Starting phenix.real_space_refine (version: dev) on Wed Feb 22 05:44:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7obq_12799/02_2023/7obq_12799_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7obq_12799/02_2023/7obq_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_12799/02_2023/7obq_12799.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7obq_12799/02_2023/7obq_12799.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7obq_12799/02_2023/7obq_12799_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7obq_12799/02_2023/7obq_12799_neut_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 10.11, per 1000 atoms: 0.61 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: 8.07 Conformation dependent library (CDL) restraints added in 1.9 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: 6.38 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: 5.59 Time building geometry restraints manager: 8.58 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: 9938 35.69 - 71.39: 170 71.39 - 107.08: 26 107.08 - 142.77: 0 142.77 - 178.47: 3 Dihedral angle restraints: 10137 sinusoidal: 5276 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 10134 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 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. 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: 4.300 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: 0.010 Extract box with map and model: 21.200 Check model and map are aligned: 0.240 Process input model: 49.800 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.160 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 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 : 12.881 178.468 6981 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 % 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 *********************** 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 : 1.681 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 outliers start: 36 outliers final: 8 residues processed: 426 average time/residue: 0.3143 time to fit residues: 193.1805 Evaluate side-chains 267 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 259 time to evaluate : 1.490 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1418 time to fit residues: 4.3267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 0.7980 chunk 137 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 73 optimal weight: 0.4980 chunk 142 optimal weight: 0.7980 chunk 55 optimal weight: 7.9990 chunk 86 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 chunk 165 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: q 43 ASN u 151 HIS 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 426 ASN y 541 ASN y 617 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1795 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= 0.164 Angle : 0.604 8.155 24117 Z= 0.295 Chirality : 0.037 0.204 2866 Planarity : 0.003 0.035 2459 Dihedral : 12.781 178.659 3806 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer Outliers : 2.78 % 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: 1.34 (0.21), residues: 1620 helix: 2.07 (0.17), residues: 897 sheet: 0.32 (0.40), residues: 157 loop : -0.91 (0.24), residues: 566 *********************** 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 317 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 279 time to evaluate : 1.767 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 outliers start: 38 outliers final: 13 residues processed: 302 average time/residue: 0.2907 time to fit residues: 132.1829 Evaluate side-chains 239 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 226 time to evaluate : 1.684 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1569 time to fit residues: 6.0929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 137 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 165 optimal weight: 0.8980 chunk 178 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 chunk 164 optimal weight: 0.9990 chunk 56 optimal weight: 9.9990 chunk 132 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: u 247 ASN v 121 HIS ** x 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 60 ASN y 412 GLN ** y 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 17274 Z= 0.201 Angle : 0.595 9.817 24117 Z= 0.298 Chirality : 0.037 0.207 2866 Planarity : 0.003 0.029 2459 Dihedral : 12.970 179.820 3806 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer Outliers : 2.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.21), residues: 1620 helix: 1.87 (0.17), residues: 896 sheet: 0.11 (0.40), residues: 162 loop : -0.98 (0.24), residues: 562 *********************** 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 284 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 247 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 16 residues processed: 268 average time/residue: 0.2883 time to fit residues: 117.0477 Evaluate side-chains 245 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 229 time to evaluate : 1.779 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1563 time to fit residues: 6.9694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 79 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 chunk 166 optimal weight: 6.9990 chunk 175 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 157 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: u 247 ASN ** x 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 338 ASN ** y 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 17274 Z= 0.240 Angle : 0.618 11.954 24117 Z= 0.311 Chirality : 0.038 0.277 2866 Planarity : 0.004 0.039 2459 Dihedral : 13.197 179.656 3806 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer Outliers : 2.27 % 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: 0.90 (0.21), residues: 1620 helix: 1.74 (0.17), residues: 893 sheet: -0.06 (0.40), residues: 162 loop : -1.05 (0.24), residues: 565 *********************** 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 273 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 242 time to evaluate : 1.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 22 residues processed: 262 average time/residue: 0.2924 time to fit residues: 114.4589 Evaluate side-chains 242 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 220 time to evaluate : 1.692 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1585 time to fit residues: 8.7076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 130 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 150 optimal weight: 9.9990 chunk 121 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 89 optimal weight: 6.9990 chunk 157 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 overall best weight: 2.9384 ------------------------------------------------------------------------------- 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 u 247 ASN ** x 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 195 HIS y 412 GLN ** y 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 17274 Z= 0.266 Angle : 0.650 11.295 24117 Z= 0.326 Chirality : 0.039 0.319 2866 Planarity : 0.004 0.038 2459 Dihedral : 13.374 179.292 3806 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer Outliers : 1.90 % 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: 0.64 (0.20), residues: 1620 helix: 1.50 (0.17), residues: 902 sheet: -0.26 (0.40), residues: 164 loop : -1.15 (0.24), residues: 554 *********************** 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 263 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 237 time to evaluate : 1.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 10 residues processed: 251 average time/residue: 0.2788 time to fit residues: 106.6077 Evaluate side-chains 225 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 215 time to evaluate : 1.671 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1502 time to fit residues: 5.0826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 0.0970 chunk 158 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 176 optimal weight: 6.9990 chunk 146 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 14 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 92 optimal weight: 0.0370 overall best weight: 0.5860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: u 247 ASN ** x 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 366 GLN y 412 GLN ** y 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 597 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.058 17274 Z= 0.152 Angle : 0.642 15.369 24117 Z= 0.312 Chirality : 0.038 0.324 2866 Planarity : 0.003 0.029 2459 Dihedral : 13.309 178.984 3806 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer Outliers : 1.24 % 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: 0.66 (0.20), residues: 1620 helix: 1.51 (0.17), residues: 899 sheet: -0.14 (0.39), residues: 164 loop : -1.13 (0.24), residues: 557 *********************** 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 275 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 258 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 269 average time/residue: 0.3081 time to fit residues: 125.5612 Evaluate side-chains 239 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 229 time to evaluate : 1.724 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1583 time to fit residues: 5.2266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 128 optimal weight: 0.6980 chunk 99 optimal weight: 7.9990 chunk 148 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 175 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 80 optimal weight: 7.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: u 247 ASN v 161 GLN ** x 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 412 GLN ** y 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3347 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= 0.231 Angle : 0.656 13.298 24117 Z= 0.324 Chirality : 0.038 0.355 2866 Planarity : 0.003 0.027 2459 Dihedral : 13.391 179.421 3806 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.20), residues: 1620 helix: 1.48 (0.17), residues: 900 sheet: -0.29 (0.39), residues: 167 loop : -1.17 (0.24), residues: 553 *********************** 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 261 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 239 time to evaluate : 1.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 14 residues processed: 251 average time/residue: 0.2802 time to fit residues: 107.8114 Evaluate side-chains 237 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 223 time to evaluate : 1.772 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1556 time to fit residues: 6.3680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 8.9990 chunk 70 optimal weight: 30.0000 chunk 104 optimal weight: 7.9990 chunk 52 optimal weight: 0.0470 chunk 34 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 137 optimal weight: 8.9990 overall best weight: 1.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 17274 Z= 0.181 Angle : 0.669 15.569 24117 Z= 0.327 Chirality : 0.038 0.453 2866 Planarity : 0.003 0.026 2459 Dihedral : 13.396 179.177 3806 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer Outliers : 0.44 % 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: 0.50 (0.20), residues: 1620 helix: 1.40 (0.17), residues: 900 sheet: -0.35 (0.39), residues: 167 loop : -1.20 (0.24), residues: 553 *********************** 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 241 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 235 time to evaluate : 1.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 240 average time/residue: 0.2780 time to fit residues: 103.0107 Evaluate side-chains 226 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 224 time to evaluate : 1.650 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1504 time to fit residues: 2.8890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 0.9980 chunk 168 optimal weight: 0.6980 chunk 153 optimal weight: 0.5980 chunk 163 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 71 optimal weight: 20.0000 chunk 128 optimal weight: 0.2980 chunk 50 optimal weight: 0.9990 chunk 147 optimal weight: 4.9990 chunk 154 optimal weight: 5.9990 chunk 162 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 412 GLN ** y 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 17274 Z= 0.161 Angle : 0.672 13.694 24117 Z= 0.329 Chirality : 0.038 0.414 2866 Planarity : 0.003 0.031 2459 Dihedral : 13.345 179.283 3806 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.20), residues: 1620 helix: 1.39 (0.17), residues: 900 sheet: -0.44 (0.39), residues: 167 loop : -1.19 (0.24), residues: 553 *********************** 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 249 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 245 time to evaluate : 1.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 245 average time/residue: 0.2944 time to fit residues: 111.6205 Evaluate side-chains 232 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 230 time to evaluate : 1.669 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1571 time to fit residues: 2.8464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 0.9980 chunk 172 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 82 optimal weight: 7.9990 chunk 120 optimal weight: 20.0000 chunk 181 optimal weight: 10.0000 chunk 166 optimal weight: 3.9990 chunk 144 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 88 optimal weight: 0.1980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 412 GLN ** y 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 17274 Z= 0.210 Angle : 0.703 19.730 24117 Z= 0.344 Chirality : 0.039 0.447 2866 Planarity : 0.003 0.028 2459 Dihedral : 13.367 179.528 3806 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.41 (0.20), residues: 1620 helix: 1.30 (0.17), residues: 901 sheet: -0.39 (0.40), residues: 165 loop : -1.20 (0.24), residues: 554 ********************** 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 234 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 231 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 232 average time/residue: 0.2762 time to fit residues: 98.9004 Evaluate side-chains 228 residues out of total 1404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 227 time to evaluate : 1.720 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1804 time to fit residues: 2.6664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 1.9990 chunk 153 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 133 optimal weight: 0.0030 chunk 21 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 148 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 26 optimal weight: 20.0000 overall best weight: 1.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: v 236 GLN ** x 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 412 GLN ** y 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.087319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.067703 restraints weight = 70400.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.069590 restraints weight = 38294.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.070900 restraints weight = 25797.764| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3717 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3717 r_free = 0.3717 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3716 r_free = 0.3716 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3716 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 17274 Z= 0.193 Angle : 0.693 19.355 24117 Z= 0.341 Chirality : 0.039 0.433 2866 Planarity : 0.003 0.033 2459 Dihedral : 13.358 179.342 3806 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.38 (0.21), residues: 1620 helix: 1.29 (0.17), residues: 901 sheet: -0.49 (0.40), residues: 167 loop : -1.20 (0.25), residues: 552 =============================================================================== Job complete usr+sys time: 3231.86 seconds wall clock time: 59 minutes 54.90 seconds (3594.90 seconds total)