Starting phenix.real_space_refine on Mon Mar 11 08:10:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9o_24330/03_2024/7r9o_24330.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9o_24330/03_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_24330/03_2024/7r9o_24330.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9o_24330/03_2024/7r9o_24330.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9o_24330/03_2024/7r9o_24330.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r9o_24330/03_2024/7r9o_24330.pdb" } 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 Residue "J ARG 382": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ARG 522": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 4.00, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 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: 8.16 Conformation dependent library (CDL) restraints added in 858.4 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: 0.81 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: 2.37 Time building geometry restraints manager: 8.35 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: 100.87 - 106.95: 59 106.95 - 113.02: 9888 113.02 - 119.10: 1576 119.10 - 125.18: 2569 125.18 - 131.26: 53 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 1.850 nonbonded pdb=" OE1 GLU J 408 " pdb=" H GLU J 408 " model vdw 1.695 1.850 nonbonded pdb=" O LEU J 317 " pdb=" HG1 THR J 321 " model vdw 1.715 1.850 nonbonded pdb=" OD1 ASN J 236 " pdb=" HZ1 LYS J 311 " model vdw 1.718 1.850 nonbonded pdb=" O ILE J 64 " pdb=" H MET J 68 " model vdw 1.729 1.850 ... (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: 0.910 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: 4.680 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 30.980 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.950 ------------------------------------------------------------------------------- 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 : 0.636 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: 0.5107 time to fit residues: 40.8795 Evaluate side-chains 45 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 44 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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: 0.9990 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 12 optimal weight: 0.0170 chunk 25 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 39 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 0.0570 chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.5536 ------------------------------------------------------------------------------- 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: 0.7594 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3809 Z= 0.167 Angle : 0.519 4.617 5126 Z= 0.276 Chirality : 0.039 0.128 630 Planarity : 0.004 0.036 663 Dihedral : 2.964 25.942 531 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.49 % Allowed : 7.13 % Favored : 92.38 % 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: -3.50 (0.31), residues: 503 helix: -2.07 (0.29), residues: 230 sheet: -3.90 (0.68), residues: 31 loop : -2.29 (0.34), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS J 375 PHE 0.012 0.001 PHE J 285 TYR 0.008 0.002 TYR J 124 ARG 0.006 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 44 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 0.601 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: 0.8977 (tp) cc_final: 0.8726 (tp) outliers start: 2 outliers final: 2 residues processed: 43 average time/residue: 0.2448 time to fit residues: 14.4087 Evaluate side-chains 36 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 34 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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 25 optimal weight: 0.2980 chunk 14 optimal weight: 0.3980 chunk 37 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 40 optimal weight: 0.0980 chunk 15 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 44 optimal weight: 0.0370 overall best weight: 0.2858 ------------------------------------------------------------------------------- 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: 0.7639 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3809 Z= 0.126 Angle : 0.440 4.291 5126 Z= 0.231 Chirality : 0.038 0.133 630 Planarity : 0.002 0.021 663 Dihedral : 2.739 25.711 531 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.74 % Allowed : 7.37 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.20 (0.34), residues: 503 helix: -0.76 (0.34), residues: 216 sheet: -3.44 (0.77), residues: 31 loop : -1.79 (0.34), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 72 PHE 0.003 0.001 PHE J 285 TYR 0.004 0.001 TYR J 124 ARG 0.003 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 35 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 32 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: 0.8906 (tp) cc_final: 0.8554 (mt) REVERT: J 213 LEU cc_start: 0.8591 (tp) cc_final: 0.8284 (mt) REVERT: J 516 ILE cc_start: 0.5221 (pt) cc_final: 0.4973 (pt) outliers start: 3 outliers final: 3 residues processed: 34 average time/residue: 0.2450 time to fit residues: 11.7957 Evaluate side-chains 32 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 29 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 23 MET 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: 2.9990 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 40 optimal weight: 0.2980 chunk 27 optimal weight: 9.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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: 0.7766 moved from start: 0.4846 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= 0.161 Angle : 0.465 5.965 5126 Z= 0.246 Chirality : 0.038 0.121 630 Planarity : 0.002 0.019 663 Dihedral : 3.012 26.612 531 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.47 % Allowed : 6.63 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.61 (0.35), residues: 503 helix: -0.14 (0.33), residues: 227 sheet: -3.21 (0.78), residues: 31 loop : -1.65 (0.37), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS J 296 PHE 0.003 0.001 PHE J 285 TYR 0.009 0.001 TYR J 124 ARG 0.002 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 33 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 27 time to evaluate : 0.590 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 68 MET cc_start: 0.8053 (ptm) cc_final: 0.7824 (ptm) REVERT: J 104 LEU cc_start: 0.9106 (tp) cc_final: 0.8766 (mt) outliers start: 6 outliers final: 4 residues processed: 32 average time/residue: 0.2301 time to fit residues: 10.7087 Evaluate side-chains 29 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 25 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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 0 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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: 0.7859 moved from start: 0.5506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3809 Z= 0.188 Angle : 0.474 4.548 5126 Z= 0.254 Chirality : 0.038 0.126 630 Planarity : 0.003 0.019 663 Dihedral : 3.172 25.150 531 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.47 % Allowed : 7.37 % 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: -1.36 (0.35), residues: 503 helix: 0.09 (0.33), residues: 232 sheet: -2.83 (0.91), residues: 31 loop : -1.61 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 116 PHE 0.003 0.001 PHE J 355 TYR 0.009 0.001 TYR J 124 ARG 0.001 0.000 ARG J 29 *********************** 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 34 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 28 time to evaluate : 0.635 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 68 MET cc_start: 0.8099 (ptm) cc_final: 0.7874 (ptm) outliers start: 6 outliers final: 5 residues processed: 32 average time/residue: 0.2664 time to fit residues: 11.8522 Evaluate side-chains 30 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 25 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 23 MET Chi-restraints excluded: chain J residue 108 GLU 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 11 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 4 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 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 474 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.5937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3809 Z= 0.158 Angle : 0.449 4.613 5126 Z= 0.237 Chirality : 0.038 0.125 630 Planarity : 0.002 0.023 663 Dihedral : 3.188 24.909 531 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.98 % Allowed : 8.35 % 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 (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: -0.99 (0.37), residues: 503 helix: 0.39 (0.33), residues: 236 sheet: -2.69 (0.96), residues: 31 loop : -1.43 (0.38), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS J 116 PHE 0.003 0.001 PHE J 285 TYR 0.008 0.001 TYR J 124 ARG 0.001 0.000 ARG J 218 *********************** 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 fitting. rotamer outliers: 4 poor density : 26 time to evaluate : 0.698 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 68 MET cc_start: 0.8085 (ptm) cc_final: 0.7853 (ptm) outliers start: 4 outliers final: 4 residues processed: 29 average time/residue: 0.2654 time to fit residues: 10.8663 Evaluate side-chains 29 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 25 time to evaluate : 0.741 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 30 optimal weight: 8.9990 chunk 29 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 9 optimal weight: 0.0270 chunk 32 optimal weight: 10.0000 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 500 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.6238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3809 Z= 0.161 Angle : 0.450 4.763 5126 Z= 0.237 Chirality : 0.038 0.120 630 Planarity : 0.002 0.027 663 Dihedral : 3.238 24.915 531 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.47 % Allowed : 8.85 % 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 (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: -0.79 (0.37), residues: 503 helix: 0.52 (0.33), residues: 242 sheet: -2.62 (0.87), residues: 36 loop : -1.28 (0.40), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS J 116 PHE 0.005 0.001 PHE J 285 TYR 0.007 0.001 TYR J 124 ARG 0.001 0.000 ARG J 29 *********************** 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 32 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 26 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 68 MET cc_start: 0.8116 (ptm) cc_final: 0.7861 (ptm) outliers start: 6 outliers final: 5 residues processed: 30 average time/residue: 0.2617 time to fit residues: 10.9733 Evaluate side-chains 30 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 25 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 23 MET Chi-restraints excluded: chain J residue 108 GLU 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: 0.7980 chunk 4 optimal weight: 0.0870 chunk 37 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 42 optimal weight: 0.0970 chunk 44 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.4956 ------------------------------------------------------------------------------- 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: 0.7881 moved from start: 0.6375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3809 Z= 0.121 Angle : 0.431 4.938 5126 Z= 0.223 Chirality : 0.038 0.123 630 Planarity : 0.002 0.025 663 Dihedral : 3.149 25.008 531 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % 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 (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: -0.55 (0.37), residues: 503 helix: 0.79 (0.34), residues: 242 sheet: -2.51 (0.98), residues: 31 loop : -1.29 (0.40), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 463 PHE 0.003 0.001 PHE J 285 TYR 0.004 0.001 TYR J 124 ARG 0.001 0.000 ARG J 218 *********************** 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 32 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 28 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 68 MET cc_start: 0.8077 (ptm) cc_final: 0.7818 (ptm) outliers start: 4 outliers final: 4 residues processed: 31 average time/residue: 0.2639 time to fit residues: 11.5184 Evaluate side-chains 29 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 25 time to evaluate : 0.675 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.0970 chunk 42 optimal weight: 0.7980 chunk 44 optimal weight: 0.0980 chunk 29 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 45 optimal weight: 0.2980 chunk 39 optimal weight: 0.5980 overall best weight: 0.3778 ------------------------------------------------------------------------------- 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: 0.7877 moved from start: 0.6477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3809 Z= 0.122 Angle : 0.444 5.062 5126 Z= 0.228 Chirality : 0.038 0.122 630 Planarity : 0.002 0.025 663 Dihedral : 3.130 25.168 531 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.23 % Allowed : 10.07 % 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 (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: -0.46 (0.37), residues: 503 helix: 0.95 (0.34), residues: 238 sheet: -2.42 (0.99), residues: 31 loop : -1.32 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 463 PHE 0.003 0.001 PHE J 285 TYR 0.004 0.001 TYR J 124 ARG 0.001 0.000 ARG J 218 *********************** 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: 5 poor density : 25 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 68 MET cc_start: 0.8082 (ptm) cc_final: 0.7854 (ptm) REVERT: J 314 MET cc_start: 0.8080 (mmm) cc_final: 0.7809 (mmm) outliers start: 5 outliers final: 5 residues processed: 28 average time/residue: 0.2602 time to fit residues: 10.2050 Evaluate side-chains 29 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 24 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 23 MET Chi-restraints excluded: chain J residue 47 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.3980 chunk 30 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 36 optimal weight: 0.3980 chunk 5 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 39 optimal weight: 0.0980 chunk 16 optimal weight: 0.6980 overall best weight: 0.5182 ------------------------------------------------------------------------------- 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: 0.7893 moved from start: 0.6629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3809 Z= 0.127 Angle : 0.446 5.205 5126 Z= 0.231 Chirality : 0.038 0.121 630 Planarity : 0.002 0.027 663 Dihedral : 3.164 24.973 531 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.98 % Allowed : 10.32 % 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 (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 (0.38), residues: 503 helix: 0.97 (0.34), residues: 242 sheet: -2.30 (0.99), residues: 31 loop : -1.30 (0.40), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 463 PHE 0.003 0.001 PHE J 285 TYR 0.005 0.001 TYR J 124 ARG 0.001 0.000 ARG J 218 ********************** 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 29 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 25 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 314 MET cc_start: 0.8090 (mmm) cc_final: 0.7801 (mmm) outliers start: 4 outliers final: 4 residues processed: 28 average time/residue: 0.3244 time to fit residues: 12.6079 Evaluate side-chains 28 residues out of total 407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 24 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.3705 r_free = 0.3705 target = 0.067598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.044301 restraints weight = 69555.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.046042 restraints weight = 32872.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.047122 restraints weight = 20191.694| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.6971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3809 Z= 0.189 Angle : 0.497 7.574 5126 Z= 0.262 Chirality : 0.038 0.124 630 Planarity : 0.003 0.030 663 Dihedral : 3.438 24.852 531 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.98 % Allowed : 10.32 % 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 (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: -0.49 (0.37), residues: 503 helix: 0.77 (0.33), residues: 242 sheet: -2.42 (0.86), residues: 36 loop : -1.12 (0.41), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS J 116 PHE 0.003 0.001 PHE J 285 TYR 0.009 0.002 TYR J 124 ARG 0.002 0.000 ARG J 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2551.03 seconds wall clock time: 45 minutes 39.85 seconds (2739.85 seconds total)