Starting phenix.real_space_refine on Tue Apr 9 14:43:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7obq_12799/04_2024/7obq_12799_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7obq_12799/04_2024/7obq_12799.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7obq_12799/04_2024/7obq_12799.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7obq_12799/04_2024/7obq_12799.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7obq_12799/04_2024/7obq_12799_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7obq_12799/04_2024/7obq_12799_neut_updated.pdb" } resolution = 3.9 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= 0.002 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 174 5.49 5 Mg 3 5.21 5 S 67 5.16 5 C 9823 2.51 5 N 2979 2.21 5 O 3622 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "u PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 16668 Number of models: 1 Model: "" Number of chains: 11 Chain: "1" Number of atoms: 3542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 3542 Classifications: {'RNA': 165} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 11, 'rna3p_pur': 79, 'rna3p_pyr': 61} Link IDs: {'rna2p': 24, 'rna3p': 140} Chain: "q" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 842 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "s" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 100 Classifications: {'peptide': 20} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'TRANS': 19} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'UNK:plan-1': 20} Unresolved non-hydrogen planarities: 20 Chain: "u" Number of atoms: 3496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3496 Classifications: {'peptide': 441} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 7, 'TRANS': 433} Chain breaks: 2 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'UNK:plan-1': 13, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 58 Chain: "v" Number of atoms: 1563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1563 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 194} Chain breaks: 1 Chain: "x" Number of atoms: 3049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3049 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 10, 'TRANS': 382} Chain breaks: 2 Chain: "y" Number of atoms: 3483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3483 Classifications: {'peptide': 454} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 10, 'TRANS': 443} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "z" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 494 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 5, 'TRANS': 56} Chain: "v" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "x" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "y" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.07, per 1000 atoms: 0.54 Number of scatterers: 16668 At special positions: 0 Unit cell: (118.77, 117.7, 189.39, 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 67 16.00 P 174 15.00 Mg 3 11.99 O 3622 8.00 N 2979 7.00 C 9823 6.00 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: 8.73 Conformation dependent library (CDL) restraints added in 2.4 seconds 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3156 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 65 helices and 5 sheets defined 54.6% alpha, 7.2% beta 39 base pairs and 89 stacking pairs defined. Time for finding SS restraints: 7.94 Creating SS restraints... Processing helix chain 'q' and resid 20 through 23 Processing helix chain 'q' and resid 46 through 54 Processing helix chain 'q' and resid 101 through 116 Proline residue: q 113 - end of helix Processing helix chain 's' and resid 2 through 19 Processing helix chain 'u' and resid 59 through 69 removed outlier: 3.783A pdb=" N GLN u 69 " --> pdb=" O GLU u 65 " (cutoff:3.500A) Processing helix chain 'u' and resid 78 through 95 Processing helix chain 'u' and resid 114 through 117 removed outlier: 3.893A pdb=" N ASP u 117 " --> pdb=" O LEU u 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 114 through 117' Processing helix chain 'u' and resid 120 through 143 removed outlier: 3.622A pdb=" N VAL u 124 " --> pdb=" O TYR u 120 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ASN u 143 " --> pdb=" O LYS u 139 " (cutoff:3.500A) Processing helix chain 'u' and resid 146 through 169 removed outlier: 4.438A pdb=" N VAL u 160 " --> pdb=" O ARG u 157 " (cutoff:3.500A) Processing helix chain 'u' and resid 177 through 197 Processing helix chain 'u' and resid 201 through 221 Processing helix chain 'u' and resid 224 through 248 removed outlier: 3.502A pdb=" N VAL u 228 " --> pdb=" O GLU u 224 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N LEU u 229 " --> pdb=" O GLU u 225 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TYR u 230 " --> pdb=" O GLN u 226 " (cutoff:3.500A) Proline residue: u 239 - end of helix Processing helix chain 'u' and resid 253 through 266 removed outlier: 3.541A pdb=" N LEU u 262 " --> pdb=" O MET u 258 " (cutoff:3.500A) Processing helix chain 'u' and resid 269 through 289 Processing helix chain 'u' and resid 304 through 319 Processing helix chain 'u' and resid 331 through 361 removed outlier: 3.715A pdb=" N GLU u 351 " --> pdb=" O ALA u 347 " (cutoff:3.500A) Proline residue: u 354 - end of helix Processing helix chain 'u' and resid 374 through 398 Processing helix chain 'u' and resid 415 through 442 removed outlier: 3.994A pdb=" N GLN u 419 " --> pdb=" O SER u 415 " (cutoff:3.500A) Proline residue: u 439 - end of helix Processing helix chain 'u' and resid 447 through 467 Processing helix chain 'u' and resid 479 through 493 removed outlier: 3.803A pdb=" N LYS u 488 " --> pdb=" O ASP u 484 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TYR u 489 " --> pdb=" O ARG u 485 " (cutoff:3.500A) Processing helix chain 'u' and resid 512 through 522 Processing helix chain 'v' and resid 77 through 86 Processing helix chain 'v' and resid 125 through 131 Processing helix chain 'v' and resid 152 through 168 removed outlier: 3.537A pdb=" N SER v 168 " --> pdb=" O ILE v 164 " (cutoff:3.500A) Processing helix chain 'v' and resid 190 through 207 removed outlier: 3.835A pdb=" N THR v 203 " --> pdb=" O LYS v 199 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG v 205 " --> pdb=" O LEU v 201 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL v 206 " --> pdb=" O ASN v 202 " (cutoff:3.500A) Processing helix chain 'v' and resid 261 through 270 Processing helix chain 'x' and resid 22 through 42 removed outlier: 3.803A pdb=" N GLU x 26 " --> pdb=" O ILE x 22 " (cutoff:3.500A) Processing helix chain 'x' and resid 46 through 63 Processing helix chain 'x' and resid 73 through 87 Processing helix chain 'x' and resid 114 through 127 Processing helix chain 'x' and resid 145 through 155 Processing helix chain 'x' and resid 168 through 182 Processing helix chain 'x' and resid 199 through 212 Processing helix chain 'x' and resid 229 through 239 Processing helix chain 'x' and resid 257 through 266 removed outlier: 3.711A pdb=" N LEU x 260 " --> pdb=" O GLY x 257 " (cutoff:3.500A) Processing helix chain 'x' and resid 287 through 295 Processing helix chain 'x' and resid 317 through 324 Processing helix chain 'x' and resid 329 through 342 Processing helix chain 'x' and resid 345 through 349 Processing helix chain 'x' and resid 365 through 381 Processing helix chain 'x' and resid 384 through 387 No H-bonds generated for 'chain 'x' and resid 384 through 387' Processing helix chain 'x' and resid 392 through 398 Processing helix chain 'x' and resid 400 through 409 Processing helix chain 'x' and resid 416 through 436 Processing helix chain 'y' and resid 28 through 37 removed outlier: 3.653A pdb=" N LEU y 32 " --> pdb=" O PRO y 28 " (cutoff:3.500A) Processing helix chain 'y' and resid 78 through 93 removed outlier: 3.927A pdb=" N HIS y 87 " --> pdb=" O ILE y 83 " (cutoff:3.500A) Processing helix chain 'y' and resid 95 through 98 No H-bonds generated for 'chain 'y' and resid 95 through 98' Processing helix chain 'y' and resid 104 through 108 Processing helix chain 'y' and resid 114 through 129 Processing helix chain 'y' and resid 134 through 146 Processing helix chain 'y' and resid 334 through 350 removed outlier: 4.565A pdb=" N SER y 339 " --> pdb=" O GLU y 335 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N VAL y 340 " --> pdb=" O ASP y 336 " (cutoff:3.500A) Processing helix chain 'y' and resid 355 through 368 Processing helix chain 'y' and resid 380 through 396 Processing helix chain 'y' and resid 404 through 413 removed outlier: 3.809A pdb=" N MET y 409 " --> pdb=" O LEU y 405 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP y 410 " --> pdb=" O ARG y 406 " (cutoff:3.500A) Processing helix chain 'y' and resid 430 through 444 Processing helix chain 'y' and resid 460 through 474 Processing helix chain 'y' and resid 497 through 511 Processing helix chain 'y' and resid 528 through 541 Processing helix chain 'y' and resid 558 through 571 Processing helix chain 'y' and resid 589 through 591 No H-bonds generated for 'chain 'y' and resid 589 through 591' Processing helix chain 'y' and resid 596 through 605 Processing helix chain 'y' and resid 627 through 635 Processing helix chain 'z' and resid 562 through 568 Proline residue: z 568 - end of helix Processing helix chain 'z' and resid 580 through 582 No H-bonds generated for 'chain 'z' and resid 580 through 582' Processing helix chain 'z' and resid 594 through 599 Processing sheet with id= A, first strand: chain 'q' and resid 16 through 18 Processing sheet with id= B, first strand: chain 'v' and resid 99 through 104 removed outlier: 7.817A pdb=" N LEU v 68 " --> pdb=" O ARG v 137 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N VAL v 139 " --> pdb=" O LEU v 68 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N LEU v 70 " --> pdb=" O VAL v 139 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N PHE v 141 " --> pdb=" O LEU v 70 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N SER v 174 " --> pdb=" O VAL v 139 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N PHE v 141 " --> pdb=" O SER v 174 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LEU v 176 " --> pdb=" O PHE v 141 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL v 143 " --> pdb=" O LEU v 176 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ALA v 178 " --> pdb=" O VAL v 143 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU v 244 " --> pdb=" O ILE v 177 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N CYS v 179 " --> pdb=" O LEU v 244 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'x' and resid 270 through 273 removed outlier: 8.258A pdb=" N VAL x 245 " --> pdb=" O ILE x 271 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE x 273 " --> pdb=" O VAL x 245 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL x 247 " --> pdb=" O ILE x 273 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'y' and resid 52 through 59 removed outlier: 6.560A pdb=" N SER y 9 " --> pdb=" O VAL y 14 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL y 14 " --> pdb=" O SER y 9 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'y' and resid 610 through 613 removed outlier: 7.644A pdb=" N ILE y 584 " --> pdb=" O VAL y 611 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL y 613 " --> pdb=" O ILE y 584 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU y 586 " --> pdb=" O VAL y 613 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR y 520 " --> pdb=" O PHE y 422 " (cutoff:3.500A) 681 hydrogen bonds defined for protein. 1875 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 98 hydrogen bonds 152 hydrogen bond angles 0 basepair planarities 39 basepair parallelities 89 stacking parallelities Total time for adding SS restraints: 5.84 Time building geometry restraints manager: 8.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4456 1.34 - 1.45: 3604 1.45 - 1.57: 8760 1.57 - 1.69: 341 1.69 - 1.81: 113 Bond restraints: 17274 Sorted by residual: bond pdb=" N3B GNP y 701 " pdb=" PG GNP y 701 " ideal model delta sigma weight residual 1.801 1.705 0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" N3B GNP x 601 " pdb=" PG GNP x 601 " ideal model delta sigma weight residual 1.801 1.706 0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" O5' GNP x 601 " pdb=" PA GNP x 601 " ideal model delta sigma weight residual 1.660 1.571 0.089 2.00e-02 2.50e+03 2.00e+01 bond pdb=" O5' GNP y 701 " pdb=" PA GNP y 701 " ideal model delta sigma weight residual 1.660 1.572 0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" N PRO y 133 " pdb=" CA PRO y 133 " ideal model delta sigma weight residual 1.474 1.456 0.018 7.40e-03 1.83e+04 5.93e+00 ... (remaining 17269 not shown) Histogram of bond angle deviations from ideal: 100.17 - 106.92: 1238 106.92 - 113.68: 9936 113.68 - 120.43: 6511 120.43 - 127.19: 6006 127.19 - 133.94: 426 Bond angle restraints: 24117 Sorted by residual: angle pdb=" N PRO y 133 " pdb=" CA PRO y 133 " pdb=" CB PRO y 133 " ideal model delta sigma weight residual 101.83 110.21 -8.38 8.40e-01 1.42e+00 9.95e+01 angle pdb=" C3' C 1 99 " pdb=" O3' C 1 99 " pdb=" P C 1 100 " ideal model delta sigma weight residual 120.20 125.60 -5.40 1.50e+00 4.44e-01 1.30e+01 angle pdb=" O1B GNP y 701 " pdb=" PB GNP y 701 " pdb=" O2B GNP y 701 " ideal model delta sigma weight residual 119.66 109.58 10.08 3.00e+00 1.11e-01 1.13e+01 angle pdb=" O3' C 1 99 " pdb=" C3' C 1 99 " pdb=" C2' C 1 99 " ideal model delta sigma weight residual 109.50 114.39 -4.89 1.50e+00 4.44e-01 1.06e+01 angle pdb=" O1B GNP x 601 " pdb=" PB GNP x 601 " pdb=" O2B GNP x 601 " ideal model delta sigma weight residual 119.66 109.88 9.78 3.00e+00 1.11e-01 1.06e+01 ... (remaining 24112 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.69: 10258 35.69 - 71.39: 486 71.39 - 107.08: 70 107.08 - 142.77: 0 142.77 - 178.47: 3 Dihedral angle restraints: 10817 sinusoidal: 5956 harmonic: 4861 Sorted by residual: dihedral pdb=" O4' C 1 242 " pdb=" C1' C 1 242 " pdb=" N1 C 1 242 " pdb=" C2 C 1 242 " ideal model delta sinusoidal sigma weight residual -128.00 50.47 -178.47 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O3B GTP v 301 " pdb=" O3A GTP v 301 " pdb=" PB GTP v 301 " pdb=" PA GTP v 301 " ideal model delta sinusoidal sigma weight residual -68.92 -171.58 102.66 1 2.00e+01 2.50e-03 2.93e+01 dihedral pdb=" O3A GTP v 301 " pdb=" O3B GTP v 301 " pdb=" PB GTP v 301 " pdb=" PG GTP v 301 " ideal model delta sinusoidal sigma weight residual -56.21 -151.21 95.01 1 2.00e+01 2.50e-03 2.61e+01 ... (remaining 10814 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2575 0.052 - 0.103: 260 0.103 - 0.155: 28 0.155 - 0.207: 2 0.207 - 0.258: 1 Chirality restraints: 2866 Sorted by residual: chirality pdb=" CA PRO y 133 " pdb=" N PRO y 133 " pdb=" C PRO y 133 " pdb=" CB PRO y 133 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" C3' C 1 99 " pdb=" C4' C 1 99 " pdb=" O3' C 1 99 " pdb=" C2' C 1 99 " both_signs ideal model delta sigma weight residual False -2.74 -2.54 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" C3' U 1 236 " pdb=" C4' U 1 236 " pdb=" O3' U 1 236 " pdb=" C2' U 1 236 " both_signs ideal model delta sigma weight residual False -2.74 -2.56 -0.18 2.00e-01 2.50e+01 8.16e-01 ... (remaining 2863 not shown) Planarity restraints: 2459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS y 343 " 0.007 2.00e-02 2.50e+03 1.46e-02 2.12e+00 pdb=" C LYS y 343 " -0.025 2.00e-02 2.50e+03 pdb=" O LYS y 343 " 0.009 2.00e-02 2.50e+03 pdb=" N MET y 344 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU y 82 " -0.007 2.00e-02 2.50e+03 1.30e-02 1.68e+00 pdb=" C LEU y 82 " 0.022 2.00e-02 2.50e+03 pdb=" O LEU y 82 " -0.008 2.00e-02 2.50e+03 pdb=" N ILE y 83 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU u 314 " -0.006 2.00e-02 2.50e+03 1.23e-02 1.51e+00 pdb=" C LEU u 314 " 0.021 2.00e-02 2.50e+03 pdb=" O LEU u 314 " -0.008 2.00e-02 2.50e+03 pdb=" N ALA u 315 " -0.007 2.00e-02 2.50e+03 ... (remaining 2456 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 390 2.66 - 3.22: 16192 3.22 - 3.78: 28921 3.78 - 4.34: 36896 4.34 - 4.90: 55841 Nonbonded interactions: 138240 Sorted by model distance: nonbonded pdb=" OG1 THR v 78 " pdb="MG MG v 300 " model vdw 2.106 2.170 nonbonded pdb=" O1B GNP x 601 " pdb="MG MG x 602 " model vdw 2.107 2.170 nonbonded pdb=" OG SER v 95 " pdb="MG MG v 300 " model vdw 2.114 2.170 nonbonded pdb=" O1G GNP x 601 " pdb="MG MG x 602 " model vdw 2.114 2.170 nonbonded pdb=" OG1 THR x 115 " pdb="MG MG x 602 " model vdw 2.120 2.170 ... (remaining 138235 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=0.57 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: 12.620 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: 0.000 Extract box with map and model: 19.560 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 51.810 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.080 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 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 : 0.003 0.096 17274 Z= 0.170 Angle : 0.483 10.077 24117 Z= 0.253 Chirality : 0.032 0.258 2866 Planarity : 0.003 0.030 2459 Dihedral : 17.779 178.468 7661 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.63 % Allowed : 6.29 % Favored : 91.08 % 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: 1.55 (0.21), residues: 1620 helix: 2.22 (0.18), residues: 905 sheet: 0.41 (0.39), residues: 166 loop : -0.83 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP y 440 HIS 0.004 0.001 HIS u 70 PHE 0.012 0.001 PHE y 8 TYR 0.006 0.001 TYR u 379 ARG 0.002 0.000 ARG q 74 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 400 time to evaluate : 1.564 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: q 48 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8633 (tt0) REVERT: q 68 TYR cc_start: 0.6149 (t80) cc_final: 0.5360 (t80) REVERT: q 75 ASP cc_start: 0.6167 (m-30) cc_final: 0.4865 (m-30) REVERT: q 77 GLN cc_start: 0.8182 (pm20) cc_final: 0.7767 (pm20) REVERT: q 102 LYS cc_start: 0.9357 (tptt) cc_final: 0.9087 (tppt) REVERT: q 107 TYR cc_start: 0.7416 (t80) cc_final: 0.7185 (t80) REVERT: u 260 MET cc_start: -0.0498 (tpt) cc_final: -0.0770 (mtm) REVERT: u 274 LYS cc_start: 0.9181 (ptpt) cc_final: 0.8929 (ptpt) REVERT: u 350 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8495 (mt-10) REVERT: u 375 TYR cc_start: 0.6252 (m-10) cc_final: 0.6009 (m-10) REVERT: u 433 VAL cc_start: 0.8747 (t) cc_final: 0.8456 (t) REVERT: u 449 LYS cc_start: 0.7139 (mppt) cc_final: 0.6436 (tmmt) REVERT: v 74 ASP cc_start: 0.8289 (t0) cc_final: 0.8080 (t70) REVERT: v 90 ARG cc_start: 0.8518 (tpp80) cc_final: 0.8307 (ttt90) REVERT: v 98 ASP cc_start: 0.8793 (p0) cc_final: 0.8583 (p0) REVERT: x 33 LYS cc_start: 0.9124 (tppt) cc_final: 0.8881 (mmtm) REVERT: x 41 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8401 (mm-30) REVERT: x 126 GLN cc_start: 0.8606 (tm-30) cc_final: 0.8314 (tm-30) REVERT: x 151 ASN cc_start: 0.8787 (m-40) cc_final: 0.8559 (m110) REVERT: x 329 LEU cc_start: 0.9187 (mm) cc_final: 0.8798 (mm) REVERT: x 374 LYS cc_start: 0.9426 (pptt) cc_final: 0.9173 (pttm) REVERT: x 396 PHE cc_start: 0.8081 (m-80) cc_final: 0.7673 (m-80) REVERT: y 40 GLU cc_start: 0.6506 (OUTLIER) cc_final: 0.5286 (mp0) REVERT: y 396 LEU cc_start: 0.8419 (tt) cc_final: 0.8130 (tt) REVERT: y 397 GLN cc_start: 0.7325 (OUTLIER) cc_final: 0.6359 (tm-30) REVERT: y 405 LEU cc_start: 0.9247 (tp) cc_final: 0.8629 (tt) REVERT: y 409 MET cc_start: 0.8545 (mpp) cc_final: 0.8311 (mpp) REVERT: y 524 MET cc_start: 0.8553 (mmm) cc_final: 0.8179 (mmt) REVERT: y 556 ASN cc_start: 0.7913 (OUTLIER) cc_final: 0.7345 (t0) REVERT: y 612 PHE cc_start: 0.8552 (m-80) cc_final: 0.8227 (m-80) outliers start: 36 outliers final: 8 residues processed: 426 average time/residue: 0.3183 time to fit residues: 195.6292 Evaluate side-chains 281 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 270 time to evaluate : 1.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain u residue 72 LEU Chi-restraints excluded: chain u residue 190 LEU Chi-restraints excluded: chain x residue 40 LEU Chi-restraints excluded: chain x residue 242 VAL Chi-restraints excluded: chain y residue 40 GLU Chi-restraints excluded: chain y residue 68 VAL Chi-restraints excluded: chain y residue 380 VAL Chi-restraints excluded: chain y residue 397 GLN Chi-restraints excluded: chain y residue 402 VAL Chi-restraints excluded: chain y residue 486 VAL Chi-restraints excluded: chain y residue 556 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 0.0570 chunk 137 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 142 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 chunk 86 optimal weight: 8.9990 chunk 106 optimal weight: 6.9990 chunk 165 optimal weight: 2.9990 overall best weight: 1.5702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: q 43 ASN u 247 ASN u 346 GLN u 431 ASN u 468 GLN v 93 GLN v 182 GLN ** x 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 338 ASN y 60 ASN y 61 GLN y 71 GLN y 444 ASN y 541 ASN y 617 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17274 Z= 0.188 Angle : 0.598 8.393 24117 Z= 0.295 Chirality : 0.037 0.226 2866 Planarity : 0.003 0.033 2459 Dihedral : 20.311 178.726 4505 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.29 % Allowed : 15.57 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.21), residues: 1620 helix: 2.10 (0.17), residues: 899 sheet: 0.29 (0.40), residues: 157 loop : -0.89 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP x 94 HIS 0.004 0.001 HIS u 70 PHE 0.022 0.002 PHE x 80 TYR 0.017 0.002 TYR y 78 ARG 0.006 0.000 ARG x 330 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 277 time to evaluate : 1.636 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: q 68 TYR cc_start: 0.6094 (t80) cc_final: 0.5718 (t80) REVERT: q 75 ASP cc_start: 0.6486 (m-30) cc_final: 0.6035 (m-30) REVERT: q 77 GLN cc_start: 0.8366 (pm20) cc_final: 0.7929 (pm20) REVERT: q 81 ARG cc_start: 0.6932 (ptp-170) cc_final: 0.6562 (ptp-170) REVERT: q 102 LYS cc_start: 0.9399 (tptt) cc_final: 0.9116 (tppt) REVERT: u 260 MET cc_start: -0.0647 (tpt) cc_final: -0.0887 (mtm) REVERT: u 449 LYS cc_start: 0.7139 (mppt) cc_final: 0.6539 (tmmt) REVERT: v 98 ASP cc_start: 0.8825 (p0) cc_final: 0.8605 (p0) REVERT: v 117 ASP cc_start: 0.8156 (t70) cc_final: 0.7935 (t0) REVERT: v 152 VAL cc_start: 0.8989 (OUTLIER) cc_final: 0.8383 (p) REVERT: x 28 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8785 (pp) REVERT: x 33 LYS cc_start: 0.9121 (tppt) cc_final: 0.8600 (mmtm) REVERT: x 41 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8499 (mm-30) REVERT: x 151 ASN cc_start: 0.8887 (m-40) cc_final: 0.8642 (m110) REVERT: y 40 GLU cc_start: 0.6593 (OUTLIER) cc_final: 0.5484 (mp0) REVERT: y 128 SER cc_start: 0.7211 (m) cc_final: 0.6954 (p) REVERT: y 397 GLN cc_start: 0.7417 (OUTLIER) cc_final: 0.6348 (tm-30) REVERT: y 405 LEU cc_start: 0.9115 (tp) cc_final: 0.8742 (tp) REVERT: y 409 MET cc_start: 0.8640 (mpp) cc_final: 0.8383 (mpp) REVERT: y 524 MET cc_start: 0.8590 (mmm) cc_final: 0.8316 (mpp) REVERT: y 556 ASN cc_start: 0.7935 (OUTLIER) cc_final: 0.7663 (t0) REVERT: y 560 ASP cc_start: 0.8474 (t70) cc_final: 0.8237 (t0) outliers start: 45 outliers final: 19 residues processed: 304 average time/residue: 0.2945 time to fit residues: 134.1536 Evaluate side-chains 264 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 240 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 18 ILE Chi-restraints excluded: chain q residue 65 ASN Chi-restraints excluded: chain u residue 60 LEU Chi-restraints excluded: chain u residue 72 LEU Chi-restraints excluded: chain u residue 181 LEU Chi-restraints excluded: chain u residue 190 LEU Chi-restraints excluded: chain u residue 198 HIS Chi-restraints excluded: chain u residue 333 LEU Chi-restraints excluded: chain u residue 453 LEU Chi-restraints excluded: chain v residue 91 ASP Chi-restraints excluded: chain v residue 152 VAL Chi-restraints excluded: chain x residue 28 LEU Chi-restraints excluded: chain x residue 40 LEU Chi-restraints excluded: chain x residue 52 LEU Chi-restraints excluded: chain x residue 117 THR Chi-restraints excluded: chain x residue 242 VAL Chi-restraints excluded: chain y residue 40 GLU Chi-restraints excluded: chain y residue 68 VAL Chi-restraints excluded: chain y residue 118 LEU Chi-restraints excluded: chain y residue 397 GLN Chi-restraints excluded: chain y residue 407 ASP Chi-restraints excluded: chain y residue 486 VAL Chi-restraints excluded: chain y residue 556 ASN Chi-restraints excluded: chain y residue 603 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 0.9990 chunk 51 optimal weight: 10.0000 chunk 137 optimal weight: 0.9980 chunk 112 optimal weight: 8.9990 chunk 45 optimal weight: 0.6980 chunk 165 optimal weight: 4.9990 chunk 178 optimal weight: 0.7980 chunk 147 optimal weight: 6.9990 chunk 164 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 chunk 132 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** u 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 247 ASN ** x 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 412 GLN y 541 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17274 Z= 0.193 Angle : 0.582 10.216 24117 Z= 0.291 Chirality : 0.037 0.209 2866 Planarity : 0.003 0.029 2459 Dihedral : 20.286 179.897 4503 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.24 % Allowed : 14.33 % Favored : 81.43 % 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: 1.14 (0.21), residues: 1620 helix: 1.93 (0.17), residues: 893 sheet: 0.20 (0.40), residues: 157 loop : -0.99 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP v 266 HIS 0.004 0.001 HIS u 70 PHE 0.026 0.002 PHE x 106 TYR 0.017 0.001 TYR y 78 ARG 0.003 0.000 ARG z 576 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 253 time to evaluate : 1.761 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: q 48 GLU cc_start: 0.9022 (mm-30) cc_final: 0.8112 (pp20) REVERT: q 68 TYR cc_start: 0.6695 (t80) cc_final: 0.5936 (t80) REVERT: q 75 ASP cc_start: 0.6622 (m-30) cc_final: 0.6012 (m-30) REVERT: q 77 GLN cc_start: 0.8663 (pm20) cc_final: 0.8345 (pm20) REVERT: q 102 LYS cc_start: 0.9423 (tptt) cc_final: 0.9114 (tppt) REVERT: u 141 GLU cc_start: 0.8711 (tp30) cc_final: 0.8468 (tp30) REVERT: u 260 MET cc_start: -0.0893 (tpt) cc_final: -0.1121 (mtm) REVERT: u 271 LEU cc_start: 0.8013 (tp) cc_final: 0.7740 (mm) REVERT: u 274 LYS cc_start: 0.9212 (ptpt) cc_final: 0.8927 (ptpt) REVERT: u 449 LYS cc_start: 0.7212 (mppt) cc_final: 0.6583 (tmmt) REVERT: v 90 ARG cc_start: 0.8535 (tpp80) cc_final: 0.8304 (tpp80) REVERT: v 98 ASP cc_start: 0.8849 (p0) cc_final: 0.8621 (p0) REVERT: v 130 GLU cc_start: 0.8205 (pp20) cc_final: 0.7987 (pp20) REVERT: x 41 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8481 (mm-30) REVERT: x 106 PHE cc_start: 0.8563 (m-10) cc_final: 0.8187 (m-10) REVERT: x 151 ASN cc_start: 0.8834 (m-40) cc_final: 0.8613 (m110) REVERT: x 187 ILE cc_start: 0.9026 (mp) cc_final: 0.8776 (mp) REVERT: x 333 TYR cc_start: 0.8477 (t80) cc_final: 0.8220 (t80) REVERT: x 376 MET cc_start: 0.9065 (mmm) cc_final: 0.8848 (mmm) REVERT: x 424 TYR cc_start: 0.7898 (t80) cc_final: 0.7582 (t80) REVERT: y 40 GLU cc_start: 0.6636 (OUTLIER) cc_final: 0.5695 (mp0) REVERT: y 397 GLN cc_start: 0.7488 (OUTLIER) cc_final: 0.6414 (tm-30) REVERT: y 405 LEU cc_start: 0.9082 (tp) cc_final: 0.8684 (tp) REVERT: y 409 MET cc_start: 0.8630 (mpp) cc_final: 0.8382 (mpp) REVERT: y 491 LYS cc_start: 0.7149 (mmtp) cc_final: 0.6905 (mmtm) REVERT: y 524 MET cc_start: 0.8583 (mmm) cc_final: 0.8300 (mpp) REVERT: y 556 ASN cc_start: 0.7956 (OUTLIER) cc_final: 0.7740 (t0) REVERT: y 560 ASP cc_start: 0.8446 (t70) cc_final: 0.8219 (t0) REVERT: y 602 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8534 (mtm) outliers start: 58 outliers final: 33 residues processed: 286 average time/residue: 0.2973 time to fit residues: 128.5294 Evaluate side-chains 272 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 235 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 65 ASN Chi-restraints excluded: chain u residue 60 LEU Chi-restraints excluded: chain u residue 72 LEU Chi-restraints excluded: chain u residue 181 LEU Chi-restraints excluded: chain u residue 190 LEU Chi-restraints excluded: chain u residue 198 HIS Chi-restraints excluded: chain u residue 317 ASN Chi-restraints excluded: chain u residue 453 LEU Chi-restraints excluded: chain v residue 80 LEU Chi-restraints excluded: chain v residue 85 LEU Chi-restraints excluded: chain v residue 91 ASP Chi-restraints excluded: chain v residue 92 THR Chi-restraints excluded: chain v residue 115 LEU Chi-restraints excluded: chain x residue 40 LEU Chi-restraints excluded: chain x residue 52 LEU Chi-restraints excluded: chain x residue 77 HIS Chi-restraints excluded: chain x residue 117 THR Chi-restraints excluded: chain x residue 136 CYS Chi-restraints excluded: chain x residue 205 MET Chi-restraints excluded: chain x residue 212 ILE Chi-restraints excluded: chain x residue 217 ILE Chi-restraints excluded: chain x residue 242 VAL Chi-restraints excluded: chain x residue 271 ILE Chi-restraints excluded: chain x residue 331 ASP Chi-restraints excluded: chain y residue 17 CYS Chi-restraints excluded: chain y residue 40 GLU Chi-restraints excluded: chain y residue 68 VAL Chi-restraints excluded: chain y residue 118 LEU Chi-restraints excluded: chain y residue 130 ILE Chi-restraints excluded: chain y residue 380 VAL Chi-restraints excluded: chain y residue 397 GLN Chi-restraints excluded: chain y residue 402 VAL Chi-restraints excluded: chain y residue 407 ASP Chi-restraints excluded: chain y residue 486 VAL Chi-restraints excluded: chain y residue 556 ASN Chi-restraints excluded: chain y residue 602 MET Chi-restraints excluded: chain y residue 603 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 111 optimal weight: 0.7980 chunk 166 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 157 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** u 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 247 ASN ** x 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 216 ASN y 60 ASN y 399 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 17274 Z= 0.315 Angle : 0.671 12.614 24117 Z= 0.340 Chirality : 0.039 0.291 2866 Planarity : 0.004 0.032 2459 Dihedral : 20.486 179.214 4503 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 19.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.61 % Allowed : 14.99 % Favored : 80.41 % 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: 0.72 (0.20), residues: 1620 helix: 1.57 (0.17), residues: 894 sheet: -0.06 (0.39), residues: 164 loop : -1.14 (0.24), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP u 295 HIS 0.006 0.001 HIS u 70 PHE 0.025 0.002 PHE x 80 TYR 0.017 0.002 TYR y 78 ARG 0.008 0.001 ARG q 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 249 time to evaluate : 1.778 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: q 68 TYR cc_start: 0.6874 (t80) cc_final: 0.6122 (t80) REVERT: q 75 ASP cc_start: 0.7647 (m-30) cc_final: 0.7040 (m-30) REVERT: q 77 GLN cc_start: 0.8771 (pm20) cc_final: 0.8544 (pm20) REVERT: q 83 ARG cc_start: 0.7029 (mpp-170) cc_final: 0.6805 (mpp-170) REVERT: q 102 LYS cc_start: 0.9489 (tptt) cc_final: 0.9214 (tppt) REVERT: u 260 MET cc_start: -0.1022 (tpt) cc_final: -0.1301 (mtm) REVERT: u 271 LEU cc_start: 0.7978 (tp) cc_final: 0.7720 (mm) REVERT: u 274 LYS cc_start: 0.9235 (ptpt) cc_final: 0.8918 (ptpt) REVERT: u 449 LYS cc_start: 0.7128 (mppt) cc_final: 0.6723 (tmmt) REVERT: v 90 ARG cc_start: 0.8549 (tpp80) cc_final: 0.8340 (tpp80) REVERT: x 41 GLU cc_start: 0.8967 (mm-30) cc_final: 0.8587 (mm-30) REVERT: x 106 PHE cc_start: 0.8731 (m-10) cc_final: 0.8174 (m-10) REVERT: x 151 ASN cc_start: 0.8750 (m-40) cc_final: 0.8531 (m110) REVERT: x 229 CYS cc_start: 0.8035 (p) cc_final: 0.7586 (p) REVERT: x 297 MET cc_start: 0.7688 (pmm) cc_final: 0.7391 (pmm) REVERT: x 332 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8497 (mtt) REVERT: x 376 MET cc_start: 0.8952 (mmm) cc_final: 0.8442 (mmm) REVERT: x 379 MET cc_start: 0.9024 (ptm) cc_final: 0.8746 (ppp) REVERT: y 40 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.6362 (mp0) REVERT: y 405 LEU cc_start: 0.9216 (tp) cc_final: 0.8675 (tt) REVERT: y 409 MET cc_start: 0.8675 (mpp) cc_final: 0.8365 (mpp) REVERT: y 491 LYS cc_start: 0.7434 (mmtp) cc_final: 0.7210 (mptt) REVERT: y 556 ASN cc_start: 0.8086 (OUTLIER) cc_final: 0.7646 (t0) REVERT: y 560 ASP cc_start: 0.8501 (t70) cc_final: 0.8294 (t0) REVERT: y 602 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8515 (mtm) outliers start: 63 outliers final: 43 residues processed: 285 average time/residue: 0.2941 time to fit residues: 125.8681 Evaluate side-chains 272 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 225 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 37 ILE Chi-restraints excluded: chain q residue 65 ASN Chi-restraints excluded: chain u residue 60 LEU Chi-restraints excluded: chain u residue 72 LEU Chi-restraints excluded: chain u residue 181 LEU Chi-restraints excluded: chain u residue 190 LEU Chi-restraints excluded: chain u residue 198 HIS Chi-restraints excluded: chain u residue 250 ASP Chi-restraints excluded: chain u residue 333 LEU Chi-restraints excluded: chain u residue 453 LEU Chi-restraints excluded: chain v residue 80 LEU Chi-restraints excluded: chain v residue 91 ASP Chi-restraints excluded: chain v residue 92 THR Chi-restraints excluded: chain v residue 126 LEU Chi-restraints excluded: chain v residue 197 LEU Chi-restraints excluded: chain x residue 28 LEU Chi-restraints excluded: chain x residue 40 LEU Chi-restraints excluded: chain x residue 77 HIS Chi-restraints excluded: chain x residue 83 LEU Chi-restraints excluded: chain x residue 117 THR Chi-restraints excluded: chain x residue 119 SER Chi-restraints excluded: chain x residue 136 CYS Chi-restraints excluded: chain x residue 183 ASN Chi-restraints excluded: chain x residue 204 GLU Chi-restraints excluded: chain x residue 205 MET Chi-restraints excluded: chain x residue 212 ILE Chi-restraints excluded: chain x residue 217 ILE Chi-restraints excluded: chain x residue 242 VAL Chi-restraints excluded: chain x residue 271 ILE Chi-restraints excluded: chain x residue 275 THR Chi-restraints excluded: chain x residue 331 ASP Chi-restraints excluded: chain x residue 332 MET Chi-restraints excluded: chain y residue 14 VAL Chi-restraints excluded: chain y residue 17 CYS Chi-restraints excluded: chain y residue 40 GLU Chi-restraints excluded: chain y residue 68 VAL Chi-restraints excluded: chain y residue 118 LEU Chi-restraints excluded: chain y residue 130 ILE Chi-restraints excluded: chain y residue 380 VAL Chi-restraints excluded: chain y residue 404 MET Chi-restraints excluded: chain y residue 407 ASP Chi-restraints excluded: chain y residue 448 VAL Chi-restraints excluded: chain y residue 486 VAL Chi-restraints excluded: chain y residue 514 ASP Chi-restraints excluded: chain y residue 556 ASN Chi-restraints excluded: chain y residue 602 MET Chi-restraints excluded: chain y residue 603 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 130 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 150 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 89 optimal weight: 6.9990 chunk 157 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: q 85 GLN ** u 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 247 ASN ** x 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 195 HIS x 216 ASN x 338 ASN y 399 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17274 Z= 0.234 Angle : 0.635 10.775 24117 Z= 0.318 Chirality : 0.038 0.212 2866 Planarity : 0.003 0.034 2459 Dihedral : 20.469 178.875 4500 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.17 % Allowed : 16.89 % Favored : 78.95 % 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: 0.63 (0.20), residues: 1620 helix: 1.51 (0.17), residues: 899 sheet: -0.07 (0.39), residues: 162 loop : -1.22 (0.24), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP u 295 HIS 0.006 0.001 HIS u 70 PHE 0.022 0.002 PHE y 70 TYR 0.014 0.002 TYR y 78 ARG 0.006 0.000 ARG q 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 250 time to evaluate : 1.731 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: q 68 TYR cc_start: 0.6875 (t80) cc_final: 0.6071 (t80) REVERT: q 75 ASP cc_start: 0.7773 (m-30) cc_final: 0.7274 (m-30) REVERT: q 102 LYS cc_start: 0.9469 (tptt) cc_final: 0.9147 (tppt) REVERT: u 260 MET cc_start: -0.1030 (tpt) cc_final: -0.1348 (mtm) REVERT: u 271 LEU cc_start: 0.7991 (tp) cc_final: 0.7742 (mm) REVERT: u 274 LYS cc_start: 0.9252 (ptpt) cc_final: 0.8946 (ptpt) REVERT: u 429 LEU cc_start: 0.9131 (pp) cc_final: 0.8703 (mm) REVERT: u 449 LYS cc_start: 0.7392 (mppt) cc_final: 0.6923 (tmmt) REVERT: v 90 ARG cc_start: 0.8477 (tpp80) cc_final: 0.8267 (tpp80) REVERT: x 41 GLU cc_start: 0.8996 (mm-30) cc_final: 0.8653 (mm-30) REVERT: x 106 PHE cc_start: 0.8731 (m-80) cc_final: 0.8229 (m-10) REVERT: x 151 ASN cc_start: 0.8768 (m-40) cc_final: 0.8518 (m110) REVERT: x 332 MET cc_start: 0.8696 (mtt) cc_final: 0.8280 (mtt) REVERT: x 376 MET cc_start: 0.9028 (mmm) cc_final: 0.8594 (mmm) REVERT: x 424 TYR cc_start: 0.8068 (t80) cc_final: 0.7476 (t80) REVERT: y 40 GLU cc_start: 0.7009 (OUTLIER) cc_final: 0.6579 (mp0) REVERT: y 122 ARG cc_start: 0.8102 (ptt90) cc_final: 0.7841 (mtm180) REVERT: y 405 LEU cc_start: 0.9215 (tp) cc_final: 0.8753 (tp) REVERT: y 556 ASN cc_start: 0.8098 (OUTLIER) cc_final: 0.7705 (t0) REVERT: y 560 ASP cc_start: 0.8412 (t70) cc_final: 0.8212 (t0) REVERT: z 597 GLN cc_start: 0.8274 (mm-40) cc_final: 0.7714 (mt0) outliers start: 57 outliers final: 42 residues processed: 286 average time/residue: 0.3083 time to fit residues: 135.0302 Evaluate side-chains 277 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 233 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 18 ILE Chi-restraints excluded: chain q residue 65 ASN Chi-restraints excluded: chain u residue 60 LEU Chi-restraints excluded: chain u residue 72 LEU Chi-restraints excluded: chain u residue 84 CYS Chi-restraints excluded: chain u residue 181 LEU Chi-restraints excluded: chain u residue 190 LEU Chi-restraints excluded: chain u residue 198 HIS Chi-restraints excluded: chain u residue 333 LEU Chi-restraints excluded: chain u residue 453 LEU Chi-restraints excluded: chain v residue 80 LEU Chi-restraints excluded: chain v residue 85 LEU Chi-restraints excluded: chain v residue 91 ASP Chi-restraints excluded: chain v residue 92 THR Chi-restraints excluded: chain v residue 115 LEU Chi-restraints excluded: chain v residue 126 LEU Chi-restraints excluded: chain v residue 154 ASP Chi-restraints excluded: chain x residue 28 LEU Chi-restraints excluded: chain x residue 40 LEU Chi-restraints excluded: chain x residue 77 HIS Chi-restraints excluded: chain x residue 83 LEU Chi-restraints excluded: chain x residue 117 THR Chi-restraints excluded: chain x residue 119 SER Chi-restraints excluded: chain x residue 136 CYS Chi-restraints excluded: chain x residue 183 ASN Chi-restraints excluded: chain x residue 204 GLU Chi-restraints excluded: chain x residue 205 MET Chi-restraints excluded: chain x residue 212 ILE Chi-restraints excluded: chain x residue 217 ILE Chi-restraints excluded: chain x residue 242 VAL Chi-restraints excluded: chain x residue 271 ILE Chi-restraints excluded: chain x residue 331 ASP Chi-restraints excluded: chain y residue 14 VAL Chi-restraints excluded: chain y residue 17 CYS Chi-restraints excluded: chain y residue 40 GLU Chi-restraints excluded: chain y residue 68 VAL Chi-restraints excluded: chain y residue 130 ILE Chi-restraints excluded: chain y residue 380 VAL Chi-restraints excluded: chain y residue 402 VAL Chi-restraints excluded: chain y residue 407 ASP Chi-restraints excluded: chain y residue 486 VAL Chi-restraints excluded: chain y residue 514 ASP Chi-restraints excluded: chain y residue 556 ASN Chi-restraints excluded: chain y residue 603 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 30.0000 chunk 158 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 176 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 92 optimal weight: 0.1980 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: u 78 GLN ** u 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 247 ASN ** x 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 444 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17274 Z= 0.214 Angle : 0.629 12.440 24117 Z= 0.315 Chirality : 0.038 0.227 2866 Planarity : 0.003 0.028 2459 Dihedral : 20.462 178.989 4500 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.53 % Allowed : 16.67 % Favored : 78.80 % 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 (0.20), residues: 1620 helix: 1.45 (0.17), residues: 899 sheet: -0.14 (0.39), residues: 162 loop : -1.26 (0.23), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP u 295 HIS 0.005 0.001 HIS u 70 PHE 0.029 0.002 PHE y 70 TYR 0.015 0.002 TYR u 379 ARG 0.006 0.000 ARG u 296 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 243 time to evaluate : 1.605 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: q 68 TYR cc_start: 0.6734 (t80) cc_final: 0.5888 (t80) REVERT: q 83 ARG cc_start: 0.8640 (mmp80) cc_final: 0.8323 (mpp-170) REVERT: q 102 LYS cc_start: 0.9474 (tptt) cc_final: 0.9164 (tppt) REVERT: u 260 MET cc_start: -0.1018 (tpt) cc_final: -0.1359 (mtm) REVERT: u 271 LEU cc_start: 0.8004 (tp) cc_final: 0.7749 (mm) REVERT: u 274 LYS cc_start: 0.9249 (ptpt) cc_final: 0.8940 (ptpt) REVERT: u 353 LYS cc_start: 0.8000 (ptpt) cc_final: 0.7234 (tppt) REVERT: u 429 LEU cc_start: 0.9063 (pp) cc_final: 0.8609 (mm) REVERT: u 449 LYS cc_start: 0.7416 (mppt) cc_final: 0.7008 (tmmt) REVERT: x 41 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8654 (mm-30) REVERT: x 106 PHE cc_start: 0.8719 (m-80) cc_final: 0.8321 (m-10) REVERT: x 151 ASN cc_start: 0.8780 (m-40) cc_final: 0.8528 (m110) REVERT: x 229 CYS cc_start: 0.8040 (p) cc_final: 0.7677 (p) REVERT: x 424 TYR cc_start: 0.7905 (t80) cc_final: 0.7413 (t80) REVERT: y 40 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6564 (mp0) REVERT: y 503 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7733 (mt-10) REVERT: y 556 ASN cc_start: 0.8081 (OUTLIER) cc_final: 0.7648 (t0) REVERT: z 597 GLN cc_start: 0.8233 (mm-40) cc_final: 0.7758 (mp10) outliers start: 62 outliers final: 48 residues processed: 277 average time/residue: 0.2764 time to fit residues: 117.0225 Evaluate side-chains 278 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 228 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 18 ILE Chi-restraints excluded: chain q residue 37 ILE Chi-restraints excluded: chain q residue 65 ASN Chi-restraints excluded: chain u residue 60 LEU Chi-restraints excluded: chain u residue 72 LEU Chi-restraints excluded: chain u residue 84 CYS Chi-restraints excluded: chain u residue 181 LEU Chi-restraints excluded: chain u residue 190 LEU Chi-restraints excluded: chain u residue 198 HIS Chi-restraints excluded: chain u residue 241 ILE Chi-restraints excluded: chain u residue 250 ASP Chi-restraints excluded: chain u residue 333 LEU Chi-restraints excluded: chain u residue 394 ASN Chi-restraints excluded: chain u residue 453 LEU Chi-restraints excluded: chain v residue 80 LEU Chi-restraints excluded: chain v residue 85 LEU Chi-restraints excluded: chain v residue 91 ASP Chi-restraints excluded: chain v residue 92 THR Chi-restraints excluded: chain v residue 126 LEU Chi-restraints excluded: chain v residue 154 ASP Chi-restraints excluded: chain x residue 28 LEU Chi-restraints excluded: chain x residue 40 LEU Chi-restraints excluded: chain x residue 52 LEU Chi-restraints excluded: chain x residue 77 HIS Chi-restraints excluded: chain x residue 83 LEU Chi-restraints excluded: chain x residue 117 THR Chi-restraints excluded: chain x residue 119 SER Chi-restraints excluded: chain x residue 136 CYS Chi-restraints excluded: chain x residue 183 ASN Chi-restraints excluded: chain x residue 204 GLU Chi-restraints excluded: chain x residue 205 MET Chi-restraints excluded: chain x residue 212 ILE Chi-restraints excluded: chain x residue 217 ILE Chi-restraints excluded: chain x residue 242 VAL Chi-restraints excluded: chain x residue 271 ILE Chi-restraints excluded: chain x residue 331 ASP Chi-restraints excluded: chain y residue 14 VAL Chi-restraints excluded: chain y residue 17 CYS Chi-restraints excluded: chain y residue 40 GLU Chi-restraints excluded: chain y residue 45 ASN Chi-restraints excluded: chain y residue 68 VAL Chi-restraints excluded: chain y residue 380 VAL Chi-restraints excluded: chain y residue 402 VAL Chi-restraints excluded: chain y residue 404 MET Chi-restraints excluded: chain y residue 407 ASP Chi-restraints excluded: chain y residue 448 VAL Chi-restraints excluded: chain y residue 486 VAL Chi-restraints excluded: chain y residue 514 ASP Chi-restraints excluded: chain y residue 556 ASN Chi-restraints excluded: chain y residue 603 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 100 optimal weight: 0.9990 chunk 128 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 148 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 chunk 175 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** u 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 247 ASN ** x 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 444 ASN y 541 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17274 Z= 0.200 Angle : 0.624 13.606 24117 Z= 0.311 Chirality : 0.038 0.209 2866 Planarity : 0.003 0.027 2459 Dihedral : 20.464 179.073 4500 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.31 % Allowed : 17.62 % Favored : 78.07 % 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: 0.52 (0.20), residues: 1620 helix: 1.43 (0.17), residues: 902 sheet: -0.16 (0.39), residues: 165 loop : -1.31 (0.24), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP u 295 HIS 0.006 0.001 HIS u 70 PHE 0.025 0.002 PHE y 70 TYR 0.013 0.001 TYR u 379 ARG 0.005 0.000 ARG q 74 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 238 time to evaluate : 1.685 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: q 48 GLU cc_start: 0.8979 (mp0) cc_final: 0.7965 (pp20) REVERT: q 68 TYR cc_start: 0.6744 (t80) cc_final: 0.5934 (t80) REVERT: q 83 ARG cc_start: 0.8557 (mmp80) cc_final: 0.8322 (mpp-170) REVERT: q 102 LYS cc_start: 0.9444 (tptt) cc_final: 0.9111 (tppt) REVERT: u 260 MET cc_start: -0.1337 (tpt) cc_final: -0.1627 (mtm) REVERT: u 271 LEU cc_start: 0.8011 (tp) cc_final: 0.7757 (mm) REVERT: u 274 LYS cc_start: 0.9265 (ptpt) cc_final: 0.8977 (ptpt) REVERT: u 429 LEU cc_start: 0.9090 (pp) cc_final: 0.8656 (mm) REVERT: u 449 LYS cc_start: 0.7404 (mppt) cc_final: 0.7011 (tmmt) REVERT: x 41 GLU cc_start: 0.8942 (mm-30) cc_final: 0.8583 (mm-30) REVERT: x 106 PHE cc_start: 0.8717 (m-80) cc_final: 0.8336 (m-10) REVERT: x 151 ASN cc_start: 0.8780 (m-40) cc_final: 0.8532 (m110) REVERT: x 229 CYS cc_start: 0.7953 (p) cc_final: 0.7593 (p) REVERT: x 396 PHE cc_start: 0.8364 (m-80) cc_final: 0.7711 (m-80) REVERT: y 40 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6537 (mp0) REVERT: y 556 ASN cc_start: 0.8065 (OUTLIER) cc_final: 0.7643 (t0) REVERT: z 597 GLN cc_start: 0.8197 (mm-40) cc_final: 0.7795 (mp10) outliers start: 59 outliers final: 45 residues processed: 270 average time/residue: 0.2866 time to fit residues: 117.0793 Evaluate side-chains 280 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 233 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 18 ILE Chi-restraints excluded: chain q residue 65 ASN Chi-restraints excluded: chain u residue 60 LEU Chi-restraints excluded: chain u residue 72 LEU Chi-restraints excluded: chain u residue 84 CYS Chi-restraints excluded: chain u residue 181 LEU Chi-restraints excluded: chain u residue 190 LEU Chi-restraints excluded: chain u residue 198 HIS Chi-restraints excluded: chain u residue 241 ILE Chi-restraints excluded: chain u residue 250 ASP Chi-restraints excluded: chain u residue 290 MET Chi-restraints excluded: chain u residue 317 ASN Chi-restraints excluded: chain u residue 333 LEU Chi-restraints excluded: chain u residue 394 ASN Chi-restraints excluded: chain v residue 80 LEU Chi-restraints excluded: chain v residue 85 LEU Chi-restraints excluded: chain v residue 91 ASP Chi-restraints excluded: chain v residue 92 THR Chi-restraints excluded: chain v residue 154 ASP Chi-restraints excluded: chain x residue 28 LEU Chi-restraints excluded: chain x residue 40 LEU Chi-restraints excluded: chain x residue 52 LEU Chi-restraints excluded: chain x residue 77 HIS Chi-restraints excluded: chain x residue 83 LEU Chi-restraints excluded: chain x residue 117 THR Chi-restraints excluded: chain x residue 119 SER Chi-restraints excluded: chain x residue 136 CYS Chi-restraints excluded: chain x residue 204 GLU Chi-restraints excluded: chain x residue 205 MET Chi-restraints excluded: chain x residue 212 ILE Chi-restraints excluded: chain x residue 242 VAL Chi-restraints excluded: chain x residue 271 ILE Chi-restraints excluded: chain x residue 275 THR Chi-restraints excluded: chain y residue 14 VAL Chi-restraints excluded: chain y residue 17 CYS Chi-restraints excluded: chain y residue 40 GLU Chi-restraints excluded: chain y residue 45 ASN Chi-restraints excluded: chain y residue 68 VAL Chi-restraints excluded: chain y residue 380 VAL Chi-restraints excluded: chain y residue 402 VAL Chi-restraints excluded: chain y residue 404 MET Chi-restraints excluded: chain y residue 407 ASP Chi-restraints excluded: chain y residue 448 VAL Chi-restraints excluded: chain y residue 486 VAL Chi-restraints excluded: chain y residue 514 ASP Chi-restraints excluded: chain y residue 541 ASN Chi-restraints excluded: chain y residue 556 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 0.8980 chunk 70 optimal weight: 30.0000 chunk 104 optimal weight: 9.9990 chunk 52 optimal weight: 0.4980 chunk 34 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 119 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 137 optimal weight: 0.6980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** u 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 77 HIS ** x 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 444 ASN y 541 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17274 Z= 0.172 Angle : 0.635 12.678 24117 Z= 0.314 Chirality : 0.037 0.217 2866 Planarity : 0.003 0.025 2459 Dihedral : 20.437 178.999 4500 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.09 % Allowed : 18.42 % Favored : 77.49 % 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: 0.48 (0.20), residues: 1620 helix: 1.39 (0.17), residues: 901 sheet: -0.23 (0.39), residues: 167 loop : -1.28 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP u 295 HIS 0.005 0.001 HIS u 70 PHE 0.029 0.001 PHE y 70 TYR 0.020 0.001 TYR x 424 ARG 0.006 0.000 ARG q 74 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 245 time to evaluate : 1.778 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: q 48 GLU cc_start: 0.9019 (mp0) cc_final: 0.7985 (pp20) REVERT: q 68 TYR cc_start: 0.6662 (t80) cc_final: 0.5867 (t80) REVERT: q 83 ARG cc_start: 0.8554 (mmp80) cc_final: 0.8333 (mpp-170) REVERT: q 102 LYS cc_start: 0.9434 (tptt) cc_final: 0.9206 (tppt) REVERT: u 271 LEU cc_start: 0.7996 (tp) cc_final: 0.7735 (mm) REVERT: u 274 LYS cc_start: 0.9225 (ptpt) cc_final: 0.8937 (ptpt) REVERT: u 353 LYS cc_start: 0.8030 (ptpt) cc_final: 0.7224 (tppt) REVERT: u 449 LYS cc_start: 0.7390 (mppt) cc_final: 0.6995 (tmmt) REVERT: x 41 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8566 (mm-30) REVERT: x 151 ASN cc_start: 0.8775 (m-40) cc_final: 0.8516 (m110) REVERT: x 187 ILE cc_start: 0.8977 (mp) cc_final: 0.8724 (mp) REVERT: x 297 MET cc_start: 0.7834 (pmm) cc_final: 0.7565 (pmm) REVERT: x 396 PHE cc_start: 0.8309 (m-80) cc_final: 0.7665 (m-80) REVERT: y 399 GLN cc_start: 0.6852 (pp30) cc_final: 0.6418 (pp30) REVERT: y 556 ASN cc_start: 0.8000 (OUTLIER) cc_final: 0.7551 (t0) REVERT: z 597 GLN cc_start: 0.8146 (mm-40) cc_final: 0.7784 (mp10) outliers start: 56 outliers final: 41 residues processed: 276 average time/residue: 0.2877 time to fit residues: 120.9861 Evaluate side-chains 274 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 232 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 18 ILE Chi-restraints excluded: chain q residue 37 ILE Chi-restraints excluded: chain q residue 65 ASN Chi-restraints excluded: chain u residue 60 LEU Chi-restraints excluded: chain u residue 72 LEU Chi-restraints excluded: chain u residue 84 CYS Chi-restraints excluded: chain u residue 181 LEU Chi-restraints excluded: chain u residue 190 LEU Chi-restraints excluded: chain u residue 198 HIS Chi-restraints excluded: chain u residue 241 ILE Chi-restraints excluded: chain u residue 279 ILE Chi-restraints excluded: chain u residue 290 MET Chi-restraints excluded: chain u residue 317 ASN Chi-restraints excluded: chain u residue 333 LEU Chi-restraints excluded: chain u residue 394 ASN Chi-restraints excluded: chain v residue 80 LEU Chi-restraints excluded: chain v residue 85 LEU Chi-restraints excluded: chain v residue 91 ASP Chi-restraints excluded: chain v residue 92 THR Chi-restraints excluded: chain v residue 126 LEU Chi-restraints excluded: chain v residue 154 ASP Chi-restraints excluded: chain x residue 40 LEU Chi-restraints excluded: chain x residue 52 LEU Chi-restraints excluded: chain x residue 77 HIS Chi-restraints excluded: chain x residue 117 THR Chi-restraints excluded: chain x residue 136 CYS Chi-restraints excluded: chain x residue 204 GLU Chi-restraints excluded: chain x residue 205 MET Chi-restraints excluded: chain x residue 242 VAL Chi-restraints excluded: chain x residue 271 ILE Chi-restraints excluded: chain y residue 14 VAL Chi-restraints excluded: chain y residue 17 CYS Chi-restraints excluded: chain y residue 45 ASN Chi-restraints excluded: chain y residue 68 VAL Chi-restraints excluded: chain y residue 380 VAL Chi-restraints excluded: chain y residue 402 VAL Chi-restraints excluded: chain y residue 404 MET Chi-restraints excluded: chain y residue 407 ASP Chi-restraints excluded: chain y residue 448 VAL Chi-restraints excluded: chain y residue 486 VAL Chi-restraints excluded: chain y residue 556 ASN Chi-restraints excluded: chain y residue 603 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 7.9990 chunk 168 optimal weight: 0.6980 chunk 153 optimal weight: 0.6980 chunk 163 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 71 optimal weight: 20.0000 chunk 128 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 162 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** u 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 236 GLN ** x 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 444 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 17274 Z= 0.179 Angle : 0.659 15.247 24117 Z= 0.324 Chirality : 0.038 0.386 2866 Planarity : 0.003 0.026 2459 Dihedral : 20.399 179.117 4497 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.58 % Allowed : 19.59 % Favored : 76.83 % 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: 0.43 (0.20), residues: 1620 helix: 1.34 (0.17), residues: 900 sheet: -0.29 (0.39), residues: 167 loop : -1.26 (0.24), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP u 295 HIS 0.005 0.001 HIS u 70 PHE 0.027 0.001 PHE y 70 TYR 0.026 0.002 TYR x 424 ARG 0.005 0.000 ARG q 74 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 248 time to evaluate : 1.637 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: q 48 GLU cc_start: 0.8995 (mp0) cc_final: 0.7946 (pp20) REVERT: q 68 TYR cc_start: 0.6707 (t80) cc_final: 0.5867 (t80) REVERT: q 83 ARG cc_start: 0.8525 (mmp80) cc_final: 0.8320 (mpp-170) REVERT: q 102 LYS cc_start: 0.9433 (tptt) cc_final: 0.9200 (tppt) REVERT: q 111 MET cc_start: 0.8366 (mmm) cc_final: 0.7802 (mmm) REVERT: u 129 GLU cc_start: 0.8316 (mm-30) cc_final: 0.8010 (mm-30) REVERT: u 271 LEU cc_start: 0.8001 (tp) cc_final: 0.7740 (mm) REVERT: u 274 LYS cc_start: 0.9221 (ptpt) cc_final: 0.8933 (ptpt) REVERT: u 353 LYS cc_start: 0.8036 (ptpt) cc_final: 0.7240 (tppt) REVERT: u 429 LEU cc_start: 0.9222 (pp) cc_final: 0.8848 (mm) REVERT: u 449 LYS cc_start: 0.7340 (mppt) cc_final: 0.6957 (tmmt) REVERT: x 41 GLU cc_start: 0.8894 (mm-30) cc_final: 0.8559 (mm-30) REVERT: x 106 PHE cc_start: 0.8713 (m-80) cc_final: 0.8258 (m-10) REVERT: x 151 ASN cc_start: 0.8774 (m-40) cc_final: 0.8519 (m110) REVERT: x 187 ILE cc_start: 0.8984 (mp) cc_final: 0.8742 (mp) REVERT: x 297 MET cc_start: 0.7849 (pmm) cc_final: 0.7618 (pmm) REVERT: x 374 LYS cc_start: 0.9000 (pttm) cc_final: 0.8747 (pttm) REVERT: x 396 PHE cc_start: 0.8323 (m-80) cc_final: 0.7713 (m-80) REVERT: y 399 GLN cc_start: 0.6858 (pp30) cc_final: 0.6440 (pp30) REVERT: y 556 ASN cc_start: 0.8023 (OUTLIER) cc_final: 0.7606 (t0) REVERT: z 597 GLN cc_start: 0.8120 (mm-40) cc_final: 0.7826 (mp10) outliers start: 49 outliers final: 43 residues processed: 271 average time/residue: 0.2864 time to fit residues: 117.7099 Evaluate side-chains 283 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 239 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 18 ILE Chi-restraints excluded: chain q residue 37 ILE Chi-restraints excluded: chain q residue 65 ASN Chi-restraints excluded: chain u residue 60 LEU Chi-restraints excluded: chain u residue 72 LEU Chi-restraints excluded: chain u residue 84 CYS Chi-restraints excluded: chain u residue 125 LEU Chi-restraints excluded: chain u residue 181 LEU Chi-restraints excluded: chain u residue 190 LEU Chi-restraints excluded: chain u residue 198 HIS Chi-restraints excluded: chain u residue 241 ILE Chi-restraints excluded: chain u residue 279 ILE Chi-restraints excluded: chain u residue 290 MET Chi-restraints excluded: chain u residue 317 ASN Chi-restraints excluded: chain u residue 333 LEU Chi-restraints excluded: chain u residue 394 ASN Chi-restraints excluded: chain v residue 80 LEU Chi-restraints excluded: chain v residue 85 LEU Chi-restraints excluded: chain v residue 91 ASP Chi-restraints excluded: chain v residue 92 THR Chi-restraints excluded: chain v residue 126 LEU Chi-restraints excluded: chain v residue 154 ASP Chi-restraints excluded: chain x residue 40 LEU Chi-restraints excluded: chain x residue 52 LEU Chi-restraints excluded: chain x residue 117 THR Chi-restraints excluded: chain x residue 119 SER Chi-restraints excluded: chain x residue 136 CYS Chi-restraints excluded: chain x residue 204 GLU Chi-restraints excluded: chain x residue 205 MET Chi-restraints excluded: chain x residue 242 VAL Chi-restraints excluded: chain x residue 271 ILE Chi-restraints excluded: chain y residue 14 VAL Chi-restraints excluded: chain y residue 17 CYS Chi-restraints excluded: chain y residue 45 ASN Chi-restraints excluded: chain y residue 68 VAL Chi-restraints excluded: chain y residue 380 VAL Chi-restraints excluded: chain y residue 402 VAL Chi-restraints excluded: chain y residue 404 MET Chi-restraints excluded: chain y residue 407 ASP Chi-restraints excluded: chain y residue 444 ASN Chi-restraints excluded: chain y residue 448 VAL Chi-restraints excluded: chain y residue 486 VAL Chi-restraints excluded: chain y residue 556 ASN Chi-restraints excluded: chain y residue 603 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 3.9990 chunk 172 optimal weight: 6.9990 chunk 105 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 120 optimal weight: 20.0000 chunk 181 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 chunk 144 optimal weight: 0.1980 chunk 14 optimal weight: 9.9990 chunk 111 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** u 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 444 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17274 Z= 0.253 Angle : 0.684 14.737 24117 Z= 0.340 Chirality : 0.040 0.406 2866 Planarity : 0.003 0.042 2459 Dihedral : 20.399 179.446 4497 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.65 % Allowed : 19.44 % Favored : 76.90 % 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: 0.34 (0.20), residues: 1620 helix: 1.27 (0.17), residues: 901 sheet: -0.36 (0.39), residues: 167 loop : -1.32 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP u 295 HIS 0.005 0.001 HIS u 70 PHE 0.025 0.002 PHE y 70 TYR 0.029 0.002 TYR x 424 ARG 0.005 0.000 ARG q 74 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 237 time to evaluate : 2.084 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: q 48 GLU cc_start: 0.8998 (mp0) cc_final: 0.7933 (pp20) REVERT: q 68 TYR cc_start: 0.6754 (t80) cc_final: 0.5924 (t80) REVERT: q 83 ARG cc_start: 0.8519 (mmp80) cc_final: 0.8282 (mpp-170) REVERT: q 102 LYS cc_start: 0.9429 (tptt) cc_final: 0.9172 (tppt) REVERT: q 111 MET cc_start: 0.8365 (mmm) cc_final: 0.7990 (tpt) REVERT: u 260 MET cc_start: -0.1312 (tpt) cc_final: -0.1601 (mtm) REVERT: u 271 LEU cc_start: 0.8013 (tp) cc_final: 0.7742 (mm) REVERT: u 274 LYS cc_start: 0.9251 (ptpt) cc_final: 0.8963 (ptpt) REVERT: u 353 LYS cc_start: 0.8049 (ptpt) cc_final: 0.7247 (tppt) REVERT: u 429 LEU cc_start: 0.9229 (pp) cc_final: 0.8868 (mm) REVERT: u 449 LYS cc_start: 0.7349 (mppt) cc_final: 0.6976 (tmmt) REVERT: x 41 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8606 (mm-30) REVERT: x 106 PHE cc_start: 0.8751 (m-80) cc_final: 0.8279 (m-10) REVERT: x 151 ASN cc_start: 0.8761 (m-40) cc_final: 0.8494 (m110) REVERT: x 187 ILE cc_start: 0.9007 (mp) cc_final: 0.8740 (mp) REVERT: x 297 MET cc_start: 0.7861 (pmm) cc_final: 0.7618 (pmm) REVERT: x 374 LYS cc_start: 0.9121 (pttm) cc_final: 0.8832 (ptpp) REVERT: x 382 MET cc_start: 0.8159 (pmm) cc_final: 0.7781 (pmm) REVERT: x 396 PHE cc_start: 0.8394 (m-80) cc_final: 0.7736 (m-80) REVERT: y 122 ARG cc_start: 0.8249 (ptp-170) cc_final: 0.7869 (ptt-90) REVERT: y 399 GLN cc_start: 0.6905 (pp30) cc_final: 0.6483 (pp30) REVERT: y 556 ASN cc_start: 0.8071 (OUTLIER) cc_final: 0.7675 (t0) REVERT: z 597 GLN cc_start: 0.8165 (mm-40) cc_final: 0.7830 (mp10) outliers start: 50 outliers final: 42 residues processed: 261 average time/residue: 0.2920 time to fit residues: 115.7289 Evaluate side-chains 278 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 235 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 18 ILE Chi-restraints excluded: chain q residue 37 ILE Chi-restraints excluded: chain q residue 65 ASN Chi-restraints excluded: chain u residue 60 LEU Chi-restraints excluded: chain u residue 72 LEU Chi-restraints excluded: chain u residue 84 CYS Chi-restraints excluded: chain u residue 181 LEU Chi-restraints excluded: chain u residue 190 LEU Chi-restraints excluded: chain u residue 198 HIS Chi-restraints excluded: chain u residue 241 ILE Chi-restraints excluded: chain u residue 279 ILE Chi-restraints excluded: chain u residue 290 MET Chi-restraints excluded: chain u residue 317 ASN Chi-restraints excluded: chain u residue 333 LEU Chi-restraints excluded: chain v residue 85 LEU Chi-restraints excluded: chain v residue 91 ASP Chi-restraints excluded: chain v residue 92 THR Chi-restraints excluded: chain v residue 126 LEU Chi-restraints excluded: chain v residue 154 ASP Chi-restraints excluded: chain x residue 40 LEU Chi-restraints excluded: chain x residue 52 LEU Chi-restraints excluded: chain x residue 117 THR Chi-restraints excluded: chain x residue 119 SER Chi-restraints excluded: chain x residue 136 CYS Chi-restraints excluded: chain x residue 204 GLU Chi-restraints excluded: chain x residue 205 MET Chi-restraints excluded: chain x residue 242 VAL Chi-restraints excluded: chain x residue 271 ILE Chi-restraints excluded: chain x residue 275 THR Chi-restraints excluded: chain x residue 329 LEU Chi-restraints excluded: chain y residue 14 VAL Chi-restraints excluded: chain y residue 17 CYS Chi-restraints excluded: chain y residue 45 ASN Chi-restraints excluded: chain y residue 68 VAL Chi-restraints excluded: chain y residue 380 VAL Chi-restraints excluded: chain y residue 402 VAL Chi-restraints excluded: chain y residue 404 MET Chi-restraints excluded: chain y residue 407 ASP Chi-restraints excluded: chain y residue 448 VAL Chi-restraints excluded: chain y residue 486 VAL Chi-restraints excluded: chain y residue 514 ASP Chi-restraints excluded: chain y residue 556 ASN Chi-restraints excluded: chain y residue 603 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 0.9990 chunk 153 optimal weight: 0.7980 chunk 44 optimal weight: 0.1980 chunk 133 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 144 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 18 optimal weight: 0.0030 chunk 26 optimal weight: 20.0000 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** u 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 183 ASN ** x 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.088166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.068213 restraints weight = 69767.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.070124 restraints weight = 39053.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.071365 restraints weight = 26675.599| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3374 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3374 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17274 Z= 0.162 Angle : 0.664 14.158 24117 Z= 0.326 Chirality : 0.039 0.409 2866 Planarity : 0.003 0.029 2459 Dihedral : 20.363 179.092 4497 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.41 % Allowed : 20.76 % Favored : 76.83 % 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: 0.37 (0.20), residues: 1620 helix: 1.28 (0.17), residues: 899 sheet: -0.31 (0.39), residues: 167 loop : -1.28 (0.24), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP u 295 HIS 0.004 0.001 HIS u 70 PHE 0.027 0.001 PHE x 80 TYR 0.025 0.001 TYR x 424 ARG 0.006 0.000 ARG q 74 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3534.56 seconds wall clock time: 66 minutes 27.69 seconds (3987.69 seconds total)