Starting phenix.real_space_refine on Tue Sep 24 10:03:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9o_24330/09_2024/7r9o_24330.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9o_24330/09_2024/7r9o_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9o_24330/09_2024/7r9o_24330.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9o_24330/09_2024/7r9o_24330.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9o_24330/09_2024/7r9o_24330.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9o_24330/09_2024/7r9o_24330.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 4.34, per 1000 atoms: 0.56 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: 1.91 Conformation dependent library (CDL) restraints added in 669.8 milliseconds 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: 0.60 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: 2.40 Time building geometry restraints manager: 2.30 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: 2.910 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: 0.140 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 19.920 Find NCS groups from input model: 0.050 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:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.930 ------------------------------------------------------------------------------- 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= 0.107 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.001 0.000 HIS J 72 PHE 0.001 0.000 PHE J 285 TYR 0.001 0.000 TYR J 418 ARG 0.001 0.000 ARG J 308 *********************** 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 fitting. rotamer outliers: 1 poor density : 68 time to evaluate : 0.637 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: 0.4968 time to fit residues: 40.0005 Evaluate side-chains 45 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 44 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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 42 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 39 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3809 Z= 0.198 Angle : 0.554 4.720 5126 Z= 0.296 Chirality : 0.040 0.129 630 Planarity : 0.004 0.038 663 Dihedral : 3.008 25.804 531 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.25 % Allowed : 6.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.32), residues: 503 helix: -1.84 (0.31), residues: 224 sheet: -4.00 (0.66), residues: 31 loop : -2.19 (0.34), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS J 375 PHE 0.013 0.001 PHE J 285 TYR 0.010 0.002 TYR J 124 ARG 0.005 0.001 ARG J 66 *********************** 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 39 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 104 LEU cc_start: 0.9053 (tp) cc_final: 0.8770 (tp) REVERT: J 213 LEU cc_start: 0.8603 (tp) cc_final: 0.8348 (mt) outliers start: 1 outliers final: 1 residues processed: 39 average time/residue: 0.2531 time to fit residues: 13.6058 Evaluate side-chains 30 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 29 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 25 optimal weight: 0.2980 chunk 14 optimal weight: 0.4980 chunk 37 optimal weight: 0.1980 chunk 30 optimal weight: 4.9990 chunk 12 optimal weight: 0.0270 chunk 45 optimal weight: 0.3980 chunk 49 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 overall best weight: 0.2838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 447 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 3809 Z= 0.138 Angle : 0.458 4.316 5126 Z= 0.241 Chirality : 0.038 0.128 630 Planarity : 0.003 0.031 663 Dihedral : 2.900 25.614 531 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.49 % Allowed : 5.90 % Favored : 93.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.34), residues: 503 helix: -0.81 (0.33), residues: 218 sheet: -3.51 (0.78), residues: 31 loop : -1.78 (0.35), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 296 PHE 0.004 0.001 PHE J 285 TYR 0.004 0.001 TYR J 124 ARG 0.005 0.000 ARG J 66 *********************** 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 33 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 31 time to evaluate : 0.732 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 104 LEU cc_start: 0.8965 (tp) cc_final: 0.8692 (tp) outliers start: 2 outliers final: 2 residues processed: 33 average time/residue: 0.2114 time to fit residues: 10.3115 Evaluate side-chains 31 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 29 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 34 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 40 optimal weight: 0.0670 chunk 27 optimal weight: 5.9990 overall best weight: 0.9324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 447 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.4881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3809 Z= 0.186 Angle : 0.474 4.492 5126 Z= 0.254 Chirality : 0.038 0.131 630 Planarity : 0.003 0.024 663 Dihedral : 3.063 26.245 531 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.74 % Allowed : 6.14 % Favored : 93.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.35), residues: 503 helix: -0.16 (0.33), residues: 226 sheet: -3.17 (0.81), residues: 31 loop : -1.55 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS J 116 PHE 0.009 0.001 PHE J 285 TYR 0.008 0.001 TYR J 124 ARG 0.004 0.000 ARG J 66 *********************** 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 32 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 29 time to evaluate : 0.604 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: J 104 LEU cc_start: 0.9149 (tp) cc_final: 0.8741 (mt) outliers start: 3 outliers final: 3 residues processed: 32 average time/residue: 0.2231 time to fit residues: 10.5006 Evaluate side-chains 29 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 26 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.5697 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= 0.197 Angle : 0.501 4.479 5126 Z= 0.267 Chirality : 0.038 0.127 630 Planarity : 0.003 0.027 663 Dihedral : 3.322 24.698 531 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.98 % Allowed : 6.88 % Favored : 92.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.36), residues: 503 helix: 0.07 (0.32), residues: 237 sheet: -2.85 (0.91), residues: 31 loop : -1.49 (0.40), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 116 PHE 0.005 0.001 PHE J 285 TYR 0.010 0.001 TYR J 124 ARG 0.002 0.000 ARG J 66 *********************** 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 31 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 27 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 104 LEU cc_start: 0.9109 (tp) cc_final: 0.8694 (mt) outliers start: 4 outliers final: 4 residues processed: 31 average time/residue: 0.2714 time to fit residues: 11.6179 Evaluate side-chains 29 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 25 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 351 ASP 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 11 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.6210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3809 Z= 0.224 Angle : 0.519 5.255 5126 Z= 0.278 Chirality : 0.039 0.130 630 Planarity : 0.003 0.030 663 Dihedral : 3.462 25.262 531 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.74 % Allowed : 8.11 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.36), residues: 503 helix: 0.29 (0.33), residues: 238 sheet: -2.80 (0.95), residues: 31 loop : -1.51 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS J 116 PHE 0.005 0.001 PHE J 285 TYR 0.009 0.001 TYR J 124 ARG 0.002 0.000 ARG J 370 *********************** 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 29 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 26 time to evaluate : 0.723 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: J 104 LEU cc_start: 0.9101 (tp) cc_final: 0.8773 (mt) REVERT: J 155 MET cc_start: 0.6438 (tpp) cc_final: 0.6219 (tpp) outliers start: 3 outliers final: 3 residues processed: 29 average time/residue: 0.3140 time to fit residues: 12.6468 Evaluate side-chains 28 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 25 time to evaluate : 0.673 ------------------------------------------------------------------------------- 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 27 optimal weight: 8.9990 chunk 40 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.6370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 3809 Z= 0.154 Angle : 0.476 4.841 5126 Z= 0.248 Chirality : 0.038 0.128 630 Planarity : 0.002 0.025 663 Dihedral : 3.335 24.729 531 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.74 % Allowed : 7.62 % Favored : 91.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.37), residues: 503 helix: 0.57 (0.33), residues: 239 sheet: -2.62 (0.98), residues: 31 loop : -1.46 (0.39), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 463 PHE 0.008 0.001 PHE J 285 TYR 0.006 0.001 TYR J 124 ARG 0.002 0.000 ARG J 370 *********************** 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 29 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 26 time to evaluate : 0.611 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: J 104 LEU cc_start: 0.9071 (tp) cc_final: 0.8795 (mt) REVERT: J 213 LEU cc_start: 0.8516 (tp) cc_final: 0.8121 (mt) outliers start: 3 outliers final: 3 residues processed: 29 average time/residue: 0.2607 time to fit residues: 10.6115 Evaluate side-chains 28 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 25 time to evaluate : 0.695 ------------------------------------------------------------------------------- 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 23 optimal weight: 0.4980 chunk 4 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 42 optimal weight: 0.1980 chunk 44 optimal weight: 0.8980 chunk 27 optimal weight: 10.0000 chunk 19 optimal weight: 0.0570 chunk 35 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 overall best weight: 0.3898 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.6491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 3809 Z= 0.131 Angle : 0.456 5.121 5126 Z= 0.235 Chirality : 0.038 0.125 630 Planarity : 0.002 0.022 663 Dihedral : 3.248 25.412 531 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.74 % Allowed : 7.13 % Favored : 92.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.37), residues: 503 helix: 0.79 (0.33), residues: 239 sheet: -2.41 (0.94), residues: 31 loop : -1.26 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 463 PHE 0.010 0.001 PHE J 285 TYR 0.004 0.001 TYR J 124 ARG 0.002 0.000 ARG J 370 *********************** 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 30 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 27 time to evaluate : 0.702 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: J 213 LEU cc_start: 0.8498 (tp) cc_final: 0.7948 (mt) REVERT: J 215 ASP cc_start: 0.8175 (m-30) cc_final: 0.7612 (p0) outliers start: 3 outliers final: 3 residues processed: 30 average time/residue: 0.2803 time to fit residues: 11.7423 Evaluate side-chains 27 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 24 time to evaluate : 0.614 ------------------------------------------------------------------------------- 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 40 optimal weight: 0.2980 chunk 42 optimal weight: 0.9990 chunk 44 optimal weight: 0.4980 chunk 29 optimal weight: 0.8980 chunk 47 optimal weight: 0.2980 chunk 28 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.6669 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= 0.142 Angle : 0.489 9.038 5126 Z= 0.249 Chirality : 0.038 0.125 630 Planarity : 0.002 0.023 663 Dihedral : 3.207 25.678 531 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.74 % Allowed : 7.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.37), residues: 503 helix: 0.79 (0.33), residues: 245 sheet: -2.41 (0.93), residues: 31 loop : -1.36 (0.39), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 463 PHE 0.010 0.001 PHE J 285 TYR 0.003 0.001 TYR J 124 ARG 0.002 0.000 ARG J 370 *********************** 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 30 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 27 time to evaluate : 0.604 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: 0.8504 (tp) cc_final: 0.7938 (mt) REVERT: J 215 ASP cc_start: 0.8191 (m-30) cc_final: 0.7654 (p0) outliers start: 3 outliers final: 3 residues processed: 30 average time/residue: 0.2129 time to fit residues: 9.4152 Evaluate side-chains 28 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 25 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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 4 optimal weight: 0.9980 chunk 30 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 16 optimal weight: 0.0370 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.6875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 3809 Z= 0.145 Angle : 0.483 7.341 5126 Z= 0.247 Chirality : 0.038 0.126 630 Planarity : 0.002 0.024 663 Dihedral : 3.204 25.705 531 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.74 % Allowed : 8.11 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.37), residues: 503 helix: 0.91 (0.33), residues: 244 sheet: -2.43 (0.91), residues: 31 loop : -1.30 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 116 PHE 0.009 0.001 PHE J 285 TYR 0.008 0.001 TYR J 124 ARG 0.002 0.000 ARG J 370 ********************** 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 28 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 25 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 215 ASP cc_start: 0.8151 (m-30) cc_final: 0.7713 (p0) REVERT: J 314 MET cc_start: 0.8140 (mmm) cc_final: 0.7722 (mmm) outliers start: 3 outliers final: 3 residues processed: 28 average time/residue: 0.2119 time to fit residues: 8.7163 Evaluate side-chains 27 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 24 time to evaluate : 0.610 ------------------------------------------------------------------------------- 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 40 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 31 optimal weight: 0.0970 chunk 30 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 222 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 = 0.3713 r_free = 0.3713 target = 0.068148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.044656 restraints weight = 68007.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.046315 restraints weight = 31284.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.047361 restraints weight = 19060.109| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.7076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3809 Z= 0.156 Angle : 0.500 7.440 5126 Z= 0.256 Chirality : 0.038 0.125 630 Planarity : 0.002 0.025 663 Dihedral : 3.265 25.698 531 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.74 % Allowed : 8.35 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.37), residues: 503 helix: 0.89 (0.33), residues: 245 sheet: -2.41 (0.89), residues: 31 loop : -1.20 (0.40), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 296 PHE 0.010 0.001 PHE J 285 TYR 0.005 0.001 TYR J 124 ARG 0.002 0.000 ARG J 370 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2471.51 seconds wall clock time: 43 minutes 37.09 seconds (2617.09 seconds total)