Starting phenix.real_space_refine on Wed Mar 4 03:52:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pmd_13529/03_2026/7pmd_13529.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pmd_13529/03_2026/7pmd_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/cci-nas-00/data/ceres_data/7pmd_13529/03_2026/7pmd_13529.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pmd_13529/03_2026/7pmd_13529.map" model { file = "/net/cci-nas-00/data/ceres_data/7pmd_13529/03_2026/7pmd_13529.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pmd_13529/03_2026/7pmd_13529.cif" } resolution = 2.9 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 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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, 'ASP:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} 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: 2.34, per 1000 atoms: 0.23 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: 0.80 Conformation dependent library (CDL) restraints added in 461.0 milliseconds 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: 0.39 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: 1.65 Time building geometry restraints manager: 1.11 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: 2.170 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.510 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.330 ------------------------------------------------------------------------------- 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 10405 Z= 0.517 Angle : 1.060 22.087 14059 Z= 0.602 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.070 0.012 ARG A 231 TYR 0.038 0.007 TYR C 306 PHE 0.083 0.004 PHE A 564 TRP 0.042 0.006 TRP A 484 HIS 0.011 0.002 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.01213 (10403) covalent geometry : angle 1.05733 (14053) hydrogen bonds : bond 0.15121 ( 512) hydrogen bonds : angle 6.71572 ( 1437) link_TRANS : bond 0.01563 ( 2) link_TRANS : angle 4.01430 ( 6) *********************** 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 to be fit. rotamer outliers: 1 poor density : 90 time to evaluate : 0.379 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: 0.6967 (m-80) outliers start: 1 outliers final: 1 residues processed: 91 average time/residue: 0.8013 time to fit residues: 77.1088 Evaluate side-chains 50 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.4980 chunk 113 optimal weight: 20.0000 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 123 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.059486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.038612 restraints weight = 41057.233| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 3.70 r_work: 0.2689 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 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 0.034 10405 Z= 0.146 Angle : 0.627 7.175 14059 Z= 0.328 Chirality : 0.043 0.200 1534 Planarity : 0.004 0.037 1792 Dihedral : 10.102 133.282 1429 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.79 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.23), residues: 1235 helix: 0.80 (0.20), residues: 609 sheet: 0.72 (0.39), residues: 162 loop : 0.77 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 343 TYR 0.012 0.001 TYR A 102 PHE 0.019 0.001 PHE A 564 TRP 0.031 0.003 TRP A 781 HIS 0.005 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00325 (10403) covalent geometry : angle 0.62742 (14053) hydrogen bonds : bond 0.04070 ( 512) hydrogen bonds : angle 4.91405 ( 1437) link_TRANS : bond 0.00017 ( 2) link_TRANS : angle 0.66921 ( 6) *********************** 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 to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: A 135 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8470 (mtp) REVERT: A 478 MET cc_start: 0.8864 (mmp) cc_final: 0.8383 (mmp) REVERT: A 484 TRP cc_start: 0.7666 (m-10) cc_final: 0.7344 (m-90) REVERT: C 299 MET cc_start: 0.9494 (OUTLIER) cc_final: 0.9164 (mtm) REVERT: B 31 GLN cc_start: 0.7684 (tp-100) cc_final: 0.7033 (tt0) REVERT: B 36 MET cc_start: 0.7441 (mtt) cc_final: 0.7186 (mpp) outliers start: 12 outliers final: 6 residues processed: 62 average time/residue: 0.7127 time to fit residues: 47.3239 Evaluate side-chains 57 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 MET 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 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 64 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 94 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.058179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.037261 restraints weight = 42055.390| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 3.69 r_work: 0.2643 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10405 Z= 0.233 Angle : 0.612 8.224 14059 Z= 0.316 Chirality : 0.043 0.188 1534 Planarity : 0.004 0.035 1792 Dihedral : 9.113 134.619 1428 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.11 % Allowed : 5.44 % Favored : 93.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.24), residues: 1235 helix: 1.35 (0.21), residues: 613 sheet: 0.88 (0.40), residues: 159 loop : 0.62 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 95 TYR 0.015 0.001 TYR C 294 PHE 0.016 0.001 PHE A 564 TRP 0.026 0.002 TRP A 781 HIS 0.004 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00536 (10403) covalent geometry : angle 0.61167 (14053) hydrogen bonds : bond 0.04126 ( 512) hydrogen bonds : angle 4.68626 ( 1437) link_TRANS : bond 0.00289 ( 2) link_TRANS : angle 0.48488 ( 6) *********************** 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 62 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8395 (mtp) REVERT: A 478 MET cc_start: 0.8936 (mmp) cc_final: 0.8406 (mmp) REVERT: A 484 TRP cc_start: 0.7816 (m-10) cc_final: 0.7477 (m-90) REVERT: A 503 MET cc_start: 0.9281 (mmp) cc_final: 0.9044 (mmp) REVERT: A 790 MET cc_start: 0.4058 (tpt) cc_final: 0.3814 (ppp) REVERT: C 47 MET cc_start: 0.8938 (mmm) cc_final: 0.8699 (tmm) REVERT: C 137 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8441 (mm-40) REVERT: C 176 MET cc_start: 0.9247 (tpp) cc_final: 0.8903 (mmm) REVERT: C 227 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.7983 (tpt) REVERT: B 31 GLN cc_start: 0.7801 (tp-100) cc_final: 0.7242 (tt0) outliers start: 12 outliers final: 5 residues processed: 56 average time/residue: 0.6886 time to fit residues: 41.4827 Evaluate side-chains 57 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 MET 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 C residue 137 GLN 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 8 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 73 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- 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 = 0.3476 r_free = 0.3476 target = 0.058288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.037487 restraints weight = 42182.934| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 3.70 r_work: 0.2656 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10405 Z= 0.182 Angle : 0.571 10.613 14059 Z= 0.290 Chirality : 0.042 0.176 1534 Planarity : 0.004 0.049 1792 Dihedral : 8.772 136.989 1428 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.92 % Allowed : 6.82 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.24), residues: 1235 helix: 1.67 (0.22), residues: 609 sheet: 0.79 (0.40), residues: 161 loop : 0.57 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 712 TYR 0.012 0.001 TYR C 294 PHE 0.010 0.001 PHE B 16 TRP 0.023 0.002 TRP A 781 HIS 0.004 0.001 HIS A 81 Details of bonding type rmsd covalent geometry : bond 0.00417 (10403) covalent geometry : angle 0.57063 (14053) hydrogen bonds : bond 0.03696 ( 512) hydrogen bonds : angle 4.57296 ( 1437) link_TRANS : bond 0.00202 ( 2) link_TRANS : angle 0.51388 ( 6) *********************** 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 63 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 135 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8476 (mtp) REVERT: A 467 MET cc_start: 0.9205 (mmm) cc_final: 0.8969 (mmm) REVERT: A 478 MET cc_start: 0.9047 (mmp) cc_final: 0.8533 (mmp) REVERT: A 484 TRP cc_start: 0.7859 (m-10) cc_final: 0.7521 (m-90) REVERT: A 503 MET cc_start: 0.9264 (mmp) cc_final: 0.9010 (mmp) REVERT: A 790 MET cc_start: 0.3944 (tpt) cc_final: 0.3686 (ppp) REVERT: C 176 MET cc_start: 0.9240 (tpp) cc_final: 0.8902 (mmm) REVERT: C 227 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.8057 (tpt) REVERT: B 31 GLN cc_start: 0.7864 (tp-100) cc_final: 0.7249 (tt0) outliers start: 10 outliers final: 6 residues processed: 58 average time/residue: 0.6675 time to fit residues: 41.7289 Evaluate side-chains 57 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 MET 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 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 11 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 120 optimal weight: 8.9990 chunk 68 optimal weight: 0.6980 chunk 79 optimal weight: 0.4980 chunk 108 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3489 r_free = 0.3489 target = 0.059022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.039068 restraints weight = 42184.510| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 3.60 r_work: 0.2684 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10405 Z= 0.119 Angle : 0.538 9.650 14059 Z= 0.272 Chirality : 0.040 0.175 1534 Planarity : 0.003 0.033 1792 Dihedral : 8.495 133.410 1428 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.01 % Allowed : 7.65 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.24), residues: 1235 helix: 1.89 (0.22), residues: 608 sheet: 0.70 (0.42), residues: 154 loop : 0.58 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 712 TYR 0.009 0.001 TYR A 79 PHE 0.013 0.001 PHE B 16 TRP 0.017 0.001 TRP A 781 HIS 0.004 0.001 HIS A 81 Details of bonding type rmsd covalent geometry : bond 0.00268 (10403) covalent geometry : angle 0.53805 (14053) hydrogen bonds : bond 0.03301 ( 512) hydrogen bonds : angle 4.46677 ( 1437) link_TRANS : bond 0.00147 ( 2) link_TRANS : angle 0.57258 ( 6) *********************** 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 to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.8474 (mtm) REVERT: A 150 MET cc_start: 0.9224 (ttp) cc_final: 0.8990 (ttm) REVERT: A 467 MET cc_start: 0.9233 (mmm) cc_final: 0.8968 (mmm) REVERT: A 478 MET cc_start: 0.9026 (mmp) cc_final: 0.8434 (mmp) REVERT: A 484 TRP cc_start: 0.7911 (m-10) cc_final: 0.7503 (m-90) REVERT: A 503 MET cc_start: 0.9224 (mmp) cc_final: 0.8956 (mmp) REVERT: A 715 MET cc_start: 0.9294 (pmt) cc_final: 0.8946 (pmm) REVERT: A 790 MET cc_start: 0.3882 (tpt) cc_final: 0.3556 (ppp) REVERT: C 167 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8513 (mp0) REVERT: C 176 MET cc_start: 0.9244 (tpp) cc_final: 0.8882 (mmm) REVERT: C 283 MET cc_start: 0.8674 (mmm) cc_final: 0.8323 (mmm) REVERT: B 29 TYR cc_start: 0.7827 (m-80) cc_final: 0.7486 (m-10) REVERT: B 31 GLN cc_start: 0.7970 (tp-100) cc_final: 0.7354 (tt0) outliers start: 11 outliers final: 7 residues processed: 57 average time/residue: 0.7075 time to fit residues: 43.3497 Evaluate side-chains 61 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 167 GLU 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 11 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.3454 r_free = 0.3454 target = 0.057406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.036608 restraints weight = 42684.877| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 3.69 r_work: 0.2623 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 10405 Z= 0.280 Angle : 0.615 9.538 14059 Z= 0.312 Chirality : 0.044 0.177 1534 Planarity : 0.004 0.035 1792 Dihedral : 8.559 126.078 1428 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.20 % Allowed : 8.39 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.24), residues: 1235 helix: 1.86 (0.22), residues: 607 sheet: 0.73 (0.41), residues: 163 loop : 0.42 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 712 TYR 0.014 0.001 TYR A 259 PHE 0.011 0.001 PHE C 255 TRP 0.013 0.002 TRP A 781 HIS 0.004 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00645 (10403) covalent geometry : angle 0.61508 (14053) hydrogen bonds : bond 0.03965 ( 512) hydrogen bonds : angle 4.58917 ( 1437) link_TRANS : bond 0.00301 ( 2) link_TRANS : angle 0.46974 ( 6) *********************** 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 65 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8888 (OUTLIER) cc_final: 0.8509 (mtm) REVERT: A 305 MET cc_start: 0.9447 (tpp) cc_final: 0.8702 (tpp) REVERT: A 467 MET cc_start: 0.9267 (mmm) cc_final: 0.9021 (mmm) REVERT: A 478 MET cc_start: 0.9096 (mmp) cc_final: 0.8533 (mmp) REVERT: A 484 TRP cc_start: 0.7940 (m-10) cc_final: 0.7527 (m-90) REVERT: A 503 MET cc_start: 0.9252 (mmp) cc_final: 0.8976 (mmp) REVERT: A 715 MET cc_start: 0.9283 (pmt) cc_final: 0.9013 (pmm) REVERT: A 790 MET cc_start: 0.3957 (tpt) cc_final: 0.3718 (ppp) REVERT: C 167 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8543 (mp0) REVERT: C 176 MET cc_start: 0.9230 (tpp) cc_final: 0.8808 (mmm) REVERT: C 227 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.8115 (tpt) REVERT: C 283 MET cc_start: 0.8641 (mmm) cc_final: 0.8351 (mmm) REVERT: B 29 TYR cc_start: 0.7737 (m-80) cc_final: 0.7404 (m-10) REVERT: B 31 GLN cc_start: 0.7790 (tp-100) cc_final: 0.7134 (tt0) outliers start: 13 outliers final: 7 residues processed: 60 average time/residue: 0.6776 time to fit residues: 43.8413 Evaluate side-chains 62 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 239 MET 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 167 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 113 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 118 optimal weight: 7.9990 chunk 117 optimal weight: 30.0000 chunk 20 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 123 optimal weight: 20.0000 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.3471 r_free = 0.3471 target = 0.058431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.038447 restraints weight = 42033.259| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 3.57 r_work: 0.2648 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10405 Z= 0.177 Angle : 0.566 9.293 14059 Z= 0.285 Chirality : 0.041 0.175 1534 Planarity : 0.003 0.034 1792 Dihedral : 8.424 125.667 1428 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.20 % Allowed : 8.76 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.24), residues: 1235 helix: 1.97 (0.22), residues: 607 sheet: 0.76 (0.41), residues: 163 loop : 0.40 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 712 TYR 0.010 0.001 TYR A 259 PHE 0.010 0.001 PHE B 16 TRP 0.013 0.002 TRP C 340 HIS 0.004 0.001 HIS A 81 Details of bonding type rmsd covalent geometry : bond 0.00407 (10403) covalent geometry : angle 0.56562 (14053) hydrogen bonds : bond 0.03582 ( 512) hydrogen bonds : angle 4.49706 ( 1437) link_TRANS : bond 0.00202 ( 2) link_TRANS : angle 0.50348 ( 6) *********************** 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 66 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8603 (mtm) REVERT: A 305 MET cc_start: 0.9451 (tpp) cc_final: 0.8872 (tpp) REVERT: A 439 TYR cc_start: 0.9403 (OUTLIER) cc_final: 0.9145 (p90) REVERT: A 467 MET cc_start: 0.9269 (mmm) cc_final: 0.9044 (mmm) REVERT: A 478 MET cc_start: 0.9089 (mmp) cc_final: 0.8534 (mmp) REVERT: A 484 TRP cc_start: 0.7914 (m-10) cc_final: 0.7505 (m-90) REVERT: A 503 MET cc_start: 0.9203 (mmp) cc_final: 0.8932 (mmp) REVERT: A 715 MET cc_start: 0.9237 (pmt) cc_final: 0.9026 (pmm) REVERT: A 790 MET cc_start: 0.4067 (tpt) cc_final: 0.3762 (ppp) REVERT: C 176 MET cc_start: 0.9232 (tpp) cc_final: 0.8801 (mmm) REVERT: C 227 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.8002 (tpt) REVERT: C 283 MET cc_start: 0.8665 (mmm) cc_final: 0.8347 (mmm) REVERT: B 29 TYR cc_start: 0.7824 (m-80) cc_final: 0.7463 (m-10) REVERT: B 31 GLN cc_start: 0.7795 (tp-100) cc_final: 0.7132 (tt0) outliers start: 13 outliers final: 7 residues processed: 59 average time/residue: 0.6804 time to fit residues: 43.2081 Evaluate side-chains 62 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 439 TYR 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 65 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 105 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3480 r_free = 0.3480 target = 0.058607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.038609 restraints weight = 42170.736| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 3.59 r_work: 0.2682 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10405 Z= 0.133 Angle : 0.545 10.278 14059 Z= 0.274 Chirality : 0.040 0.173 1534 Planarity : 0.003 0.034 1792 Dihedral : 8.190 121.600 1428 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.11 % Allowed : 9.03 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.24), residues: 1235 helix: 2.03 (0.22), residues: 615 sheet: 0.78 (0.42), residues: 152 loop : 0.40 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 712 TYR 0.009 0.001 TYR A 79 PHE 0.011 0.001 PHE B 16 TRP 0.013 0.001 TRP C 340 HIS 0.004 0.001 HIS A 81 Details of bonding type rmsd covalent geometry : bond 0.00302 (10403) covalent geometry : angle 0.54512 (14053) hydrogen bonds : bond 0.03293 ( 512) hydrogen bonds : angle 4.41915 ( 1437) link_TRANS : bond 0.00160 ( 2) link_TRANS : angle 0.53880 ( 6) *********************** 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 65 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.9454 (tpp) cc_final: 0.8888 (tpp) REVERT: A 418 HIS cc_start: 0.8561 (OUTLIER) cc_final: 0.8298 (m-70) REVERT: A 467 MET cc_start: 0.9283 (mmm) cc_final: 0.9014 (mmm) REVERT: A 478 MET cc_start: 0.9070 (mmp) cc_final: 0.8493 (mmp) REVERT: A 484 TRP cc_start: 0.7901 (m-10) cc_final: 0.7507 (m-90) REVERT: A 503 MET cc_start: 0.9205 (mmp) cc_final: 0.8950 (mmp) REVERT: A 790 MET cc_start: 0.4330 (tpt) cc_final: 0.4036 (ppp) REVERT: C 176 MET cc_start: 0.9223 (tpp) cc_final: 0.8806 (mmm) REVERT: C 283 MET cc_start: 0.8661 (mmm) cc_final: 0.8302 (mmm) REVERT: C 355 MET cc_start: 0.9535 (OUTLIER) cc_final: 0.9080 (mmm) REVERT: B 29 TYR cc_start: 0.7806 (m-80) cc_final: 0.7474 (m-10) REVERT: B 31 GLN cc_start: 0.7732 (tp-100) cc_final: 0.7111 (tt0) REVERT: B 105 MET cc_start: 0.9097 (mmp) cc_final: 0.8788 (tpp) outliers start: 12 outliers final: 8 residues processed: 59 average time/residue: 0.6236 time to fit residues: 39.8002 Evaluate side-chains 61 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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 418 HIS 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 C residue 355 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 11 optimal weight: 0.0470 chunk 47 optimal weight: 3.9990 chunk 117 optimal weight: 30.0000 chunk 22 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 95 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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 = 0.3494 r_free = 0.3494 target = 0.058823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.038069 restraints weight = 42102.784| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 3.74 r_work: 0.2687 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10405 Z= 0.112 Angle : 0.544 11.562 14059 Z= 0.269 Chirality : 0.040 0.172 1534 Planarity : 0.003 0.037 1792 Dihedral : 8.014 117.125 1428 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.83 % Allowed : 9.40 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.24), residues: 1235 helix: 2.07 (0.22), residues: 613 sheet: 0.75 (0.42), residues: 153 loop : 0.48 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 712 TYR 0.010 0.001 TYR A 79 PHE 0.011 0.001 PHE B 12 TRP 0.013 0.001 TRP C 340 HIS 0.003 0.001 HIS A 81 Details of bonding type rmsd covalent geometry : bond 0.00257 (10403) covalent geometry : angle 0.54386 (14053) hydrogen bonds : bond 0.03169 ( 512) hydrogen bonds : angle 4.35911 ( 1437) link_TRANS : bond 0.00136 ( 2) link_TRANS : angle 0.58168 ( 6) *********************** 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 60 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.9222 (ttp) cc_final: 0.8986 (ttm) REVERT: A 305 MET cc_start: 0.9464 (tpp) cc_final: 0.8876 (tpp) REVERT: A 418 HIS cc_start: 0.8558 (OUTLIER) cc_final: 0.8272 (m-70) REVERT: A 467 MET cc_start: 0.9299 (mmm) cc_final: 0.9053 (mmm) REVERT: A 478 MET cc_start: 0.9077 (mmp) cc_final: 0.8554 (mmp) REVERT: A 484 TRP cc_start: 0.7991 (m-10) cc_final: 0.7636 (m-90) REVERT: A 503 MET cc_start: 0.9189 (mmp) cc_final: 0.8844 (mmp) REVERT: A 790 MET cc_start: 0.3922 (tpt) cc_final: 0.3328 (mmm) REVERT: C 283 MET cc_start: 0.8659 (mmm) cc_final: 0.8385 (mmm) REVERT: B 29 TYR cc_start: 0.7783 (m-80) cc_final: 0.7498 (m-10) REVERT: B 31 GLN cc_start: 0.7639 (tp-100) cc_final: 0.7015 (tt0) outliers start: 9 outliers final: 6 residues processed: 55 average time/residue: 0.6485 time to fit residues: 38.5824 Evaluate side-chains 58 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 HIS 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 103 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 1 optimal weight: 0.4980 chunk 8 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3493 r_free = 0.3493 target = 0.059148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.039020 restraints weight = 41414.296| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 3.60 r_work: 0.2697 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10405 Z= 0.121 Angle : 0.544 10.327 14059 Z= 0.271 Chirality : 0.040 0.173 1534 Planarity : 0.003 0.038 1792 Dihedral : 7.897 115.598 1428 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.55 % Allowed : 9.77 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.25), residues: 1235 helix: 2.10 (0.22), residues: 614 sheet: 0.72 (0.42), residues: 153 loop : 0.49 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 712 TYR 0.009 0.001 TYR A 79 PHE 0.011 0.001 PHE B 16 TRP 0.012 0.001 TRP C 340 HIS 0.003 0.001 HIS A 81 Details of bonding type rmsd covalent geometry : bond 0.00278 (10403) covalent geometry : angle 0.54412 (14053) hydrogen bonds : bond 0.03213 ( 512) hydrogen bonds : angle 4.33657 ( 1437) link_TRANS : bond 0.00129 ( 2) link_TRANS : angle 0.58265 ( 6) ********************** 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 59 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.9232 (ttp) cc_final: 0.8986 (ttm) REVERT: A 418 HIS cc_start: 0.8565 (OUTLIER) cc_final: 0.8282 (m-70) REVERT: A 467 MET cc_start: 0.9300 (mmm) cc_final: 0.9052 (mmm) REVERT: A 478 MET cc_start: 0.9081 (mmp) cc_final: 0.8599 (mmp) REVERT: A 484 TRP cc_start: 0.7940 (m-10) cc_final: 0.7563 (m-90) REVERT: A 503 MET cc_start: 0.9197 (mmp) cc_final: 0.8852 (mmp) REVERT: A 788 MET cc_start: 0.8219 (mpp) cc_final: 0.7738 (mmm) REVERT: A 790 MET cc_start: 0.3801 (tpt) cc_final: 0.3430 (mmm) REVERT: C 176 MET cc_start: 0.9235 (tpp) cc_final: 0.8990 (mmm) REVERT: C 283 MET cc_start: 0.8641 (mmm) cc_final: 0.8386 (mmm) REVERT: B 29 TYR cc_start: 0.7803 (m-80) cc_final: 0.7499 (m-10) REVERT: B 31 GLN cc_start: 0.7639 (tp-100) cc_final: 0.6977 (tt0) REVERT: B 105 MET cc_start: 0.9087 (mmp) cc_final: 0.8802 (tpp) outliers start: 6 outliers final: 6 residues processed: 57 average time/residue: 0.6204 time to fit residues: 38.2975 Evaluate side-chains 58 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 HIS 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 6 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.3472 r_free = 0.3472 target = 0.058024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.037295 restraints weight = 42091.215| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 3.68 r_work: 0.2658 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10405 Z= 0.187 Angle : 0.581 12.255 14059 Z= 0.287 Chirality : 0.041 0.175 1534 Planarity : 0.003 0.039 1792 Dihedral : 7.948 115.703 1428 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.55 % Allowed : 10.05 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.24), residues: 1235 helix: 2.10 (0.22), residues: 612 sheet: 0.77 (0.41), residues: 163 loop : 0.43 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 712 TYR 0.012 0.001 TYR A 259 PHE 0.010 0.001 PHE B 16 TRP 0.010 0.001 TRP C 340 HIS 0.003 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00432 (10403) covalent geometry : angle 0.58079 (14053) hydrogen bonds : bond 0.03514 ( 512) hydrogen bonds : angle 4.38362 ( 1437) link_TRANS : bond 0.00188 ( 2) link_TRANS : angle 0.52839 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3572.40 seconds wall clock time: 61 minutes 39.50 seconds (3699.50 seconds total)