints excluded: chain 2 residue 423 SER Chi-restraints excluded: chain 2 residue 471 ILE Chi-restraints excluded: chain 3 residue 84 LEU Chi-restraints excluded: chain 3 residue 141 ILE Chi-restraints excluded: chain 3 residue 143 VAL Chi-restraints excluded: chain 3 residue 176 THR Chi-restraints excluded: chain 3 residue 186 THR Chi-restraints excluded: chain 3 residue 300 ASN Chi-restraints excluded: chain 3 residue 318 CYS Chi-restraints excluded: chain 3 residue 338 VAL Chi-restraints excluded: chain 3 residue 391 VAL Chi-restraints excluded: chain 3 residue 416 THR Chi-restraints excluded: chain 3 residue 430 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 5 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 60 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 76 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 198 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.198025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.170991 restraints weight = 30731.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.175382 restraints weight = 9504.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.177625 restraints weight = 4561.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.178639 restraints weight = 3112.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.178965 restraints weight = 2628.847| |-----------------------------------------------------------------------------| r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4029 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4029 r_free = 0.4029 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 69 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4029 r_free = 0.4029 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 72 | |-----------------------------------------------------------------------------| r_final: 0.4029 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6824 Z= 0.182 Angle : 0.547 4.500 9324 Z= 0.293 Chirality : 0.044 0.159 1030 Planarity : 0.005 0.051 1206 Dihedral : 5.133 51.396 928 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 4.21 % Allowed : 21.47 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % 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 aren not related in a simple way. whole: -2.45 (0.27), residues: 832 helix: -0.69 (0.98), residues: 22 sheet: -1.35 (0.25), residues: 382 loop : -1.89 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 3 446 TYR 0.012 0.001 TYR 2 355 PHE 0.019 0.002 PHE 2 468 TRP 0.007 0.001 TRP 2 356 HIS 0.002 0.001 HIS 3 170 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 6824) covalent geometry : angle 0.54740 ( 9324) hydrogen bonds : bond 0.03391 ( 195) hydrogen bonds : angle 5.71691 ( 486) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 152 TYR cc_start: 0.4867 (OUTLIER) cc_final: 0.3447 (m-80) REVERT: 2 175 TYR cc_start: 0.4557 (m-80) cc_final: 0.4144 (m-80) REVERT: 2 200 THR cc_start: 0.8238 (t) cc_final: 0.7840 (m) REVERT: 2 374 ASN cc_start: 0.7617 (m-40) cc_final: 0.7120 (p0) REVERT: 2 396 VAL cc_start: 0.6545 (OUTLIER) cc_final: 0.6262 (m) REVERT: 2 456 ASN cc_start: 0.8250 (m-40) cc_final: 0.8012 (t0) REVERT: 3 70 GLN cc_start: 0.7090 (pt0) cc_final: 0.6780 (pp30) REVERT: 3 154 GLN cc_start: 0.5329 (mt0) cc_final: 0.3278 (pm20) REVERT: 3 187 LYS cc_start: 0.6640 (mttt) cc_final: 0.6244 (tptt) REVERT: 3 213 GLU cc_start: 0.7447 (pt0) cc_final: 0.7015 (tm-30) REVERT: 3 292 SER cc_start: 0.8943 (t) cc_final: 0.8504 (p) REVERT: 3 297 LYS cc_start: 0.8780 (tttt) cc_final: 0.8399 (ttmt) outliers start: 31 outliers final: 26 residues processed: 161 average time/residue: 0.1536 time to fit residues: 34.8602 Evaluate side-chains 167 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 81 TRP Chi-restraints excluded: chain 2 residue 100 ASP Chi-restraints excluded: chain 2 residue 105 THR Chi-restraints excluded: chain 2 residue 134 SER Chi-restraints excluded: chain 2 residue 147 THR Chi-restraints excluded: chain 2 residue 152 TYR Chi-restraints excluded: chain 2 residue 176 THR Chi-restraints excluded: chain 2 residue 191 THR Chi-restraints excluded: chain 2 residue 221 ASN Chi-restraints excluded: chain 2 residue 280 SER Chi-restraints excluded: chain 2 residue 292 SER Chi-restraints excluded: chain 2 residue 304 THR Chi-restraints excluded: chain 2 residue 306 THR Chi-restraints excluded: chain 2 residue 327 ASN Chi-restraints excluded: chain 2 residue 366 VAL Chi-restraints excluded: chain 2 residue 391 VAL Chi-restraints excluded: chain 2 residue 396 VAL Chi-restraints excluded: chain 2 residue 423 SER Chi-restraints excluded: chain 2 residue 471 ILE Chi-restraints excluded: chain 3 residue 84 LEU Chi-restraints excluded: chain 3 residue 141 ILE Chi-restraints excluded: chain 3 residue 143 VAL Chi-restraints excluded: chain 3 residue 176 THR Chi-restraints excluded: chain 3 residue 186 THR Chi-restraints excluded: chain 3 residue 318 CYS Chi-restraints excluded: chain 3 residue 338 VAL Chi-restraints excluded: chain 3 residue 391 VAL Chi-restraints excluded: chain 3 residue 430 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 79 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.198679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.171476 restraints weight = 30405.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.175974 restraints weight = 9339.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.178267 restraints weight = 4423.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.179214 restraints weight = 2983.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.179763 restraints weight = 2544.156| |-----------------------------------------------------------------------------| r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4053 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4053 r_free = 0.4053 target_work(ls_wunit_k1) = 0.177 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 72 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4053 r_free = 0.4053 target_work(ls_wunit_k1) = 0.177 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 72 | |-----------------------------------------------------------------------------| r_final: 0.4053 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6824 Z= 0.109 Angle : 0.517 4.461 9324 Z= 0.274 Chirality : 0.044 0.167 1030 Planarity : 0.004 0.052 1206 Dihedral : 4.943 51.835 928 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 2.45 % Allowed : 23.78 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % 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 aren not related in a simple way. whole: -2.25 (0.28), residues: 832 helix: -0.09 (1.11), residues: 22 sheet: -1.28 (0.25), residues: 392 loop : -1.71 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 3 446 TYR 0.018 0.001 TYR 3 289 PHE 0.024 0.002 PHE 2 140 TRP 0.005 0.001 TRP 3 50 HIS 0.003 0.001 HIS 2 315 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 6824) covalent geometry : angle 0.51719 ( 9324) hydrogen bonds : bond 0.03058 ( 195) hydrogen bonds : angle 5.57910 ( 486) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 175 TYR cc_start: 0.4548 (m-80) cc_final: 0.4138 (m-80) REVERT: 2 200 THR cc_start: 0.8181 (t) cc_final: 0.7811 (m) REVERT: 2 374 ASN cc_start: 0.7580 (m-40) cc_final: 0.7010 (p0) REVERT: 2 396 VAL cc_start: 0.6517 (OUTLIER) cc_final: 0.6226 (m) REVERT: 2 456 ASN cc_start: 0.8231 (m-40) cc_final: 0.8003 (t0) REVERT: 3 70 GLN cc_start: 0.7092 (pt0) cc_final: 0.6711 (pp30) REVERT: 3 154 GLN cc_start: 0.5196 (mt0) cc_final: 0.3315 (pm20) REVERT: 3 187 LYS cc_start: 0.6606 (mttt) cc_final: 0.6205 (tptt) REVERT: 3 213 GLU cc_start: 0.7303 (pt0) cc_final: 0.6901 (tm-30) REVERT: 3 292 SER cc_start: 0.8916 (t) cc_final: 0.8457 (p) REVERT: 3 297 LYS cc_start: 0.8772 (tttt) cc_final: 0.8389 (ttmt) outliers start: 18 outliers final: 16 residues processed: 153 average time/residue: 0.1515 time to fit residues: 32.7140 Evaluate side-chains 156 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 81 TRP Chi-restraints excluded: chain 2 residue 100 ASP Chi-restraints excluded: chain 2 residue 105 THR Chi-restraints excluded: chain 2 residue 134 SER Chi-restraints excluded: chain 2 residue 221 ASN Chi-restraints excluded: chain 2 residue 304 THR Chi-restraints excluded: chain 2 residue 306 THR Chi-restraints excluded: chain 2 residue 391 VAL Chi-restraints excluded: chain 2 residue 396 VAL Chi-restraints excluded: chain 2 residue 471 ILE Chi-restraints excluded: chain 3 residue 84 LEU Chi-restraints excluded: chain 3 residue 141 ILE Chi-restraints excluded: chain 3 residue 143 VAL Chi-restraints excluded: chain 3 residue 176 THR Chi-restraints excluded: chain 3 residue 318 CYS Chi-restraints excluded: chain 3 residue 338 VAL Chi-restraints excluded: chain 3 residue 391 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 12 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.197868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.171022 restraints weight = 30545.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.175439 restraints weight = 9419.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.177638 restraints weight = 4476.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.178676 restraints weight = 3050.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.179004 restraints weight = 2574.344| |-----------------------------------------------------------------------------| r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4043 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4043 r_free = 0.4043 target_work(ls_wunit_k1) = 0.176 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 72 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4043 r_free = 0.4043 target_work(ls_wunit_k1) = 0.176 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 73 | |-----------------------------------------------------------------------------| r_final: 0.4043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6824 Z= 0.149 Angle : 0.523 4.471 9324 Z= 0.277 Chirality : 0.044 0.161 1030 Planarity : 0.004 0.049 1206 Dihedral : 4.952 52.005 928 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 2.58 % Allowed : 23.78 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % 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 aren not related in a simple way. whole: -2.28 (0.28), residues: 832 helix: -0.00 (1.13), residues: 22 sheet: -1.33 (0.25), residues: 390 loop : -1.71 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 3 446 TYR 0.019 0.001 TYR 3 289 PHE 0.015 0.002 PHE 2 140 TRP 0.007 0.001 TRP 2 356 HIS 0.003 0.001 HIS 3 170 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 6824) covalent geometry : angle 0.52278 ( 9324) hydrogen bonds : bond 0.03145 ( 195) hydrogen bonds : angle 5.58392 ( 486) =============================================================================== Job complete usr+sys time: 2860.07 seconds wall clock time: 49 minutes 31.22 seconds (2971.22 seconds total)