Starting phenix.real_space_refine on Sat Feb 17 18:42:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m33_23641/02_2024/7m33_23641_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m33_23641/02_2024/7m33_23641.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m33_23641/02_2024/7m33_23641.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m33_23641/02_2024/7m33_23641.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m33_23641/02_2024/7m33_23641_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m33_23641/02_2024/7m33_23641_trim_updated.pdb" } resolution = 3.55 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 S 40 5.16 5 C 6328 2.51 5 N 1657 2.21 5 O 1802 1.98 5 H 9742 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 137": "OE1" <-> "OE2" Residue "D PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19575 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 8993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 8993 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 19, 'TRANS': 553} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'TYR:plan': 2, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "D" Number of atoms: 10452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 10452 Classifications: {'peptide': 664} Link IDs: {'PTRANS': 13, 'TRANS': 650} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 99 Unusual residues: {'ATP': 1, 'HT1': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.85, per 1000 atoms: 0.45 Number of scatterers: 19575 At special positions: 0 Unit cell: (100.605, 151.437, 96.369, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 40 16.00 P 6 15.00 O 1802 8.00 N 1657 7.00 C 6328 6.00 H 9742 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: 15.81 Conformation dependent library (CDL) restraints added in 2.0 seconds 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2294 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 8 sheets defined 60.0% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.29 Creating SS restraints... Processing helix chain 'C' and resid 3 through 7 Processing helix chain 'C' and resid 9 through 14 Processing helix chain 'C' and resid 16 through 48 removed outlier: 4.215A pdb=" N MET C 34 " --> pdb=" O ASN C 30 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE C 35 " --> pdb=" O VAL C 31 " (cutoff:3.500A) Proline residue: C 36 - end of helix Processing helix chain 'C' and resid 54 through 102 Processing helix chain 'C' and resid 106 through 111 Processing helix chain 'C' and resid 114 through 120 Processing helix chain 'C' and resid 123 through 132 Processing helix chain 'C' and resid 134 through 155 removed outlier: 4.120A pdb=" N PHE C 145 " --> pdb=" O ASP C 141 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N MET C 146 " --> pdb=" O SER C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 165 Processing helix chain 'C' and resid 167 through 206 removed outlier: 4.161A pdb=" N VAL C 171 " --> pdb=" O ILE C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 213 Processing helix chain 'C' and resid 221 through 242 removed outlier: 3.864A pdb=" N LYS C 234 " --> pdb=" O ASP C 230 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ASN C 235 " --> pdb=" O VAL C 231 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N MET C 236 " --> pdb=" O TYR C 232 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N LYS C 237 " --> pdb=" O GLN C 233 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N VAL C 238 " --> pdb=" O LYS C 234 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE C 241 " --> pdb=" O LYS C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 269 removed outlier: 3.617A pdb=" N PHE C 269 " --> pdb=" O ALA C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 287 Processing helix chain 'C' and resid 289 through 316 removed outlier: 3.564A pdb=" N PHE C 293 " --> pdb=" O ILE C 289 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLY C 296 " --> pdb=" O MET C 292 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR C 315 " --> pdb=" O ARG C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 384 removed outlier: 4.064A pdb=" N ILE C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 413 Processing helix chain 'C' and resid 428 through 433 Processing helix chain 'C' and resid 442 through 450 removed outlier: 3.526A pdb=" N ILE C 448 " --> pdb=" O GLN C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 457 No H-bonds generated for 'chain 'C' and resid 454 through 457' Processing helix chain 'C' and resid 477 through 491 Processing helix chain 'C' and resid 501 through 504 removed outlier: 3.815A pdb=" N ALA C 504 " --> pdb=" O SER C 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 501 through 504' Processing helix chain 'C' and resid 507 through 521 removed outlier: 4.013A pdb=" N ALA C 512 " --> pdb=" O LYS C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 538 removed outlier: 4.037A pdb=" N HIS C 538 " --> pdb=" O SER C 534 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 534 through 538' Processing helix chain 'C' and resid 556 through 561 Processing helix chain 'C' and resid 564 through 573 Processing helix chain 'D' and resid 3 through 12 Processing helix chain 'D' and resid 15 through 44 removed outlier: 3.935A pdb=" N GLY D 35 " --> pdb=" O ALA D 31 " (cutoff:3.500A) Proline residue: D 36 - end of helix Processing helix chain 'D' and resid 49 through 51 No H-bonds generated for 'chain 'D' and resid 49 through 51' Processing helix chain 'D' and resid 135 through 158 Proline residue: D 144 - end of helix removed outlier: 4.200A pdb=" N LYS D 147 " --> pdb=" O GLN D 143 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N GLY D 148 " --> pdb=" O PRO D 144 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL D 150 " --> pdb=" O ILE D 146 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N LEU D 151 " --> pdb=" O LYS D 147 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU D 152 " --> pdb=" O GLY D 148 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ALA D 154 " --> pdb=" O VAL D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 195 Processing helix chain 'D' and resid 198 through 203 Processing helix chain 'D' and resid 206 through 213 Processing helix chain 'D' and resid 215 through 229 Processing helix chain 'D' and resid 231 through 248 Processing helix chain 'D' and resid 250 through 297 removed outlier: 3.665A pdb=" N VAL D 255 " --> pdb=" O LYS D 251 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA D 258 " --> pdb=" O PHE D 254 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE D 259 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL D 260 " --> pdb=" O ALA D 256 " (cutoff:3.500A) Proline residue: D 261 - end of helix removed outlier: 4.289A pdb=" N TYR D 276 " --> pdb=" O ARG D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 305 Processing helix chain 'D' and resid 308 through 336 Processing helix chain 'D' and resid 339 through 360 Processing helix chain 'D' and resid 369 through 384 removed outlier: 3.671A pdb=" N ASN D 380 " --> pdb=" O VAL D 376 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG D 381 " --> pdb=" O ASP D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 410 removed outlier: 4.690A pdb=" N GLU D 397 " --> pdb=" O PHE D 393 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LEU D 398 " --> pdb=" O SER D 394 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA D 399 " --> pdb=" O LYS D 395 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU D 409 " --> pdb=" O ARG D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 475 Processing helix chain 'D' and resid 499 through 503 Processing helix chain 'D' and resid 520 through 525 Processing helix chain 'D' and resid 532 through 545 removed outlier: 3.725A pdb=" N ILE D 536 " --> pdb=" O THR D 532 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG D 541 " --> pdb=" O LYS D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 583 removed outlier: 3.756A pdb=" N GLN D 573 " --> pdb=" O SER D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 614 removed outlier: 4.242A pdb=" N GLN D 614 " --> pdb=" O ASP D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 629 Processing helix chain 'D' and resid 649 through 653 Processing helix chain 'D' and resid 655 through 664 Processing sheet with id= A, first strand: chain 'C' and resid 337 through 339 Processing sheet with id= B, first strand: chain 'C' and resid 342 through 344 Processing sheet with id= C, first strand: chain 'C' and resid 550 through 554 removed outlier: 7.112A pdb=" N VAL C 544 " --> pdb=" O ALA C 551 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ARG C 553 " --> pdb=" O ILE C 542 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ILE C 542 " --> pdb=" O ARG C 553 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 54 through 56 Processing sheet with id= E, first strand: chain 'D' and resid 89 through 92 Processing sheet with id= F, first strand: chain 'D' and resid 109 through 113 Processing sheet with id= G, first strand: chain 'D' and resid 430 through 433 Processing sheet with id= H, first strand: chain 'D' and resid 506 through 508 removed outlier: 6.824A pdb=" N ILE D 587 " --> pdb=" O GLY D 507 " (cutoff:3.500A) 544 hydrogen bonds defined for protein. 1575 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: 7.27 Time building geometry restraints manager: 16.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 9742 1.04 - 1.24: 1338 1.24 - 1.45: 3032 1.45 - 1.65: 5588 1.65 - 1.85: 80 Bond restraints: 19780 Sorted by residual: bond pdb=" C4 ATP D 701 " pdb=" C5 ATP D 701 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.82e+01 bond pdb=" C4 ATP C 801 " pdb=" C5 ATP C 801 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.52e+01 bond pdb=" C5 ATP D 701 " pdb=" C6 ATP D 701 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.47e+01 bond pdb=" C5 ATP C 801 " pdb=" C6 ATP C 801 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.37e+01 bond pdb=" C5 ATP C 801 " pdb=" N7 ATP C 801 " ideal model delta sigma weight residual 1.387 1.340 0.047 1.00e-02 1.00e+04 2.19e+01 ... (remaining 19775 not shown) Histogram of bond angle deviations from ideal: 96.57 - 104.45: 136 104.45 - 112.34: 22390 112.34 - 120.22: 7387 120.22 - 128.10: 5689 128.10 - 135.98: 96 Bond angle restraints: 35698 Sorted by residual: angle pdb=" PB ATP C 801 " pdb=" O3B ATP C 801 " pdb=" PG ATP C 801 " ideal model delta sigma weight residual 139.87 119.68 20.19 1.00e+00 1.00e+00 4.08e+02 angle pdb=" PB ATP D 701 " pdb=" O3B ATP D 701 " pdb=" PG ATP D 701 " ideal model delta sigma weight residual 139.87 125.37 14.50 1.00e+00 1.00e+00 2.10e+02 angle pdb=" PA ATP D 701 " pdb=" O3A ATP D 701 " pdb=" PB ATP D 701 " ideal model delta sigma weight residual 136.83 122.52 14.31 1.00e+00 1.00e+00 2.05e+02 angle pdb=" PA ATP C 801 " pdb=" O3A ATP C 801 " pdb=" PB ATP C 801 " ideal model delta sigma weight residual 136.83 123.50 13.33 1.00e+00 1.00e+00 1.78e+02 angle pdb=" C5 ATP C 801 " pdb=" C4 ATP C 801 " pdb=" N3 ATP C 801 " ideal model delta sigma weight residual 126.80 118.76 8.04 1.00e+00 1.00e+00 6.47e+01 ... (remaining 35693 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 8368 17.79 - 35.58: 595 35.58 - 53.37: 192 53.37 - 71.16: 100 71.16 - 88.95: 15 Dihedral angle restraints: 9270 sinusoidal: 5032 harmonic: 4238 Sorted by residual: dihedral pdb=" CA SER C 340 " pdb=" C SER C 340 " pdb=" N HIS C 341 " pdb=" CA HIS C 341 " ideal model delta harmonic sigma weight residual 180.00 152.82 27.18 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA TYR D 439 " pdb=" C TYR D 439 " pdb=" N GLN D 440 " pdb=" CA GLN D 440 " ideal model delta harmonic sigma weight residual 180.00 155.29 24.71 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA LEU D 335 " pdb=" C LEU D 335 " pdb=" N MET D 336 " pdb=" CA MET D 336 " ideal model delta harmonic sigma weight residual -180.00 -158.02 -21.98 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 9267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1269 0.088 - 0.177: 231 0.177 - 0.265: 34 0.265 - 0.353: 4 0.353 - 0.441: 2 Chirality restraints: 1540 Sorted by residual: chirality pdb=" CG LEU D 340 " pdb=" CB LEU D 340 " pdb=" CD1 LEU D 340 " pdb=" CD2 LEU D 340 " both_signs ideal model delta sigma weight residual False -2.59 -2.15 -0.44 2.00e-01 2.50e+01 4.87e+00 chirality pdb=" CG LEU C 137 " pdb=" CB LEU C 137 " pdb=" CD1 LEU C 137 " pdb=" CD2 LEU C 137 " both_signs ideal model delta sigma weight residual False -2.59 -2.17 -0.42 2.00e-01 2.50e+01 4.38e+00 chirality pdb=" CB VAL D 620 " pdb=" CA VAL D 620 " pdb=" CG1 VAL D 620 " pdb=" CG2 VAL D 620 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.54e+00 ... (remaining 1537 not shown) Planarity restraints: 2916 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN D 175 " -0.017 2.00e-02 2.50e+03 3.52e-02 1.24e+01 pdb=" C GLN D 175 " 0.061 2.00e-02 2.50e+03 pdb=" O GLN D 175 " -0.023 2.00e-02 2.50e+03 pdb=" N MET D 176 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 282 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.68e+00 pdb=" C ASN C 282 " -0.048 2.00e-02 2.50e+03 pdb=" O ASN C 282 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL C 283 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 361 " -0.013 2.00e-02 2.50e+03 2.66e-02 7.06e+00 pdb=" C LEU D 361 " 0.046 2.00e-02 2.50e+03 pdb=" O LEU D 361 " -0.017 2.00e-02 2.50e+03 pdb=" N ASN D 362 " -0.015 2.00e-02 2.50e+03 ... (remaining 2913 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 1720 2.23 - 2.83: 43469 2.83 - 3.42: 51671 3.42 - 4.01: 69117 4.01 - 4.60: 108414 Nonbonded interactions: 274391 Sorted by model distance: nonbonded pdb=" OE1 GLU C 537 " pdb=" HH TYR C 566 " model vdw 1.643 1.850 nonbonded pdb=" HG1 THR C 95 " pdb=" OE2 GLU D 316 " model vdw 1.659 1.850 nonbonded pdb=" HZ1 LYS C 250 " pdb=" OE2 GLU D 32 " model vdw 1.677 1.850 nonbonded pdb=" O ALA C 165 " pdb=" HG SER C 256 " model vdw 1.688 1.850 nonbonded pdb=" O VAL C 71 " pdb=" HG SER C 75 " model vdw 1.695 1.850 ... (remaining 274386 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.400 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: 0.290 Extract box with map and model: 6.200 Check model and map are aligned: 0.290 Set scattering table: 0.190 Process input model: 63.620 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 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 : 0.014 0.129 10038 Z= 0.876 Angle : 1.138 20.187 13607 Z= 0.662 Chirality : 0.071 0.441 1540 Planarity : 0.006 0.064 1713 Dihedral : 14.886 88.954 3681 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.23 % Allowed : 9.70 % Favored : 87.07 % 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: -2.02 (0.21), residues: 1233 helix: -0.54 (0.16), residues: 778 sheet: -1.99 (0.58), residues: 74 loop : -2.71 (0.27), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP C 78 HIS 0.017 0.002 HIS D 322 PHE 0.036 0.003 PHE D 141 TYR 0.027 0.003 TYR C 257 ARG 0.018 0.002 ARG D 345 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue TYR 232 is missing expected H atoms. Skipping. Residue TYR 318 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 458 is missing expected H atoms. Skipping. Residue VAL 487 is missing expected H atoms. Skipping. Residue LYS 550 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Evaluate side-chains 215 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 182 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 108 PHE cc_start: 0.7654 (t80) cc_final: 0.7136 (t80) REVERT: C 258 LEU cc_start: 0.8455 (tm) cc_final: 0.8157 (tp) REVERT: C 517 ILE cc_start: 0.8775 (mt) cc_final: 0.8575 (mt) REVERT: C 543 LEU cc_start: 0.8253 (pp) cc_final: 0.7973 (pp) REVERT: D 259 ILE cc_start: 0.5515 (OUTLIER) cc_final: 0.5212 (mt) REVERT: D 588 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8104 (pp) outliers start: 33 outliers final: 4 residues processed: 207 average time/residue: 0.4608 time to fit residues: 134.6243 Evaluate side-chains 117 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 111 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 266 TRP Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain D residue 588 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 96 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 111 optimal weight: 10.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 355 GLN C 520 ASN D 46 HIS ** D 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10038 Z= 0.225 Angle : 0.550 6.480 13607 Z= 0.301 Chirality : 0.039 0.166 1540 Planarity : 0.005 0.059 1713 Dihedral : 9.657 84.493 1438 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.18 % Allowed : 13.22 % Favored : 85.60 % 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 (0.22), residues: 1233 helix: 0.47 (0.17), residues: 785 sheet: -1.97 (0.52), residues: 83 loop : -2.43 (0.28), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 78 HIS 0.007 0.001 HIS D 68 PHE 0.016 0.001 PHE D 139 TYR 0.011 0.001 TYR D 237 ARG 0.006 0.000 ARG D 126 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue TYR 232 is missing expected H atoms. Skipping. Residue TYR 318 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 458 is missing expected H atoms. Skipping. Residue VAL 487 is missing expected H atoms. Skipping. Residue LYS 550 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 114 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 258 LEU cc_start: 0.8472 (tm) cc_final: 0.8267 (tp) REVERT: D 259 ILE cc_start: 0.5724 (OUTLIER) cc_final: 0.5319 (mt) REVERT: D 588 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.8038 (pp) REVERT: D 661 MET cc_start: 0.4364 (OUTLIER) cc_final: 0.3968 (mpp) outliers start: 12 outliers final: 7 residues processed: 123 average time/residue: 0.4264 time to fit residues: 78.8692 Evaluate side-chains 116 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 106 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 266 TRP Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 610 ASP Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 661 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 120 optimal weight: 7.9990 chunk 99 optimal weight: 0.8980 chunk 110 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 89 optimal weight: 0.3980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 184 HIS ** D 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 542 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10038 Z= 0.297 Angle : 0.533 7.130 13607 Z= 0.296 Chirality : 0.039 0.146 1540 Planarity : 0.004 0.064 1713 Dihedral : 8.803 79.579 1436 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.47 % Allowed : 13.81 % Favored : 84.72 % 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: -0.54 (0.23), residues: 1233 helix: 0.76 (0.18), residues: 783 sheet: -1.94 (0.52), residues: 83 loop : -2.38 (0.29), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 78 HIS 0.007 0.001 HIS D 307 PHE 0.025 0.001 PHE C 344 TYR 0.029 0.001 TYR D 495 ARG 0.002 0.000 ARG D 74 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue TYR 232 is missing expected H atoms. Skipping. Residue TYR 318 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 458 is missing expected H atoms. Skipping. Residue VAL 487 is missing expected H atoms. Skipping. Residue LYS 550 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 111 time to evaluate : 1.593 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: C 89 MET cc_start: 0.7675 (tpp) cc_final: 0.7253 (tpp) REVERT: D 139 PHE cc_start: 0.7900 (t80) cc_final: 0.7691 (t80) REVERT: D 259 ILE cc_start: 0.5886 (OUTLIER) cc_final: 0.5461 (mt) REVERT: D 661 MET cc_start: 0.4301 (OUTLIER) cc_final: 0.3915 (mpp) outliers start: 15 outliers final: 7 residues processed: 120 average time/residue: 0.4547 time to fit residues: 80.2319 Evaluate side-chains 111 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 102 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 344 PHE Chi-restraints excluded: chain D residue 141 PHE Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 610 ASP Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 661 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 53 optimal weight: 20.0000 chunk 75 optimal weight: 0.9990 chunk 112 optimal weight: 9.9990 chunk 118 optimal weight: 8.9990 chunk 106 optimal weight: 8.9990 chunk 32 optimal weight: 0.4980 chunk 99 optimal weight: 2.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10038 Z= 0.240 Angle : 0.499 6.271 13607 Z= 0.274 Chirality : 0.038 0.138 1540 Planarity : 0.004 0.063 1713 Dihedral : 8.246 82.306 1430 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.27 % Allowed : 13.61 % Favored : 85.11 % 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: -0.22 (0.23), residues: 1233 helix: 0.99 (0.18), residues: 782 sheet: -1.67 (0.53), residues: 83 loop : -2.25 (0.29), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 78 HIS 0.009 0.001 HIS C 452 PHE 0.011 0.001 PHE C 77 TYR 0.009 0.001 TYR C 346 ARG 0.008 0.000 ARG C 120 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue TYR 232 is missing expected H atoms. Skipping. Residue TYR 318 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 458 is missing expected H atoms. Skipping. Residue VAL 487 is missing expected H atoms. Skipping. Residue LYS 550 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Evaluate side-chains 120 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 107 time to evaluate : 1.528 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: C 89 MET cc_start: 0.7748 (tpp) cc_final: 0.7307 (tpp) REVERT: C 344 PHE cc_start: 0.5768 (OUTLIER) cc_final: 0.5041 (p90) REVERT: D 259 ILE cc_start: 0.5798 (OUTLIER) cc_final: 0.5480 (mt) REVERT: D 661 MET cc_start: 0.4293 (OUTLIER) cc_final: 0.3901 (mpp) outliers start: 13 outliers final: 7 residues processed: 116 average time/residue: 0.4256 time to fit residues: 76.1189 Evaluate side-chains 112 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 102 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 344 PHE Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 610 ASP Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 661 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 101 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 106 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10038 Z= 0.276 Angle : 0.509 6.837 13607 Z= 0.281 Chirality : 0.038 0.210 1540 Planarity : 0.004 0.063 1713 Dihedral : 8.161 85.300 1430 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.47 % Allowed : 13.52 % Favored : 85.01 % 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: -0.10 (0.23), residues: 1233 helix: 1.07 (0.18), residues: 776 sheet: -1.48 (0.53), residues: 88 loop : -2.15 (0.29), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 78 HIS 0.005 0.001 HIS C 452 PHE 0.023 0.001 PHE D 139 TYR 0.009 0.001 TYR C 346 ARG 0.005 0.000 ARG C 120 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue TYR 232 is missing expected H atoms. Skipping. Residue TYR 318 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 458 is missing expected H atoms. Skipping. Residue VAL 487 is missing expected H atoms. Skipping. Residue LYS 550 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Evaluate side-chains 122 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 107 time to evaluate : 1.386 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: C 172 MET cc_start: 0.7730 (ttm) cc_final: 0.7496 (ttp) REVERT: C 191 GLN cc_start: 0.6778 (tp-100) cc_final: 0.6466 (tp40) REVERT: C 344 PHE cc_start: 0.5862 (OUTLIER) cc_final: 0.4893 (p90) REVERT: C 383 GLN cc_start: 0.7064 (mm110) cc_final: 0.6577 (mm110) REVERT: D 259 ILE cc_start: 0.5910 (OUTLIER) cc_final: 0.5575 (mt) REVERT: D 661 MET cc_start: 0.4283 (OUTLIER) cc_final: 0.3912 (mpp) outliers start: 15 outliers final: 8 residues processed: 118 average time/residue: 0.4033 time to fit residues: 72.1575 Evaluate side-chains 114 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 103 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 344 PHE Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 610 ASP Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 661 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 119 optimal weight: 9.9990 chunk 98 optimal weight: 7.9990 chunk 55 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 20.0000 chunk 62 optimal weight: 9.9990 chunk 114 optimal weight: 9.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 ASN ** C 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.091 10038 Z= 0.681 Angle : 0.739 10.768 13607 Z= 0.414 Chirality : 0.048 0.243 1540 Planarity : 0.006 0.070 1713 Dihedral : 8.599 87.467 1429 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 1.86 % Allowed : 13.52 % Favored : 84.62 % 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: -1.21 (0.22), residues: 1233 helix: -0.02 (0.17), residues: 773 sheet: -1.43 (0.56), residues: 83 loop : -2.13 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 78 HIS 0.010 0.002 HIS C 452 PHE 0.027 0.002 PHE C 145 TYR 0.028 0.003 TYR D 495 ARG 0.008 0.001 ARG C 120 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue TYR 232 is missing expected H atoms. Skipping. Residue TYR 318 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 458 is missing expected H atoms. Skipping. Residue VAL 487 is missing expected H atoms. Skipping. Residue LYS 550 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 108 time to evaluate : 1.527 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: C 344 PHE cc_start: 0.5955 (OUTLIER) cc_final: 0.4564 (p90) REVERT: C 383 GLN cc_start: 0.7009 (mm110) cc_final: 0.6632 (mm110) REVERT: D 259 ILE cc_start: 0.6206 (OUTLIER) cc_final: 0.5995 (mt) REVERT: D 527 ASP cc_start: 0.6167 (OUTLIER) cc_final: 0.5490 (t0) REVERT: D 661 MET cc_start: 0.4292 (OUTLIER) cc_final: 0.3882 (mpp) outliers start: 19 outliers final: 11 residues processed: 122 average time/residue: 0.4294 time to fit residues: 79.0766 Evaluate side-chains 119 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 104 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 344 PHE Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 266 TRP Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 527 ASP Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 661 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 0.6980 chunk 67 optimal weight: 8.9990 chunk 86 optimal weight: 0.6980 chunk 100 optimal weight: 9.9990 chunk 66 optimal weight: 0.8980 chunk 118 optimal weight: 0.0050 chunk 74 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 73 optimal weight: 0.5980 chunk 47 optimal weight: 10.0000 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10038 Z= 0.167 Angle : 0.502 5.618 13607 Z= 0.274 Chirality : 0.037 0.134 1540 Planarity : 0.005 0.061 1713 Dihedral : 8.075 88.683 1429 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.08 % Allowed : 15.08 % Favored : 83.84 % 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: -0.36 (0.23), residues: 1233 helix: 0.67 (0.18), residues: 774 sheet: -1.06 (0.60), residues: 71 loop : -1.88 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 78 HIS 0.006 0.001 HIS C 452 PHE 0.028 0.001 PHE D 139 TYR 0.022 0.001 TYR D 495 ARG 0.009 0.000 ARG D 221 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue TYR 232 is missing expected H atoms. Skipping. Residue TYR 318 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 458 is missing expected H atoms. Skipping. Residue VAL 487 is missing expected H atoms. Skipping. Residue LYS 550 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 103 time to evaluate : 1.488 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: C 344 PHE cc_start: 0.5859 (OUTLIER) cc_final: 0.4331 (p90) REVERT: C 383 GLN cc_start: 0.6976 (mm110) cc_final: 0.6635 (mm110) REVERT: D 259 ILE cc_start: 0.5985 (OUTLIER) cc_final: 0.5722 (mt) REVERT: D 661 MET cc_start: 0.4227 (OUTLIER) cc_final: 0.3861 (mpp) outliers start: 11 outliers final: 7 residues processed: 112 average time/residue: 0.4302 time to fit residues: 71.8554 Evaluate side-chains 107 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 344 PHE Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 661 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10038 Z= 0.251 Angle : 0.507 6.982 13607 Z= 0.279 Chirality : 0.038 0.133 1540 Planarity : 0.004 0.061 1713 Dihedral : 8.000 86.916 1429 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.37 % Allowed : 14.99 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.15 (0.23), residues: 1233 helix: 0.90 (0.18), residues: 771 sheet: -1.08 (0.59), residues: 71 loop : -1.91 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 78 HIS 0.005 0.001 HIS C 452 PHE 0.015 0.001 PHE D 139 TYR 0.014 0.001 TYR D 495 ARG 0.006 0.000 ARG D 221 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue TYR 232 is missing expected H atoms. Skipping. Residue TYR 318 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 458 is missing expected H atoms. Skipping. Residue VAL 487 is missing expected H atoms. Skipping. Residue LYS 550 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Evaluate side-chains 109 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 89 MET cc_start: 0.7975 (tpp) cc_final: 0.7460 (tpp) REVERT: C 344 PHE cc_start: 0.5882 (OUTLIER) cc_final: 0.4288 (p90) REVERT: C 383 GLN cc_start: 0.6987 (mm110) cc_final: 0.6667 (mm110) REVERT: D 259 ILE cc_start: 0.5961 (OUTLIER) cc_final: 0.5703 (mt) REVERT: D 661 MET cc_start: 0.4380 (OUTLIER) cc_final: 0.4033 (mpp) outliers start: 14 outliers final: 9 residues processed: 107 average time/residue: 0.4068 time to fit residues: 65.2024 Evaluate side-chains 106 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 94 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 344 PHE Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 661 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 9.9990 chunk 110 optimal weight: 0.9990 chunk 113 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 0.0370 chunk 99 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 116 optimal weight: 0.0980 overall best weight: 1.2264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10038 Z= 0.225 Angle : 0.489 5.852 13607 Z= 0.269 Chirality : 0.038 0.145 1540 Planarity : 0.004 0.060 1713 Dihedral : 7.888 86.801 1429 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.18 % Allowed : 14.99 % Favored : 83.84 % 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: 0.02 (0.23), residues: 1233 helix: 1.05 (0.18), residues: 771 sheet: -1.13 (0.58), residues: 71 loop : -1.85 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 78 HIS 0.005 0.001 HIS C 452 PHE 0.036 0.001 PHE D 139 TYR 0.013 0.001 TYR D 495 ARG 0.006 0.000 ARG D 221 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue TYR 232 is missing expected H atoms. Skipping. Residue TYR 318 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 458 is missing expected H atoms. Skipping. Residue VAL 487 is missing expected H atoms. Skipping. Residue LYS 550 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 100 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 89 MET cc_start: 0.7963 (tpp) cc_final: 0.7456 (tpp) REVERT: C 344 PHE cc_start: 0.5662 (OUTLIER) cc_final: 0.4084 (p90) REVERT: D 259 ILE cc_start: 0.6084 (OUTLIER) cc_final: 0.5860 (mt) REVERT: D 661 MET cc_start: 0.4355 (OUTLIER) cc_final: 0.4030 (mpp) outliers start: 12 outliers final: 9 residues processed: 109 average time/residue: 0.4075 time to fit residues: 67.1763 Evaluate side-chains 110 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 344 PHE Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 661 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 112 optimal weight: 0.0980 chunk 97 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 103 optimal weight: 9.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10038 Z= 0.195 Angle : 0.484 5.547 13607 Z= 0.265 Chirality : 0.037 0.133 1540 Planarity : 0.004 0.068 1713 Dihedral : 7.803 86.298 1429 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.27 % Allowed : 15.48 % Favored : 83.25 % 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: 0.18 (0.24), residues: 1233 helix: 1.20 (0.18), residues: 771 sheet: -1.17 (0.63), residues: 64 loop : -1.82 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 78 HIS 0.004 0.001 HIS C 452 PHE 0.034 0.001 PHE D 139 TYR 0.011 0.001 TYR D 495 ARG 0.006 0.000 ARG D 221 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue TYR 232 is missing expected H atoms. Skipping. Residue TYR 318 is missing expected H atoms. Skipping. Residue LYS 326 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LYS 62 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue LYS 147 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 458 is missing expected H atoms. Skipping. Residue VAL 487 is missing expected H atoms. Skipping. Residue LYS 550 is missing expected H atoms. Skipping. Residue LYS 554 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 99 time to evaluate : 1.506 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: C 344 PHE cc_start: 0.5155 (OUTLIER) cc_final: 0.4492 (p90) REVERT: D 661 MET cc_start: 0.4312 (OUTLIER) cc_final: 0.4002 (mpp) outliers start: 13 outliers final: 8 residues processed: 110 average time/residue: 0.4039 time to fit residues: 67.1888 Evaluate side-chains 109 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 99 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 344 PHE Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 661 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 14 optimal weight: 0.0980 chunk 27 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 100 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 573 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 = 0.4322 r_free = 0.4322 target = 0.195477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.146157 restraints weight = 34468.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.143612 restraints weight = 29856.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.146558 restraints weight = 24554.407| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10038 Z= 0.163 Angle : 0.464 5.431 13607 Z= 0.253 Chirality : 0.037 0.132 1540 Planarity : 0.004 0.058 1713 Dihedral : 7.513 86.298 1427 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.18 % Allowed : 15.48 % Favored : 83.35 % 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 (0.24), residues: 1233 helix: 1.45 (0.18), residues: 766 sheet: -1.38 (0.58), residues: 74 loop : -1.66 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 78 HIS 0.004 0.001 HIS C 452 PHE 0.013 0.001 PHE C 266 TYR 0.010 0.001 TYR D 495 ARG 0.006 0.000 ARG D 221 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3661.60 seconds wall clock time: 65 minutes 50.76 seconds (3950.76 seconds total)