Starting phenix.real_space_refine on Wed Sep 25 15:39:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmd_13529/09_2024/7pmd_13529.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmd_13529/09_2024/7pmd_13529.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmd_13529/09_2024/7pmd_13529.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmd_13529/09_2024/7pmd_13529.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmd_13529/09_2024/7pmd_13529.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmd_13529/09_2024/7pmd_13529.cif" } resolution = 2.9 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 5 5.49 5 Mg 3 5.21 5 S 63 5.16 5 C 6482 2.51 5 N 1730 2.21 5 O 1906 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 10189 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 6105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 6105 Classifications: {'peptide': 747} Link IDs: {'PTRANS': 27, 'TRANS': 719} Chain breaks: 5 Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1059 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.16, per 1000 atoms: 0.60 Number of scatterers: 10189 At special positions: 0 Unit cell: (103.4, 128.7, 154, 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 63 16.00 P 5 15.00 Mg 3 11.99 O 1906 8.00 N 1730 7.00 C 6482 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied TRANS " TRP H 1 " - " ALA H 7 " " DTH H 4 " - " ALA H 3 " Time building additional restraints: 2.53 Conformation dependent library (CDL) restraints added in 1.3 seconds 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH H 4 " Number of C-beta restraints generated: 2382 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 14 sheets defined 55.5% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 73 through 77 Processing helix chain 'A' and resid 81 through 95 Processing helix chain 'A' and resid 116 through 119 removed outlier: 4.450A pdb=" N TYR A 119 " --> pdb=" O LEU A 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 116 through 119' Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 138 through 153 removed outlier: 3.541A pdb=" N VAL A 142 " --> pdb=" O HIS A 138 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 185 removed outlier: 3.526A pdb=" N PHE A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 207 removed outlier: 3.758A pdb=" N LYS A 195 " --> pdb=" O ASN A 191 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 245 through 250 removed outlier: 3.531A pdb=" N ARG A 248 " --> pdb=" O GLU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 269 removed outlier: 4.216A pdb=" N TYR A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 271 No H-bonds generated for 'chain 'A' and resid 270 through 271' Processing helix chain 'A' and resid 272 through 278 removed outlier: 4.149A pdb=" N THR A 276 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 removed outlier: 3.806A pdb=" N GLN A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 315 removed outlier: 4.018A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 337 removed outlier: 3.754A pdb=" N ASN A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 365 Processing helix chain 'A' and resid 367 through 375 Processing helix chain 'A' and resid 392 through 424 removed outlier: 3.572A pdb=" N ALA A 422 " --> pdb=" O HIS A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 480 Processing helix chain 'A' and resid 483 through 487 removed outlier: 3.747A pdb=" N LEU A 486 " --> pdb=" O PRO A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 501 Processing helix chain 'A' and resid 504 through 515 removed outlier: 3.794A pdb=" N LYS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 532 removed outlier: 3.504A pdb=" N ALA A 524 " --> pdb=" O ASP A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 569 removed outlier: 3.521A pdb=" N LYS A 569 " --> pdb=" O LEU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 582 removed outlier: 3.571A pdb=" N LEU A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 594 removed outlier: 4.142A pdb=" N PHE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 635 through 653 Processing helix chain 'A' and resid 674 through 685 removed outlier: 3.884A pdb=" N GLN A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 696 Processing helix chain 'A' and resid 704 through 712 Processing helix chain 'A' and resid 713 through 715 No H-bonds generated for 'chain 'A' and resid 713 through 715' Processing helix chain 'A' and resid 723 through 736 removed outlier: 3.809A pdb=" N GLU A 733 " --> pdb=" O LYS A 729 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS A 734 " --> pdb=" O ASN A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 740 No H-bonds generated for 'chain 'A' and resid 738 through 740' Processing helix chain 'A' and resid 754 through 792 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.534A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.132A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.609A pdb=" N SER C 141 " --> pdb=" O GLN C 137 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.706A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 183 through 196 removed outlier: 3.772A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.568A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 232 Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 273 through 283 Processing helix chain 'C' and resid 289 through 295 Processing helix chain 'C' and resid 301 through 306 removed outlier: 4.286A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 347 Processing helix chain 'C' and resid 348 through 349 No H-bonds generated for 'chain 'C' and resid 348 through 349' Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.854A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 4.266A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 19 Processing helix chain 'B' and resid 29 through 39 removed outlier: 4.234A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ASP B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 53 Processing helix chain 'B' and resid 56 through 63 Processing helix chain 'B' and resid 67 through 79 Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 87 through 95 Processing helix chain 'B' and resid 105 through 116 Processing helix chain 'B' and resid 121 through 130 Processing helix chain 'B' and resid 140 through 150 Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 16 removed outlier: 4.229A pdb=" N ALA A 11 " --> pdb=" O LEU A 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 103 removed outlier: 6.314A pdb=" N LEU A 107 " --> pdb=" O ARG A 660 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ILE A 662 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ALA A 109 " --> pdb=" O ILE A 662 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N VAL A 659 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ILE A 160 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N CYS A 661 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N SER A 162 " --> pdb=" O CYS A 661 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLN A 157 " --> pdb=" O GLY A 434 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N LEU A 436 " --> pdb=" O GLN A 157 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE A 159 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ILE A 438 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N VAL A 161 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 208 through 211 removed outlier: 5.841A pdb=" N ALA A 209 " --> pdb=" O ASN A 216 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN A 216 " --> pdb=" O ALA A 209 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 341 through 344 removed outlier: 6.183A pdb=" N SER A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 377 through 382 Processing sheet with id=AA6, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA7, first strand: chain 'A' and resid 700 through 703 Processing sheet with id=AA8, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.678A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB1, first strand: chain 'C' and resid 71 through 72 removed outlier: 3.712A pdb=" N ILE C 75 " --> pdb=" O GLU C 72 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 170 removed outlier: 5.978A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB5, first strand: chain 'B' and resid 26 through 28 514 hydrogen bonds defined for protein. 1437 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.17 Time building geometry restraints manager: 2.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1707 1.31 - 1.44: 2745 1.44 - 1.56: 5840 1.56 - 1.69: 9 1.69 - 1.81: 102 Bond restraints: 10403 Sorted by residual: bond pdb=" O3A ANP A1901 " pdb=" PB ANP A1901 " ideal model delta sigma weight residual 1.700 1.548 0.152 2.00e-02 2.50e+03 5.77e+01 bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.572 1.438 0.134 2.00e-02 2.50e+03 4.52e+01 bond pdb=" N3B ANP A1901 " pdb=" PG ANP A1901 " ideal model delta sigma weight residual 1.795 1.684 0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" O5' ANP A1901 " pdb=" PA ANP A1901 " ideal model delta sigma weight residual 1.655 1.571 0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C EEP H 2 " pdb=" O EEP H 2 " ideal model delta sigma weight residual 1.263 1.190 0.073 2.00e-02 2.50e+03 1.32e+01 ... (remaining 10398 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.42: 13950 4.42 - 8.83: 96 8.83 - 13.25: 6 13.25 - 17.67: 0 17.67 - 22.09: 1 Bond angle restraints: 14053 Sorted by residual: angle pdb=" PB ANP A1901 " pdb=" N3B ANP A1901 " pdb=" PG ANP A1901 " ideal model delta sigma weight residual 126.95 104.86 22.09 3.00e+00 1.11e-01 5.42e+01 angle pdb=" N GLY A 563 " pdb=" CA GLY A 563 " pdb=" C GLY A 563 " ideal model delta sigma weight residual 113.86 122.92 -9.06 1.50e+00 4.44e-01 3.65e+01 angle pdb=" C HYP H 6 " pdb=" N ALA H 7 " pdb=" CA ALA H 7 " ideal model delta sigma weight residual 121.70 112.34 9.36 1.80e+00 3.09e-01 2.70e+01 angle pdb=" N DTH H 4 " pdb=" CA DTH H 4 " pdb=" CB DTH H 4 " ideal model delta sigma weight residual 111.50 103.32 8.18 1.70e+00 3.46e-01 2.31e+01 angle pdb=" N HIS A 531 " pdb=" CA HIS A 531 " pdb=" C HIS A 531 " ideal model delta sigma weight residual 112.45 118.49 -6.04 1.39e+00 5.18e-01 1.89e+01 ... (remaining 14048 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.40: 6005 25.40 - 50.79: 220 50.79 - 76.18: 53 76.18 - 101.58: 18 101.58 - 126.97: 3 Dihedral angle restraints: 6299 sinusoidal: 2605 harmonic: 3694 Sorted by residual: dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 173.03 126.97 1 2.00e+01 2.50e-03 3.84e+01 dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 62.50 -122.51 1 2.00e+01 2.50e-03 3.69e+01 dihedral pdb=" CA HIS A 531 " pdb=" C HIS A 531 " pdb=" N LEU A 532 " pdb=" CA LEU A 532 " ideal model delta harmonic sigma weight residual -180.00 -150.17 -29.83 0 5.00e+00 4.00e-02 3.56e+01 ... (remaining 6296 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1093 0.064 - 0.129: 373 0.129 - 0.193: 57 0.193 - 0.258: 9 0.258 - 0.322: 2 Chirality restraints: 1534 Sorted by residual: chirality pdb=" CA GLU C 316 " pdb=" N GLU C 316 " pdb=" C GLU C 316 " pdb=" CB GLU C 316 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" C3' ANP A1901 " pdb=" C2' ANP A1901 " pdb=" C4' ANP A1901 " pdb=" O3' ANP A1901 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CB ILE C 151 " pdb=" CA ILE C 151 " pdb=" CG1 ILE C 151 " pdb=" CG2 ILE C 151 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 1531 not shown) Planarity restraints: 1794 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 231 " 0.326 9.50e-02 1.11e+02 1.51e-01 2.93e+01 pdb=" NE ARG A 231 " 0.004 2.00e-02 2.50e+03 pdb=" CZ ARG A 231 " -0.073 2.00e-02 2.50e+03 pdb=" NH1 ARG A 231 " 0.019 2.00e-02 2.50e+03 pdb=" NH2 ARG A 231 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 564 " -0.039 2.00e-02 2.50e+03 3.61e-02 2.28e+01 pdb=" CG PHE A 564 " 0.083 2.00e-02 2.50e+03 pdb=" CD1 PHE A 564 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE A 564 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE A 564 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 564 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 564 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 89 " -0.023 2.00e-02 2.50e+03 4.69e-02 2.20e+01 pdb=" C THR C 89 " 0.081 2.00e-02 2.50e+03 pdb=" O THR C 89 " -0.030 2.00e-02 2.50e+03 pdb=" N PHE C 90 " -0.027 2.00e-02 2.50e+03 ... (remaining 1791 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.36: 14 2.36 - 3.00: 5490 3.00 - 3.63: 14794 3.63 - 4.27: 22950 4.27 - 4.90: 39298 Nonbonded interactions: 82546 Sorted by model distance: nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.728 3.620 nonbonded pdb=" O3B ADP C 401 " pdb="MG MG C 402 " model vdw 1.934 2.170 nonbonded pdb=" O3G ANP A1901 " pdb="MG MG A1902 " model vdw 1.934 2.170 nonbonded pdb=" O1B ANP A1901 " pdb="MG MG A1903 " model vdw 1.955 2.170 nonbonded pdb=" OG SER A 165 " pdb=" O2G ANP A1901 " model vdw 2.052 3.040 ... (remaining 82541 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 24.580 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:10.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 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 : 0.012 0.152 10403 Z= 0.785 Angle : 1.057 22.087 14053 Z= 0.600 Chirality : 0.064 0.322 1534 Planarity : 0.009 0.151 1792 Dihedral : 15.522 126.974 3911 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 0.09 % Allowed : 0.18 % Favored : 99.72 % Cbeta Deviations : 0.08 % 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: -1.33 (0.21), residues: 1235 helix: -1.77 (0.16), residues: 606 sheet: 0.43 (0.39), residues: 161 loop : 0.26 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.006 TRP A 484 HIS 0.011 0.002 HIS A 418 PHE 0.083 0.004 PHE A 564 TYR 0.038 0.007 TYR C 306 ARG 0.070 0.012 ARG A 231 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 90 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.8627 (tpp) cc_final: 0.8115 (tpp) REVERT: C 325 MET cc_start: 0.7465 (mtm) cc_final: 0.7226 (mtt) REVERT: B 19 PHE cc_start: 0.7284 (m-80) cc_final: 0.6986 (m-80) outliers start: 1 outliers final: 1 residues processed: 91 average time/residue: 1.6386 time to fit residues: 158.1222 Evaluate side-chains 50 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 49 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 112 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 GLN A 354 HIS A 398 ASN A 493 GLN A 775 GLN C 162 ASN C 280 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10403 Z= 0.205 Angle : 0.623 6.777 14053 Z= 0.326 Chirality : 0.043 0.210 1534 Planarity : 0.004 0.037 1792 Dihedral : 10.134 133.156 1429 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 1.11 % Allowed : 3.78 % Favored : 95.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.23), residues: 1235 helix: 0.77 (0.20), residues: 613 sheet: 0.72 (0.40), residues: 162 loop : 0.77 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 781 HIS 0.005 0.001 HIS C 101 PHE 0.017 0.001 PHE A 564 TYR 0.013 0.001 TYR A 102 ARG 0.007 0.001 ARG A 343 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 58 time to evaluate : 1.225 Fit side-chains revert: symmetry clash REVERT: A 478 MET cc_start: 0.8298 (mmp) cc_final: 0.7997 (mmp) REVERT: C 299 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.7817 (mtm) REVERT: B 31 GLN cc_start: 0.7861 (tp-100) cc_final: 0.7191 (tt0) REVERT: B 120 MET cc_start: 0.5906 (mtm) cc_final: 0.5633 (mmt) outliers start: 12 outliers final: 7 residues processed: 62 average time/residue: 1.4395 time to fit residues: 96.2446 Evaluate side-chains 57 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 49 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 139 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 0.8980 chunk 34 optimal weight: 0.2980 chunk 93 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 chunk 121 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10403 Z= 0.193 Angle : 0.555 7.123 14053 Z= 0.287 Chirality : 0.041 0.184 1534 Planarity : 0.004 0.033 1792 Dihedral : 9.024 134.579 1429 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.20 % Allowed : 5.25 % Favored : 93.55 % 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: 1.56 (0.24), residues: 1235 helix: 1.45 (0.21), residues: 621 sheet: 0.79 (0.42), residues: 156 loop : 0.74 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 781 HIS 0.004 0.001 HIS A 81 PHE 0.011 0.001 PHE B 16 TYR 0.014 0.001 TYR B 29 ARG 0.006 0.000 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 51 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.8999 (ttp) cc_final: 0.8775 (ttm) REVERT: A 305 MET cc_start: 0.8395 (tpp) cc_final: 0.7911 (tpp) REVERT: A 478 MET cc_start: 0.8292 (mmp) cc_final: 0.7916 (mmp) REVERT: C 227 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.7555 (tpt) REVERT: C 299 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.7871 (mtm) REVERT: B 31 GLN cc_start: 0.8013 (tp-100) cc_final: 0.7313 (tt0) REVERT: B 120 MET cc_start: 0.5535 (OUTLIER) cc_final: 0.5124 (mmt) outliers start: 13 outliers final: 7 residues processed: 55 average time/residue: 1.4116 time to fit residues: 84.0807 Evaluate side-chains 59 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 49 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain B residue 139 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 58 optimal weight: 0.0060 chunk 12 optimal weight: 8.9990 chunk 53 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 chunk 119 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 overall best weight: 1.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10403 Z= 0.268 Angle : 0.562 7.346 14053 Z= 0.288 Chirality : 0.041 0.187 1534 Planarity : 0.004 0.050 1792 Dihedral : 8.707 132.800 1429 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.83 % Allowed : 6.91 % Favored : 92.26 % 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: 1.78 (0.24), residues: 1235 helix: 1.74 (0.22), residues: 609 sheet: 0.94 (0.40), residues: 164 loop : 0.68 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 781 HIS 0.004 0.001 HIS A 81 PHE 0.010 0.001 PHE C 255 TYR 0.012 0.001 TYR C 294 ARG 0.014 0.000 ARG A 712 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 51 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 478 MET cc_start: 0.8322 (mmp) cc_final: 0.8059 (mmp) REVERT: C 227 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.7661 (tpt) REVERT: C 283 MET cc_start: 0.7727 (mmm) cc_final: 0.7466 (mmm) REVERT: B 31 GLN cc_start: 0.8026 (tp-100) cc_final: 0.7376 (tt0) outliers start: 9 outliers final: 5 residues processed: 54 average time/residue: 1.3459 time to fit residues: 78.7328 Evaluate side-chains 56 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 50 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 139 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 102 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10403 Z= 0.198 Angle : 0.541 9.777 14053 Z= 0.274 Chirality : 0.040 0.182 1534 Planarity : 0.003 0.036 1792 Dihedral : 8.443 129.342 1429 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.11 % Allowed : 7.00 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.24), residues: 1235 helix: 1.88 (0.22), residues: 613 sheet: 0.91 (0.42), residues: 154 loop : 0.57 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 781 HIS 0.004 0.001 HIS A 81 PHE 0.010 0.001 PHE B 16 TYR 0.010 0.001 TYR C 294 ARG 0.010 0.000 ARG A 712 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 52 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.8998 (ttp) cc_final: 0.8786 (ttm) REVERT: A 305 MET cc_start: 0.8382 (tpp) cc_final: 0.7960 (tpp) REVERT: A 478 MET cc_start: 0.8353 (mmp) cc_final: 0.8131 (mmp) REVERT: B 31 GLN cc_start: 0.8053 (tp-100) cc_final: 0.7472 (tt0) REVERT: B 105 MET cc_start: 0.8903 (mmp) cc_final: 0.8577 (mmm) outliers start: 12 outliers final: 8 residues processed: 58 average time/residue: 1.3234 time to fit residues: 83.3654 Evaluate side-chains 58 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 50 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 139 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 23 optimal weight: 0.4980 chunk 70 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 119 optimal weight: 8.9990 chunk 99 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 62 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10403 Z= 0.183 Angle : 0.547 10.133 14053 Z= 0.273 Chirality : 0.040 0.183 1534 Planarity : 0.003 0.033 1792 Dihedral : 8.154 122.517 1428 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.01 % Allowed : 7.93 % Favored : 91.06 % 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: 1.85 (0.24), residues: 1235 helix: 1.95 (0.22), residues: 613 sheet: 0.72 (0.43), residues: 155 loop : 0.56 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 781 HIS 0.004 0.001 HIS A 81 PHE 0.011 0.001 PHE B 16 TYR 0.009 0.001 TYR A 456 ARG 0.005 0.000 ARG A 712 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 52 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.8992 (ttp) cc_final: 0.8784 (ttm) REVERT: B 31 GLN cc_start: 0.8123 (tp-100) cc_final: 0.7484 (tt0) outliers start: 11 outliers final: 8 residues processed: 59 average time/residue: 1.3028 time to fit residues: 83.4553 Evaluate side-chains 59 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 51 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 139 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 67 optimal weight: 0.3980 chunk 100 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 119 optimal weight: 9.9990 chunk 74 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 55 optimal weight: 0.3980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10403 Z= 0.238 Angle : 0.576 10.498 14053 Z= 0.286 Chirality : 0.041 0.175 1534 Planarity : 0.003 0.033 1792 Dihedral : 8.073 115.665 1428 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.01 % Allowed : 8.20 % Favored : 90.78 % 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: 1.80 (0.24), residues: 1235 helix: 1.96 (0.22), residues: 611 sheet: 0.62 (0.43), residues: 156 loop : 0.51 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 484 HIS 0.003 0.001 HIS A 81 PHE 0.010 0.001 PHE B 16 TYR 0.011 0.001 TYR A 259 ARG 0.005 0.000 ARG A 712 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 51 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.8996 (ttp) cc_final: 0.8794 (ttm) REVERT: A 305 MET cc_start: 0.8324 (tpp) cc_final: 0.8000 (tpp) REVERT: A 790 MET cc_start: 0.3317 (ppp) cc_final: 0.0598 (mmm) REVERT: B 31 GLN cc_start: 0.8055 (tp-100) cc_final: 0.7383 (tt0) REVERT: B 36 MET cc_start: 0.7317 (mpp) cc_final: 0.7094 (pmm) REVERT: B 120 MET cc_start: 0.5330 (mmt) cc_final: 0.5003 (mmt) outliers start: 11 outliers final: 8 residues processed: 59 average time/residue: 1.3343 time to fit residues: 85.5761 Evaluate side-chains 57 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 49 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 139 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 23 optimal weight: 0.0020 chunk 75 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 93 optimal weight: 0.1980 chunk 108 optimal weight: 1.9990 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10403 Z= 0.181 Angle : 0.569 10.821 14053 Z= 0.281 Chirality : 0.040 0.171 1534 Planarity : 0.003 0.033 1792 Dihedral : 7.934 116.032 1428 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.92 % Allowed : 8.57 % Favored : 90.51 % 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: 1.90 (0.24), residues: 1235 helix: 2.04 (0.22), residues: 613 sheet: 0.74 (0.43), residues: 153 loop : 0.52 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP A 484 HIS 0.003 0.001 HIS A 81 PHE 0.011 0.001 PHE B 16 TYR 0.009 0.001 TYR A 456 ARG 0.004 0.000 ARG A 712 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 54 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.8982 (ttp) cc_final: 0.8777 (ttm) REVERT: A 478 MET cc_start: 0.8287 (mmp) cc_final: 0.7135 (mmp) REVERT: A 790 MET cc_start: 0.3260 (ppp) cc_final: 0.0640 (mmm) REVERT: C 283 MET cc_start: 0.7724 (mmm) cc_final: 0.7389 (mmm) REVERT: B 29 TYR cc_start: 0.8086 (m-80) cc_final: 0.7580 (m-10) REVERT: B 31 GLN cc_start: 0.7981 (tp-100) cc_final: 0.7317 (tt0) outliers start: 10 outliers final: 8 residues processed: 60 average time/residue: 1.3433 time to fit residues: 87.5143 Evaluate side-chains 59 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 51 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 139 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 20.0000 chunk 104 optimal weight: 0.7980 chunk 111 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 105 optimal weight: 0.6980 chunk 110 optimal weight: 0.9980 chunk 73 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10403 Z= 0.191 Angle : 0.587 11.951 14053 Z= 0.288 Chirality : 0.041 0.173 1534 Planarity : 0.003 0.033 1792 Dihedral : 7.857 115.311 1428 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.83 % Allowed : 8.85 % Favored : 90.32 % 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: 1.88 (0.24), residues: 1235 helix: 2.02 (0.22), residues: 613 sheet: 0.74 (0.43), residues: 153 loop : 0.52 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A 484 HIS 0.003 0.001 HIS A 81 PHE 0.009 0.001 PHE B 12 TYR 0.009 0.001 TYR A 259 ARG 0.004 0.000 ARG A 712 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 52 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.8983 (ttp) cc_final: 0.8775 (ttm) REVERT: A 790 MET cc_start: 0.3087 (ppp) cc_final: 0.0565 (mmm) REVERT: C 283 MET cc_start: 0.7707 (mmm) cc_final: 0.7382 (mmm) REVERT: B 29 TYR cc_start: 0.8066 (m-80) cc_final: 0.7608 (m-10) REVERT: B 31 GLN cc_start: 0.7907 (tp-100) cc_final: 0.7235 (tt0) REVERT: B 36 MET cc_start: 0.7271 (mpp) cc_final: 0.6969 (pmm) outliers start: 9 outliers final: 8 residues processed: 57 average time/residue: 1.3942 time to fit residues: 86.2709 Evaluate side-chains 60 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 52 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 139 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 20.0000 chunk 71 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 123 optimal weight: 20.0000 chunk 113 optimal weight: 3.9990 chunk 98 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 10403 Z= 0.363 Angle : 0.634 11.115 14053 Z= 0.316 Chirality : 0.043 0.178 1534 Planarity : 0.003 0.034 1792 Dihedral : 7.993 115.358 1428 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.65 % Allowed : 9.03 % Favored : 90.32 % 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: 1.75 (0.24), residues: 1235 helix: 1.95 (0.22), residues: 610 sheet: 0.68 (0.41), residues: 163 loop : 0.39 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 484 HIS 0.004 0.001 HIS A 260 PHE 0.010 0.001 PHE C 255 TYR 0.015 0.001 TYR A 259 ARG 0.003 0.000 ARG A 712 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 53 time to evaluate : 1.174 Fit side-chains revert: symmetry clash REVERT: A 788 MET cc_start: 0.8102 (mpp) cc_final: 0.7318 (mmm) REVERT: A 790 MET cc_start: 0.3049 (ppp) cc_final: 0.0573 (mmm) REVERT: C 283 MET cc_start: 0.7759 (mmm) cc_final: 0.7469 (mmm) REVERT: B 29 TYR cc_start: 0.8072 (m-80) cc_final: 0.7599 (m-10) REVERT: B 31 GLN cc_start: 0.7910 (tp-100) cc_final: 0.7229 (tt0) REVERT: B 36 MET cc_start: 0.7436 (mpp) cc_final: 0.7097 (pmm) REVERT: B 105 MET cc_start: 0.8681 (tpp) cc_final: 0.8420 (tpp) outliers start: 7 outliers final: 6 residues processed: 57 average time/residue: 1.3094 time to fit residues: 81.2458 Evaluate side-chains 55 residues out of total 1096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 49 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 139 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 101 optimal weight: 0.6980 chunk 12 optimal weight: 0.4980 chunk 18 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.058856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.038734 restraints weight = 41815.761| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 3.60 r_work: 0.2679 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10403 Z= 0.193 Angle : 0.604 12.293 14053 Z= 0.298 Chirality : 0.041 0.171 1534 Planarity : 0.003 0.042 1792 Dihedral : 7.874 117.185 1428 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.74 % Allowed : 9.31 % Favored : 89.95 % 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: 1.76 (0.24), residues: 1235 helix: 1.95 (0.22), residues: 612 sheet: 0.64 (0.43), residues: 153 loop : 0.42 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 484 HIS 0.003 0.001 HIS A 81 PHE 0.019 0.001 PHE B 12 TYR 0.010 0.001 TYR A 79 ARG 0.003 0.000 ARG A 712 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2778.91 seconds wall clock time: 49 minutes 51.78 seconds (2991.78 seconds total)