Starting phenix.real_space_refine on Wed Sep 17 09:40:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r9o_24330/09_2025/7r9o_24330.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r9o_24330/09_2025/7r9o_24330.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7r9o_24330/09_2025/7r9o_24330.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r9o_24330/09_2025/7r9o_24330.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7r9o_24330/09_2025/7r9o_24330.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r9o_24330/09_2025/7r9o_24330.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 23 5.16 5 C 2351 2.51 5 N 655 2.21 5 O 759 1.98 5 H 3938 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 7726 Number of models: 1 Model: "" Number of chains: 1 Chain: "J" Number of atoms: 7726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 7726 Classifications: {'peptide': 505} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 8, 'TRANS': 496} Time building chain proxies: 1.61, per 1000 atoms: 0.21 Number of scatterers: 7726 At special positions: 0 Unit cell: (82.08, 70.2, 111.24, 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 23 16.00 O 759 8.00 N 655 7.00 C 2351 6.00 H 3938 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: 0.70 Conformation dependent library (CDL) restraints added in 355.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 938 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 4 sheets defined 52.3% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'J' and resid 20 through 34 removed outlier: 3.628A pdb=" N ASN J 24 " --> pdb=" O ALA J 20 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU J 26 " --> pdb=" O ARG J 22 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG J 29 " --> pdb=" O ILE J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 66 Processing helix chain 'J' and resid 72 through 74 No H-bonds generated for 'chain 'J' and resid 72 through 74' Processing helix chain 'J' and resid 75 through 87 removed outlier: 3.779A pdb=" N ILE J 79 " --> pdb=" O ALA J 75 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL J 81 " --> pdb=" O MET J 77 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA J 82 " --> pdb=" O LEU J 78 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR J 84 " --> pdb=" O GLU J 80 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN J 85 " --> pdb=" O VAL J 81 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS J 87 " --> pdb=" O LYS J 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 112 removed outlier: 3.502A pdb=" N VAL J 98 " --> pdb=" O THR J 94 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL J 99 " --> pdb=" O THR J 95 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA J 100 " --> pdb=" O ALA J 96 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU J 102 " --> pdb=" O VAL J 98 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA J 107 " --> pdb=" O LEU J 103 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLU J 108 " --> pdb=" O LEU J 104 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLU J 109 " --> pdb=" O ARG J 105 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU J 110 " --> pdb=" O LYS J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 116 through 139 removed outlier: 3.848A pdb=" N VAL J 120 " --> pdb=" O HIS J 116 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS J 122 " --> pdb=" O THR J 118 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY J 123 " --> pdb=" O ILE J 119 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR J 124 " --> pdb=" O VAL J 120 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN J 125 " --> pdb=" O VAL J 121 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN J 132 " --> pdb=" O ALA J 128 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU J 133 " --> pdb=" O GLN J 129 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU J 134 " --> pdb=" O LYS J 130 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS J 136 " --> pdb=" O GLN J 132 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR J 137 " --> pdb=" O GLU J 133 " (cutoff:3.500A) Processing helix chain 'J' and resid 146 through 162 removed outlier: 3.729A pdb=" N LYS J 152 " --> pdb=" O GLU J 148 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR J 156 " --> pdb=" O LYS J 152 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY J 162 " --> pdb=" O ILE J 158 " (cutoff:3.500A) Processing helix chain 'J' and resid 167 through 180 removed outlier: 3.608A pdb=" N ALA J 171 " --> pdb=" O LYS J 167 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU J 172 " --> pdb=" O GLU J 168 " (cutoff:3.500A) Processing helix chain 'J' and resid 189 through 193 Processing helix chain 'J' and resid 257 through 279 removed outlier: 3.671A pdb=" N PHE J 261 " --> pdb=" O LYS J 257 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU J 263 " --> pdb=" O MET J 259 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU J 266 " --> pdb=" O ILE J 262 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET J 272 " --> pdb=" O MET J 268 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU J 275 " --> pdb=" O ASP J 271 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE J 276 " --> pdb=" O MET J 272 " (cutoff:3.500A) Processing helix chain 'J' and resid 293 through 301 removed outlier: 3.785A pdb=" N TYR J 297 " --> pdb=" O LEU J 293 " (cutoff:3.500A) Processing helix chain 'J' and resid 310 through 322 removed outlier: 3.653A pdb=" N MET J 314 " --> pdb=" O LYS J 310 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS J 316 " --> pdb=" O SER J 312 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU J 317 " --> pdb=" O ASP J 313 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA J 318 " --> pdb=" O MET J 314 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS J 319 " --> pdb=" O GLU J 315 " (cutoff:3.500A) Processing helix chain 'J' and resid 373 through 383 removed outlier: 3.723A pdb=" N GLU J 378 " --> pdb=" O GLU J 374 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL J 380 " --> pdb=" O VAL J 376 " (cutoff:3.500A) Processing helix chain 'J' and resid 386 through 398 Processing helix chain 'J' and resid 405 through 420 removed outlier: 3.592A pdb=" N VAL J 409 " --> pdb=" O GLY J 405 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU J 410 " --> pdb=" O SER J 406 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER J 412 " --> pdb=" O GLU J 408 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N MET J 413 " --> pdb=" O VAL J 409 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU J 417 " --> pdb=" O MET J 413 " (cutoff:3.500A) Processing helix chain 'J' and resid 424 through 427 removed outlier: 3.578A pdb=" N GLN J 427 " --> pdb=" O GLY J 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 424 through 427' Processing helix chain 'J' and resid 428 through 437 removed outlier: 3.803A pdb=" N LEU J 437 " --> pdb=" O PHE J 433 " (cutoff:3.500A) Processing helix chain 'J' and resid 438 through 448 removed outlier: 3.946A pdb=" N ARG J 442 " --> pdb=" O GLU J 438 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA J 448 " --> pdb=" O LEU J 444 " (cutoff:3.500A) Processing helix chain 'J' and resid 455 through 463 removed outlier: 3.823A pdb=" N ARG J 460 " --> pdb=" O LEU J 456 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA J 461 " --> pdb=" O VAL J 457 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA J 462 " --> pdb=" O LYS J 458 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N HIS J 463 " --> pdb=" O VAL J 459 " (cutoff:3.500A) Processing helix chain 'J' and resid 482 through 487 Processing helix chain 'J' and resid 492 through 512 removed outlier: 3.550A pdb=" N ALA J 503 " --> pdb=" O ILE J 499 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU J 507 " --> pdb=" O ALA J 503 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N MET J 508 " --> pdb=" O GLU J 504 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LEU J 509 " --> pdb=" O SER J 505 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE J 512 " --> pdb=" O MET J 508 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 140 through 141 removed outlier: 3.716A pdb=" N ILE J 400 " --> pdb=" O CYS J 140 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL J 401 " --> pdb=" O GLU J 490 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU J 490 " --> pdb=" O VAL J 401 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 196 through 197 removed outlier: 3.560A pdb=" N THR J 366 " --> pdb=" O ILE J 209 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE J 209 " --> pdb=" O THR J 366 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 228 through 230 removed outlier: 7.653A pdb=" N THR J 228 " --> pdb=" O LEU J 342 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LEU J 342 " --> pdb=" O THR J 228 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU J 344 " --> pdb=" O PHE J 355 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE J 355 " --> pdb=" O GLU J 344 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 472 through 473 126 hydrogen bonds defined for protein. 360 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.31 Time building geometry restraints manager: 1.02 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: 3931 1.03 - 1.23: 7 1.23 - 1.42: 1405 1.42 - 1.61: 2365 1.61 - 1.81: 39 Bond restraints: 7747 Sorted by residual: bond pdb=" CA LEU J 368 " pdb=" CB LEU J 368 " ideal model delta sigma weight residual 1.530 1.541 -0.011 1.69e-02 3.50e+03 4.05e-01 bond pdb=" N LYS J 161 " pdb=" CA LYS J 161 " ideal model delta sigma weight residual 1.468 1.461 0.008 1.24e-02 6.50e+03 3.82e-01 bond pdb=" CA GLU J 358 " pdb=" C GLU J 358 " ideal model delta sigma weight residual 1.523 1.531 -0.008 1.34e-02 5.57e+03 3.59e-01 bond pdb=" N VAL J 384 " pdb=" CA VAL J 384 " ideal model delta sigma weight residual 1.452 1.459 -0.007 1.18e-02 7.18e+03 3.57e-01 bond pdb=" CA VAL J 439 " pdb=" C VAL J 439 " ideal model delta sigma weight residual 1.519 1.526 -0.007 1.14e-02 7.69e+03 3.45e-01 ... (remaining 7742 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.80: 12716 0.80 - 1.60: 1376 1.60 - 2.40: 36 2.40 - 3.19: 9 3.19 - 3.99: 8 Bond angle restraints: 14145 Sorted by residual: angle pdb=" N VAL J 384 " pdb=" CA VAL J 384 " pdb=" C VAL J 384 " ideal model delta sigma weight residual 112.96 109.07 3.89 1.00e+00 1.00e+00 1.52e+01 angle pdb=" N THR J 253 " pdb=" CA THR J 253 " pdb=" C THR J 253 " ideal model delta sigma weight residual 114.62 111.25 3.37 1.14e+00 7.69e-01 8.74e+00 angle pdb=" CA THR J 253 " pdb=" C THR J 253 " pdb=" N ASP J 254 " ideal model delta sigma weight residual 119.71 117.13 2.58 1.17e+00 7.31e-01 4.86e+00 angle pdb=" CA VAL J 384 " pdb=" C VAL J 384 " pdb=" N ASP J 385 " ideal model delta sigma weight residual 118.65 116.71 1.94 1.07e+00 8.73e-01 3.30e+00 angle pdb=" CA VAL J 384 " pdb=" C VAL J 384 " pdb=" O VAL J 384 " ideal model delta sigma weight residual 119.29 120.73 -1.44 8.40e-01 1.42e+00 2.93e+00 ... (remaining 14140 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.03: 3369 13.03 - 26.06: 82 26.06 - 39.09: 44 39.09 - 52.12: 22 52.12 - 65.15: 19 Dihedral angle restraints: 3536 sinusoidal: 2036 harmonic: 1500 Sorted by residual: dihedral pdb=" CA ARG J 18 " pdb=" CB ARG J 18 " pdb=" CG ARG J 18 " pdb=" CD ARG J 18 " ideal model delta sinusoidal sigma weight residual -60.00 -93.31 33.31 3 1.50e+01 4.44e-03 5.56e+00 dihedral pdb=" CB MET J 77 " pdb=" CG MET J 77 " pdb=" SD MET J 77 " pdb=" CE MET J 77 " ideal model delta sinusoidal sigma weight residual 60.00 89.03 -29.03 3 1.50e+01 4.44e-03 4.50e+00 dihedral pdb=" CA VAL J 401 " pdb=" CB VAL J 401 " pdb=" CG1 VAL J 401 " pdb="HG13 VAL J 401 " ideal model delta sinusoidal sigma weight residual -120.00 -54.85 -65.15 2 3.00e+01 1.11e-03 4.39e+00 ... (remaining 3533 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 397 0.025 - 0.051: 140 0.051 - 0.076: 44 0.076 - 0.102: 30 0.102 - 0.127: 19 Chirality restraints: 630 Sorted by residual: chirality pdb=" CA ILE J 303 " pdb=" N ILE J 303 " pdb=" C ILE J 303 " pdb=" CB ILE J 303 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA ILE J 195 " pdb=" N ILE J 195 " pdb=" C ILE J 195 " pdb=" CB ILE J 195 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.90e-01 chirality pdb=" CA ILE J 209 " pdb=" N ILE J 209 " pdb=" C ILE J 209 " pdb=" CB ILE J 209 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.63e-01 ... (remaining 627 not shown) Planarity restraints: 1159 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS J 116 " 0.008 5.00e-02 4.00e+02 1.22e-02 2.36e-01 pdb=" N PRO J 117 " -0.021 5.00e-02 4.00e+02 pdb=" CA PRO J 117 " 0.006 5.00e-02 4.00e+02 pdb=" CD PRO J 117 " 0.007 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY J 40 " 0.007 5.00e-02 4.00e+02 1.05e-02 1.78e-01 pdb=" N PRO J 41 " -0.018 5.00e-02 4.00e+02 pdb=" CA PRO J 41 " 0.005 5.00e-02 4.00e+02 pdb=" CD PRO J 41 " 0.006 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP J 254 " -0.007 5.00e-02 4.00e+02 1.05e-02 1.78e-01 pdb=" N PRO J 255 " 0.018 5.00e-02 4.00e+02 pdb=" CA PRO J 255 " -0.005 5.00e-02 4.00e+02 pdb=" CD PRO J 255 " -0.006 5.00e-02 4.00e+02 ... (remaining 1156 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.27: 846 2.27 - 2.85: 18213 2.85 - 3.43: 17566 3.43 - 4.02: 22640 4.02 - 4.60: 35430 Nonbonded interactions: 94695 Sorted by model distance: nonbonded pdb=" HZ1 LYS J 169 " pdb=" O ASP J 204 " model vdw 1.687 2.450 nonbonded pdb=" OE1 GLU J 408 " pdb=" H GLU J 408 " model vdw 1.695 2.450 nonbonded pdb=" O LEU J 317 " pdb=" HG1 THR J 321 " model vdw 1.715 2.450 nonbonded pdb=" OD1 ASN J 236 " pdb=" HZ1 LYS J 311 " model vdw 1.718 2.450 nonbonded pdb=" O ILE J 64 " pdb=" H MET J 68 " model vdw 1.729 2.450 ... (remaining 94690 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.940 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: 0.050 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.020 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 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 : 0.002 0.012 3809 Z= 0.086 Angle : 0.381 3.992 5126 Z= 0.231 Chirality : 0.038 0.127 630 Planarity : 0.001 0.012 663 Dihedral : 4.489 61.236 1463 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.80 % Allowed : 10.54 % Favored : 88.67 % Rotamer: Outliers : 0.25 % Allowed : 1.72 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.93 (0.27), residues: 503 helix: -3.96 (0.20), residues: 212 sheet: -4.24 (0.66), residues: 31 loop : -2.47 (0.32), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 308 TYR 0.001 0.000 TYR J 418 PHE 0.001 0.000 PHE J 285 HIS 0.001 0.000 HIS J 72 Details of bonding type rmsd covalent geometry : bond 0.00158 ( 3809) covalent geometry : angle 0.38126 ( 5126) hydrogen bonds : bond 0.35264 ( 126) hydrogen bonds : angle 9.24905 ( 360) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 104 LEU cc_start: 0.8847 (tp) cc_final: 0.8537 (mm) REVERT: J 314 MET cc_start: 0.8272 (mmm) cc_final: 0.7959 (mmt) outliers start: 1 outliers final: 1 residues processed: 69 average time/residue: 0.2352 time to fit residues: 18.6791 Evaluate side-chains 45 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 368 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.0980 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 447 ASN J 486 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.072238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.048961 restraints weight = 71052.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.050940 restraints weight = 33844.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.052150 restraints weight = 20547.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.052895 restraints weight = 14872.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.053255 restraints weight = 12225.657| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3809 Z= 0.159 Angle : 0.564 4.585 5126 Z= 0.303 Chirality : 0.040 0.136 630 Planarity : 0.004 0.040 663 Dihedral : 3.079 25.706 531 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.49 % Allowed : 6.14 % Favored : 93.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.22 (0.32), residues: 503 helix: -1.79 (0.31), residues: 224 sheet: -3.99 (0.66), residues: 31 loop : -2.16 (0.34), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 66 TYR 0.011 0.002 TYR J 124 PHE 0.013 0.001 PHE J 285 HIS 0.003 0.001 HIS J 375 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 3809) covalent geometry : angle 0.56368 ( 5126) hydrogen bonds : bond 0.05234 ( 126) hydrogen bonds : angle 5.11763 ( 360) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 104 LEU cc_start: 0.9480 (tp) cc_final: 0.9070 (tp) REVERT: J 155 MET cc_start: 0.8576 (tpp) cc_final: 0.8277 (tpp) REVERT: J 213 LEU cc_start: 0.9263 (tp) cc_final: 0.8701 (mt) REVERT: J 285 PHE cc_start: 0.8932 (t80) cc_final: 0.8667 (t80) REVERT: J 504 GLU cc_start: 0.9060 (tt0) cc_final: 0.8519 (tp30) REVERT: J 508 MET cc_start: 0.8700 (mmm) cc_final: 0.8317 (mmp) outliers start: 2 outliers final: 2 residues processed: 40 average time/residue: 0.1027 time to fit residues: 5.6322 Evaluate side-chains 32 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 23 MET Chi-restraints excluded: chain J residue 368 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 18 optimal weight: 4.9990 chunk 36 optimal weight: 0.2980 chunk 39 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 17 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.070907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.047080 restraints weight = 70624.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.048920 restraints weight = 33038.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.050091 restraints weight = 20155.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.050826 restraints weight = 14678.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.051245 restraints weight = 12140.492| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3809 Z= 0.135 Angle : 0.471 4.472 5126 Z= 0.255 Chirality : 0.038 0.128 630 Planarity : 0.003 0.031 663 Dihedral : 3.039 25.642 531 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.74 % Allowed : 6.39 % Favored : 92.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.98 (0.35), residues: 503 helix: -0.56 (0.33), residues: 220 sheet: -3.50 (0.76), residues: 31 loop : -1.68 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 370 TYR 0.008 0.001 TYR J 124 PHE 0.004 0.001 PHE J 285 HIS 0.003 0.001 HIS J 116 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 3809) covalent geometry : angle 0.47059 ( 5126) hydrogen bonds : bond 0.04307 ( 126) hydrogen bonds : angle 4.40612 ( 360) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 27 time to evaluate : 0.192 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: J 285 PHE cc_start: 0.8804 (t80) cc_final: 0.8569 (t80) REVERT: J 504 GLU cc_start: 0.9102 (tt0) cc_final: 0.8566 (tp30) REVERT: J 508 MET cc_start: 0.8953 (mmm) cc_final: 0.8651 (mmm) outliers start: 3 outliers final: 3 residues processed: 30 average time/residue: 0.0829 time to fit residues: 3.7763 Evaluate side-chains 30 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 27 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 521 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 486 ASN J 500 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.066661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.043345 restraints weight = 70112.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.045022 restraints weight = 32601.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.046107 restraints weight = 20002.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.046675 restraints weight = 14591.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.047112 restraints weight = 12269.293| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.6159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3809 Z= 0.219 Angle : 0.572 4.554 5126 Z= 0.313 Chirality : 0.040 0.131 630 Planarity : 0.003 0.036 663 Dihedral : 3.743 24.057 531 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.98 % Allowed : 7.62 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.64 (0.35), residues: 503 helix: -0.30 (0.31), residues: 238 sheet: -3.06 (0.77), residues: 38 loop : -1.51 (0.39), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 399 TYR 0.014 0.002 TYR J 124 PHE 0.004 0.001 PHE J 285 HIS 0.005 0.001 HIS J 116 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 3809) covalent geometry : angle 0.57210 ( 5126) hydrogen bonds : bond 0.03817 ( 126) hydrogen bonds : angle 4.34712 ( 360) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.177 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: J 285 PHE cc_start: 0.8611 (t80) cc_final: 0.8367 (t80) REVERT: J 504 GLU cc_start: 0.9111 (tt0) cc_final: 0.8890 (tm-30) REVERT: J 508 MET cc_start: 0.9048 (mmm) cc_final: 0.8845 (mmm) outliers start: 4 outliers final: 4 residues processed: 29 average time/residue: 0.0897 time to fit residues: 3.5640 Evaluate side-chains 28 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 23 MET Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 521 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 19 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 10 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 474 ASN J 486 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.067504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.043837 restraints weight = 70674.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.045521 restraints weight = 33150.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.046568 restraints weight = 20408.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.047187 restraints weight = 15119.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.047458 restraints weight = 12766.386| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.6365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3809 Z= 0.133 Angle : 0.467 4.407 5126 Z= 0.249 Chirality : 0.038 0.133 630 Planarity : 0.003 0.030 663 Dihedral : 3.434 24.040 531 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.74 % Allowed : 8.60 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.37), residues: 503 helix: 0.19 (0.33), residues: 238 sheet: -2.93 (0.78), residues: 38 loop : -1.37 (0.40), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 370 TYR 0.007 0.001 TYR J 124 PHE 0.002 0.001 PHE J 355 HIS 0.002 0.001 HIS J 463 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 3809) covalent geometry : angle 0.46675 ( 5126) hydrogen bonds : bond 0.03232 ( 126) hydrogen bonds : angle 4.03847 ( 360) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 27 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 213 LEU cc_start: 0.9300 (tp) cc_final: 0.8842 (mt) REVERT: J 285 PHE cc_start: 0.8798 (t80) cc_final: 0.8597 (t80) REVERT: J 351 ASP cc_start: 0.9023 (m-30) cc_final: 0.8794 (t0) REVERT: J 353 MET cc_start: 0.8995 (mpp) cc_final: 0.8141 (mpp) outliers start: 3 outliers final: 3 residues processed: 30 average time/residue: 0.1023 time to fit residues: 4.2773 Evaluate side-chains 29 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 521 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 23 optimal weight: 0.2980 chunk 15 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 31 optimal weight: 0.0470 chunk 4 optimal weight: 0.5980 chunk 17 optimal weight: 0.2980 chunk 27 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 486 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.068075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.044717 restraints weight = 69126.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.046397 restraints weight = 31303.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.047440 restraints weight = 18905.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.047957 restraints weight = 13860.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.048362 restraints weight = 11793.843| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.6436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3809 Z= 0.083 Angle : 0.440 4.590 5126 Z= 0.228 Chirality : 0.038 0.129 630 Planarity : 0.002 0.024 663 Dihedral : 3.215 24.756 531 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.74 % Allowed : 8.60 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.37), residues: 503 helix: 0.56 (0.33), residues: 239 sheet: -2.98 (0.91), residues: 31 loop : -1.39 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 370 TYR 0.004 0.001 TYR J 124 PHE 0.002 0.000 PHE J 355 HIS 0.002 0.000 HIS J 463 Details of bonding type rmsd covalent geometry : bond 0.00188 ( 3809) covalent geometry : angle 0.44038 ( 5126) hydrogen bonds : bond 0.02748 ( 126) hydrogen bonds : angle 3.69366 ( 360) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 27 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 213 LEU cc_start: 0.9270 (tp) cc_final: 0.8766 (mt) REVERT: J 285 PHE cc_start: 0.8780 (t80) cc_final: 0.8577 (t80) REVERT: J 351 ASP cc_start: 0.9004 (m-30) cc_final: 0.8767 (t0) REVERT: J 353 MET cc_start: 0.8961 (mpp) cc_final: 0.8094 (mpp) outliers start: 3 outliers final: 3 residues processed: 30 average time/residue: 0.1134 time to fit residues: 4.7597 Evaluate side-chains 28 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 521 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 20 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 42 optimal weight: 0.4980 chunk 33 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 447 ASN J 486 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.067474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.044028 restraints weight = 69713.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.045713 restraints weight = 31919.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.046735 restraints weight = 19479.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.047257 restraints weight = 14313.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.047665 restraints weight = 12159.194| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.6647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 3809 Z= 0.117 Angle : 0.476 5.009 5126 Z= 0.248 Chirality : 0.038 0.129 630 Planarity : 0.002 0.026 663 Dihedral : 3.248 24.750 531 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.98 % Allowed : 9.09 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.37), residues: 503 helix: 0.72 (0.34), residues: 242 sheet: -3.04 (0.91), residues: 31 loop : -1.37 (0.40), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 370 TYR 0.006 0.001 TYR J 124 PHE 0.001 0.000 PHE J 285 HIS 0.002 0.001 HIS J 116 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 3809) covalent geometry : angle 0.47600 ( 5126) hydrogen bonds : bond 0.02821 ( 126) hydrogen bonds : angle 3.70741 ( 360) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 213 LEU cc_start: 0.9261 (tp) cc_final: 0.8817 (mt) REVERT: J 351 ASP cc_start: 0.8998 (m-30) cc_final: 0.8764 (t0) REVERT: J 353 MET cc_start: 0.8955 (mpp) cc_final: 0.8113 (mpp) outliers start: 4 outliers final: 3 residues processed: 30 average time/residue: 0.0944 time to fit residues: 4.0393 Evaluate side-chains 27 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 521 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 14 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 2 optimal weight: 0.1980 chunk 43 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 486 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.067807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.043996 restraints weight = 71289.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.045721 restraints weight = 32701.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.046767 restraints weight = 19908.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.047386 restraints weight = 14689.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.047699 restraints weight = 12445.671| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.6811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 3809 Z= 0.113 Angle : 0.489 7.487 5126 Z= 0.253 Chirality : 0.038 0.129 630 Planarity : 0.002 0.026 663 Dihedral : 3.289 24.546 531 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.74 % Allowed : 9.58 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.38), residues: 503 helix: 0.80 (0.34), residues: 242 sheet: -2.87 (0.78), residues: 38 loop : -1.18 (0.41), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 370 TYR 0.004 0.001 TYR J 124 PHE 0.005 0.001 PHE J 285 HIS 0.001 0.000 HIS J 116 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 3809) covalent geometry : angle 0.48933 ( 5126) hydrogen bonds : bond 0.02674 ( 126) hydrogen bonds : angle 3.65701 ( 360) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 213 LEU cc_start: 0.9303 (tp) cc_final: 0.8833 (mt) outliers start: 3 outliers final: 3 residues processed: 28 average time/residue: 0.0923 time to fit residues: 3.8313 Evaluate side-chains 25 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 521 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 33 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 18 optimal weight: 0.0570 chunk 27 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 486 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.067387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.044044 restraints weight = 68993.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.045719 restraints weight = 31347.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.046755 restraints weight = 19016.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.047292 restraints weight = 13939.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.047687 restraints weight = 11830.817| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.6967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3809 Z= 0.105 Angle : 0.493 6.495 5126 Z= 0.256 Chirality : 0.039 0.129 630 Planarity : 0.002 0.025 663 Dihedral : 3.334 24.911 531 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.74 % Allowed : 10.32 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.38), residues: 503 helix: 0.83 (0.34), residues: 244 sheet: -3.02 (0.89), residues: 31 loop : -1.28 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 370 TYR 0.005 0.001 TYR J 124 PHE 0.023 0.002 PHE J 285 HIS 0.001 0.000 HIS J 116 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 3809) covalent geometry : angle 0.49290 ( 5126) hydrogen bonds : bond 0.02624 ( 126) hydrogen bonds : angle 3.59421 ( 360) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 213 LEU cc_start: 0.9270 (tp) cc_final: 0.8768 (mt) REVERT: J 284 LEU cc_start: 0.9379 (tt) cc_final: 0.9159 (mt) outliers start: 3 outliers final: 3 residues processed: 29 average time/residue: 0.0911 time to fit residues: 3.9666 Evaluate side-chains 27 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 521 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 10 optimal weight: 0.2980 chunk 44 optimal weight: 0.3980 chunk 17 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 486 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.067702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.044375 restraints weight = 69668.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.046118 restraints weight = 31377.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.047175 restraints weight = 18908.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.047805 restraints weight = 13867.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.048061 restraints weight = 11652.024| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.7086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3809 Z= 0.095 Angle : 0.496 6.177 5126 Z= 0.254 Chirality : 0.039 0.128 630 Planarity : 0.002 0.025 663 Dihedral : 3.275 25.078 531 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.74 % Allowed : 10.32 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.38), residues: 503 helix: 0.94 (0.34), residues: 248 sheet: -2.84 (1.00), residues: 21 loop : -1.41 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 370 TYR 0.004 0.001 TYR J 124 PHE 0.021 0.002 PHE J 285 HIS 0.001 0.000 HIS J 463 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 3809) covalent geometry : angle 0.49566 ( 5126) hydrogen bonds : bond 0.02511 ( 126) hydrogen bonds : angle 3.50485 ( 360) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.129 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: J 284 LEU cc_start: 0.9380 (tt) cc_final: 0.9156 (mt) outliers start: 3 outliers final: 1 residues processed: 27 average time/residue: 0.0936 time to fit residues: 3.6681 Evaluate side-chains 25 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 239 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 4 optimal weight: 0.0670 chunk 48 optimal weight: 0.8980 overall best weight: 0.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 486 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.066741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.043331 restraints weight = 70515.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.045054 restraints weight = 31977.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.045966 restraints weight = 19378.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.046659 restraints weight = 14465.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.046929 restraints weight = 12099.488| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.7377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3809 Z= 0.134 Angle : 0.518 5.397 5126 Z= 0.269 Chirality : 0.039 0.128 630 Planarity : 0.002 0.027 663 Dihedral : 3.231 12.791 529 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.49 % Allowed : 10.81 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.38), residues: 503 helix: 0.79 (0.34), residues: 249 sheet: -2.84 (0.78), residues: 33 loop : -1.25 (0.41), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 105 TYR 0.006 0.001 TYR J 124 PHE 0.016 0.001 PHE J 285 HIS 0.002 0.001 HIS J 116 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 3809) covalent geometry : angle 0.51796 ( 5126) hydrogen bonds : bond 0.02764 ( 126) hydrogen bonds : angle 3.66620 ( 360) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1811.26 seconds wall clock time: 31 minutes 27.28 seconds (1887.28 seconds total)