Starting phenix.real_space_refine on Mon Jul 28 19:55:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pmd_13529/07_2025/7pmd_13529.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pmd_13529/07_2025/7pmd_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_13529/07_2025/7pmd_13529.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pmd_13529/07_2025/7pmd_13529.map" model { file = "/net/cci-nas-00/data/ceres_data/7pmd_13529/07_2025/7pmd_13529.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pmd_13529/07_2025/7pmd_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 7.34, per 1000 atoms: 0.72 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: 2.57 Conformation dependent library (CDL) restraints added in 1.6 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: 1.31 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: 3.41 Time building geometry restraints manager: 3.01 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: 1.500 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: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 28.200 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 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:11.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.050 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd link_TRANS : bond 0.01563 ( 2) link_TRANS : angle 4.01430 ( 6) hydrogen bonds : bond 0.15121 ( 512) hydrogen bonds : angle 6.71572 ( 1437) covalent geometry : bond 0.01213 (10403) covalent geometry : angle 1.05733 (14053) *********************** 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 : 1.420 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: 1.7049 time to fit residues: 164.7598 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 : 1.279 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.059555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.038699 restraints weight = 40822.972| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 3.67 r_work: 0.2692 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 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 10405 Z= 0.143 Angle : 0.623 6.777 14059 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 Details of bonding type rmsd link_TRANS : bond 0.00059 ( 2) link_TRANS : angle 0.55688 ( 6) hydrogen bonds : bond 0.04092 ( 512) hydrogen bonds : angle 4.91908 ( 1437) covalent geometry : bond 0.00319 (10403) covalent geometry : angle 0.62320 (14053) *********************** 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 : 1.304 Fit side-chains revert: symmetry clash REVERT: A 135 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8487 (mtp) REVERT: A 478 MET cc_start: 0.8839 (mmp) cc_final: 0.8405 (mmp) REVERT: A 484 TRP cc_start: 0.7607 (m-10) cc_final: 0.7292 (m-90) REVERT: C 299 MET cc_start: 0.9495 (OUTLIER) cc_final: 0.9159 (mtm) REVERT: B 31 GLN cc_start: 0.7646 (tp-100) cc_final: 0.7006 (tt0) REVERT: B 36 MET cc_start: 0.7424 (mtt) cc_final: 0.7191 (mpp) outliers start: 12 outliers final: 7 residues processed: 62 average time/residue: 1.5845 time to fit residues: 105.7228 Evaluate side-chains 58 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 1.287 ------------------------------------------------------------------------------- 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 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 37 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 2 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 122 optimal weight: 8.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.3496 r_free = 0.3496 target = 0.059607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.039258 restraints weight = 42222.398| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 3.68 r_work: 0.2674 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10405 Z= 0.162 Angle : 0.577 10.042 14059 Z= 0.296 Chirality : 0.041 0.186 1534 Planarity : 0.004 0.034 1792 Dihedral : 9.052 134.564 1429 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.01 % Allowed : 5.25 % Favored : 93.73 % 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: 1.57 (0.24), residues: 1235 helix: 1.47 (0.21), residues: 606 sheet: 0.96 (0.41), residues: 161 loop : 0.69 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 781 HIS 0.004 0.001 HIS A 81 PHE 0.011 0.001 PHE A 564 TYR 0.014 0.001 TYR C 294 ARG 0.006 0.000 ARG C 95 Details of bonding type rmsd link_TRANS : bond 0.00160 ( 2) link_TRANS : angle 0.53828 ( 6) hydrogen bonds : bond 0.03777 ( 512) hydrogen bonds : angle 4.60127 ( 1437) covalent geometry : bond 0.00371 (10403) covalent geometry : angle 0.57717 (14053) *********************** 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: 11 poor density : 51 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8376 (mtm) REVERT: A 478 MET cc_start: 0.8941 (mmp) cc_final: 0.8386 (mmp) REVERT: A 484 TRP cc_start: 0.7826 (m-10) cc_final: 0.7456 (m-90) REVERT: A 503 MET cc_start: 0.9251 (mmp) cc_final: 0.9035 (mmp) REVERT: A 790 MET cc_start: 0.4134 (tpt) cc_final: 0.3889 (ppp) REVERT: C 47 MET cc_start: 0.8863 (mmm) cc_final: 0.8621 (tmm) REVERT: C 82 MET cc_start: 0.9106 (tpt) cc_final: 0.8905 (tpt) REVERT: C 227 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.7941 (tpt) REVERT: B 31 GLN cc_start: 0.7768 (tp-100) cc_final: 0.7144 (tt0) outliers start: 11 outliers final: 7 residues processed: 55 average time/residue: 1.4413 time to fit residues: 85.6512 Evaluate side-chains 58 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 1.177 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 49 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 117 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 56 optimal weight: 0.4980 chunk 11 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.058938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.038358 restraints weight = 41621.323| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 3.67 r_work: 0.2686 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10405 Z= 0.126 Angle : 0.526 7.473 14059 Z= 0.270 Chirality : 0.040 0.182 1534 Planarity : 0.004 0.060 1792 Dihedral : 8.651 134.224 1429 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.74 % Allowed : 7.19 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.24), residues: 1235 helix: 1.71 (0.22), residues: 617 sheet: 0.98 (0.42), residues: 152 loop : 0.69 (0.29), residues: 466 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 0.011 0.001 PHE B 16 TYR 0.010 0.001 TYR C 294 ARG 0.014 0.000 ARG A 712 Details of bonding type rmsd link_TRANS : bond 0.00138 ( 2) link_TRANS : angle 0.58217 ( 6) hydrogen bonds : bond 0.03417 ( 512) hydrogen bonds : angle 4.49976 ( 1437) covalent geometry : bond 0.00287 (10403) covalent geometry : angle 0.52589 (14053) *********************** 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 to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8437 (mtm) REVERT: A 150 MET cc_start: 0.9223 (ttp) cc_final: 0.8972 (ttm) REVERT: A 467 MET cc_start: 0.9497 (ttp) cc_final: 0.9213 (mmm) REVERT: A 478 MET cc_start: 0.9017 (mmp) cc_final: 0.8464 (mmp) REVERT: A 484 TRP cc_start: 0.7863 (m-10) cc_final: 0.7485 (m-90) REVERT: A 503 MET cc_start: 0.9251 (mmp) cc_final: 0.9034 (mmp) REVERT: A 790 MET cc_start: 0.4004 (tpt) cc_final: 0.3745 (ppp) REVERT: C 47 MET cc_start: 0.8914 (mmm) cc_final: 0.8684 (mmm) REVERT: C 176 MET cc_start: 0.9262 (tpp) cc_final: 0.8944 (mmm) REVERT: B 31 GLN cc_start: 0.7884 (tp-100) cc_final: 0.7280 (tt0) outliers start: 8 outliers final: 6 residues processed: 55 average time/residue: 1.4371 time to fit residues: 85.6045 Evaluate side-chains 57 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 1.175 ------------------------------------------------------------------------------- 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 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 65 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 112 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 68 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 = 0.3467 r_free = 0.3467 target = 0.057934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.037211 restraints weight = 41941.741| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 3.68 r_work: 0.2646 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10405 Z= 0.228 Angle : 0.579 10.456 14059 Z= 0.294 Chirality : 0.042 0.185 1534 Planarity : 0.004 0.039 1792 Dihedral : 8.521 128.179 1428 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.11 % Allowed : 7.10 % Favored : 91.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.24), residues: 1235 helix: 1.87 (0.22), residues: 606 sheet: 0.88 (0.41), residues: 164 loop : 0.57 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 781 HIS 0.003 0.001 HIS A 81 PHE 0.011 0.001 PHE C 255 TYR 0.013 0.001 TYR A 259 ARG 0.008 0.000 ARG A 712 Details of bonding type rmsd link_TRANS : bond 0.00246 ( 2) link_TRANS : angle 0.51124 ( 6) hydrogen bonds : bond 0.03800 ( 512) hydrogen bonds : angle 4.53781 ( 1437) covalent geometry : bond 0.00525 (10403) covalent geometry : angle 0.57877 (14053) *********************** 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: 12 poor density : 52 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8487 (mtm) REVERT: A 305 MET cc_start: 0.9451 (tpp) cc_final: 0.8809 (tpp) REVERT: A 478 MET cc_start: 0.9079 (mmp) cc_final: 0.8526 (mmp) REVERT: A 484 TRP cc_start: 0.7932 (m-10) cc_final: 0.7509 (m-90) REVERT: A 503 MET cc_start: 0.9222 (mmp) cc_final: 0.8996 (mmp) REVERT: A 790 MET cc_start: 0.3912 (tpt) cc_final: 0.3666 (ppp) REVERT: C 47 MET cc_start: 0.8965 (mmm) cc_final: 0.8740 (mmm) REVERT: C 137 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.7463 (mp10) REVERT: C 167 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8580 (mp0) REVERT: C 176 MET cc_start: 0.9258 (tpp) cc_final: 0.8933 (mmm) REVERT: C 227 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.8047 (tpt) REVERT: C 283 MET cc_start: 0.8636 (mmm) cc_final: 0.8405 (mmm) REVERT: C 355 MET cc_start: 0.9524 (OUTLIER) cc_final: 0.9019 (mmm) REVERT: B 31 GLN cc_start: 0.7609 (tp-100) cc_final: 0.6940 (tt0) REVERT: B 36 MET cc_start: 0.7323 (mpp) cc_final: 0.7084 (mpp) REVERT: B 73 MET cc_start: 0.7833 (ptm) cc_final: 0.7627 (ppp) outliers start: 12 outliers final: 7 residues processed: 58 average time/residue: 1.3756 time to fit residues: 86.4743 Evaluate side-chains 63 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 1.282 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 13 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 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 = 0.3489 r_free = 0.3489 target = 0.059049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.039132 restraints weight = 42272.735| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 3.61 r_work: 0.2684 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10405 Z= 0.124 Angle : 0.527 9.003 14059 Z= 0.267 Chirality : 0.040 0.173 1534 Planarity : 0.003 0.033 1792 Dihedral : 8.257 125.654 1428 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.20 % Allowed : 8.02 % 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: 1.85 (0.24), residues: 1235 helix: 1.98 (0.22), residues: 608 sheet: 0.77 (0.42), residues: 150 loop : 0.52 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 781 HIS 0.003 0.001 HIS A 81 PHE 0.011 0.001 PHE B 12 TYR 0.009 0.001 TYR A 456 ARG 0.007 0.000 ARG A 712 Details of bonding type rmsd link_TRANS : bond 0.00160 ( 2) link_TRANS : angle 0.58030 ( 6) hydrogen bonds : bond 0.03271 ( 512) hydrogen bonds : angle 4.42847 ( 1437) covalent geometry : bond 0.00283 (10403) covalent geometry : angle 0.52700 (14053) *********************** 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 : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.8527 (mtm) REVERT: A 150 MET cc_start: 0.9219 (ttp) cc_final: 0.8980 (ttm) REVERT: A 305 MET cc_start: 0.9481 (tpp) cc_final: 0.8844 (tpp) REVERT: A 467 MET cc_start: 0.9498 (ttp) cc_final: 0.9207 (mmm) REVERT: A 478 MET cc_start: 0.9077 (mmp) cc_final: 0.8543 (mmp) REVERT: A 484 TRP cc_start: 0.7944 (m-10) cc_final: 0.7504 (m-90) REVERT: A 503 MET cc_start: 0.9192 (mmp) cc_final: 0.8916 (mmp) REVERT: A 790 MET cc_start: 0.3934 (tpt) cc_final: 0.3572 (ppp) REVERT: C 47 MET cc_start: 0.8981 (mmm) cc_final: 0.8726 (tmm) REVERT: C 137 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8328 (mm-40) REVERT: C 167 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8542 (mp0) REVERT: C 176 MET cc_start: 0.9255 (tpp) cc_final: 0.8927 (mmm) REVERT: C 283 MET cc_start: 0.8634 (mmm) cc_final: 0.8308 (mmm) REVERT: B 31 GLN cc_start: 0.7631 (tp-100) cc_final: 0.7027 (tt0) outliers start: 13 outliers final: 7 residues processed: 59 average time/residue: 1.3681 time to fit residues: 87.3139 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 : 1.138 ------------------------------------------------------------------------------- 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 691 ILE Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain C residue 137 GLN 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 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 7 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 93 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 62 optimal weight: 0.4980 chunk 50 optimal weight: 0.3980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3496 r_free = 0.3496 target = 0.059265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.039240 restraints weight = 42349.343| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 3.64 r_work: 0.2690 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2954 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= 0.116 Angle : 0.528 9.080 14059 Z= 0.265 Chirality : 0.040 0.171 1534 Planarity : 0.003 0.033 1792 Dihedral : 8.042 118.783 1428 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.47 % Allowed : 7.74 % 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: 1.88 (0.24), residues: 1235 helix: 2.02 (0.22), residues: 612 sheet: 0.71 (0.42), residues: 153 loop : 0.52 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 781 HIS 0.004 0.001 HIS A 81 PHE 0.014 0.001 PHE B 70 TYR 0.010 0.001 TYR A 79 ARG 0.005 0.000 ARG A 712 Details of bonding type rmsd link_TRANS : bond 0.00137 ( 2) link_TRANS : angle 0.58447 ( 6) hydrogen bonds : bond 0.03190 ( 512) hydrogen bonds : angle 4.36858 ( 1437) covalent geometry : bond 0.00265 (10403) covalent geometry : angle 0.52836 (14053) *********************** 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 70 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.9225 (ttp) cc_final: 0.8981 (ttm) REVERT: A 467 MET cc_start: 0.9500 (ttp) cc_final: 0.9211 (mmm) REVERT: A 478 MET cc_start: 0.9081 (mmp) cc_final: 0.8507 (mmp) REVERT: A 484 TRP cc_start: 0.7977 (m-10) cc_final: 0.7590 (m-90) REVERT: A 503 MET cc_start: 0.9174 (mmp) cc_final: 0.8901 (mmp) REVERT: A 790 MET cc_start: 0.3923 (tpt) cc_final: 0.3656 (ppp) REVERT: C 47 MET cc_start: 0.8981 (mmm) cc_final: 0.8734 (tmm) REVERT: C 137 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8318 (mm-40) REVERT: C 167 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8548 (mp0) REVERT: C 176 MET cc_start: 0.9262 (tpp) cc_final: 0.8925 (mmm) REVERT: C 283 MET cc_start: 0.8653 (mmm) cc_final: 0.8327 (mmm) REVERT: B 31 GLN cc_start: 0.7782 (tp-100) cc_final: 0.7099 (tt0) REVERT: B 105 MET cc_start: 0.9148 (mmp) cc_final: 0.8840 (tpp) outliers start: 16 outliers final: 8 residues processed: 64 average time/residue: 1.5213 time to fit residues: 105.3098 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 : 1.177 ------------------------------------------------------------------------------- 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 137 GLN 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 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 14 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 120 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 33 optimal weight: 0.0020 chunk 66 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.7192 ------------------------------------------------------------------------------- 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 = 0.3497 r_free = 0.3497 target = 0.059054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.038391 restraints weight = 41747.721| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 3.68 r_work: 0.2693 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10405 Z= 0.118 Angle : 0.533 10.124 14059 Z= 0.268 Chirality : 0.040 0.172 1534 Planarity : 0.003 0.033 1792 Dihedral : 7.919 115.726 1428 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.20 % Allowed : 8.11 % Favored : 90.69 % 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: 1.94 (0.24), residues: 1235 helix: 2.08 (0.22), residues: 613 sheet: 0.77 (0.43), residues: 153 loop : 0.53 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 781 HIS 0.003 0.001 HIS A 81 PHE 0.011 0.001 PHE B 16 TYR 0.009 0.001 TYR A 79 ARG 0.003 0.000 ARG A 712 Details of bonding type rmsd link_TRANS : bond 0.00129 ( 2) link_TRANS : angle 0.58747 ( 6) hydrogen bonds : bond 0.03143 ( 512) hydrogen bonds : angle 4.33800 ( 1437) covalent geometry : bond 0.00270 (10403) covalent geometry : angle 0.53305 (14053) *********************** 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 66 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.9215 (ttp) cc_final: 0.8967 (ttm) REVERT: A 305 MET cc_start: 0.9456 (tpp) cc_final: 0.8751 (tpp) REVERT: A 467 MET cc_start: 0.9500 (ttp) cc_final: 0.9215 (mmm) REVERT: A 478 MET cc_start: 0.9091 (mmp) cc_final: 0.8558 (mmp) REVERT: A 484 TRP cc_start: 0.8000 (m-10) cc_final: 0.7608 (m-90) REVERT: A 503 MET cc_start: 0.9180 (mmp) cc_final: 0.8890 (mmp) REVERT: A 790 MET cc_start: 0.3980 (tpt) cc_final: 0.3719 (ppp) REVERT: C 47 MET cc_start: 0.9014 (mmm) cc_final: 0.8747 (tmm) REVERT: C 137 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8331 (mm-40) REVERT: C 167 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8548 (mp0) REVERT: C 176 MET cc_start: 0.9264 (tpp) cc_final: 0.8885 (mmm) REVERT: C 283 MET cc_start: 0.8648 (mmm) cc_final: 0.8308 (mmm) REVERT: B 29 TYR cc_start: 0.7833 (m-80) cc_final: 0.7497 (m-10) REVERT: B 31 GLN cc_start: 0.7927 (tp-100) cc_final: 0.7231 (tt0) REVERT: B 105 MET cc_start: 0.9159 (mmp) cc_final: 0.8854 (tpp) outliers start: 13 outliers final: 7 residues processed: 61 average time/residue: 1.8015 time to fit residues: 118.4328 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 : 1.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain C residue 137 GLN 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 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 57 optimal weight: 0.0670 chunk 41 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 121 optimal weight: 0.0020 chunk 46 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.9328 ------------------------------------------------------------------------------- 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 = 0.3490 r_free = 0.3490 target = 0.058997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.038824 restraints weight = 42206.393| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 3.62 r_work: 0.2683 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10405 Z= 0.138 Angle : 0.545 11.797 14059 Z= 0.271 Chirality : 0.040 0.173 1534 Planarity : 0.003 0.033 1792 Dihedral : 7.852 115.241 1428 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.11 % Allowed : 8.20 % Favored : 90.69 % 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: 1.99 (0.24), residues: 1235 helix: 2.13 (0.22), residues: 611 sheet: 0.78 (0.43), residues: 153 loop : 0.55 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 781 HIS 0.003 0.001 HIS A 81 PHE 0.010 0.001 PHE B 12 TYR 0.009 0.001 TYR A 259 ARG 0.004 0.000 ARG A 712 Details of bonding type rmsd link_TRANS : bond 0.00138 ( 2) link_TRANS : angle 0.56695 ( 6) hydrogen bonds : bond 0.03270 ( 512) hydrogen bonds : angle 4.33906 ( 1437) covalent geometry : bond 0.00319 (10403) covalent geometry : angle 0.54505 (14053) *********************** 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 64 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.9222 (ttp) cc_final: 0.8972 (ttm) REVERT: A 305 MET cc_start: 0.9451 (tpp) cc_final: 0.8708 (tpp) REVERT: A 467 MET cc_start: 0.9481 (ttp) cc_final: 0.9191 (mmm) REVERT: A 478 MET cc_start: 0.9096 (mmp) cc_final: 0.8585 (mmp) REVERT: A 484 TRP cc_start: 0.8017 (m-10) cc_final: 0.7624 (m-90) REVERT: A 503 MET cc_start: 0.9177 (mmp) cc_final: 0.8873 (mmp) REVERT: A 790 MET cc_start: 0.3885 (tpt) cc_final: 0.3054 (mmm) REVERT: C 47 MET cc_start: 0.9005 (mmm) cc_final: 0.8738 (tmm) REVERT: C 137 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.7463 (mp10) REVERT: C 167 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8534 (mp0) REVERT: C 176 MET cc_start: 0.9265 (tpp) cc_final: 0.8896 (mmm) REVERT: C 283 MET cc_start: 0.8653 (mmm) cc_final: 0.8328 (mmm) REVERT: B 29 TYR cc_start: 0.7821 (m-80) cc_final: 0.7496 (m-10) REVERT: B 31 GLN cc_start: 0.7706 (tp-100) cc_final: 0.7000 (tt0) REVERT: B 105 MET cc_start: 0.9142 (mmp) cc_final: 0.8840 (tpp) outliers start: 12 outliers final: 6 residues processed: 59 average time/residue: 1.4232 time to fit residues: 91.3365 Evaluate side-chains 60 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain C residue 137 GLN 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 B residue 44 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 2 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 115 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 76 optimal weight: 0.0570 chunk 1 optimal weight: 0.3980 chunk 44 optimal weight: 0.7980 overall best weight: 0.9900 ------------------------------------------------------------------------------- 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 = 0.3490 r_free = 0.3490 target = 0.058731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.038009 restraints weight = 41954.181| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 3.68 r_work: 0.2682 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10405 Z= 0.143 Angle : 0.545 10.556 14059 Z= 0.273 Chirality : 0.040 0.172 1534 Planarity : 0.003 0.033 1792 Dihedral : 7.802 115.839 1428 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.83 % Allowed : 8.76 % 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 (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: 1.99 (0.25), residues: 1235 helix: 2.15 (0.22), residues: 611 sheet: 0.70 (0.43), residues: 154 loop : 0.56 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 340 HIS 0.003 0.001 HIS A 81 PHE 0.010 0.001 PHE B 16 TYR 0.009 0.001 TYR A 259 ARG 0.004 0.000 ARG A 712 Details of bonding type rmsd link_TRANS : bond 0.00148 ( 2) link_TRANS : angle 0.56269 ( 6) hydrogen bonds : bond 0.03287 ( 512) hydrogen bonds : angle 4.33817 ( 1437) covalent geometry : bond 0.00331 (10403) covalent geometry : angle 0.54477 (14053) ********************** 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 61 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.9228 (ttp) cc_final: 0.8976 (ttm) REVERT: A 305 MET cc_start: 0.9468 (tpp) cc_final: 0.8763 (tpp) REVERT: A 478 MET cc_start: 0.9101 (mmp) cc_final: 0.8594 (mmp) REVERT: A 484 TRP cc_start: 0.8047 (m-10) cc_final: 0.7649 (m-90) REVERT: A 503 MET cc_start: 0.9192 (mmp) cc_final: 0.8883 (mmp) REVERT: A 788 MET cc_start: 0.8296 (mpp) cc_final: 0.7811 (mmm) REVERT: A 790 MET cc_start: 0.3757 (tpt) cc_final: 0.3330 (mmm) REVERT: C 47 MET cc_start: 0.8994 (mmm) cc_final: 0.8728 (tmm) REVERT: C 137 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.7486 (mp10) REVERT: C 167 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8553 (mp0) REVERT: C 176 MET cc_start: 0.9261 (tpp) cc_final: 0.8870 (mmm) REVERT: C 283 MET cc_start: 0.8626 (mmm) cc_final: 0.8304 (mmm) REVERT: B 29 TYR cc_start: 0.7837 (m-80) cc_final: 0.7515 (m-10) REVERT: B 31 GLN cc_start: 0.7585 (tp-100) cc_final: 0.6921 (tt0) REVERT: B 105 MET cc_start: 0.8965 (mmp) cc_final: 0.8757 (tpp) outliers start: 9 outliers final: 6 residues processed: 58 average time/residue: 1.4110 time to fit residues: 88.7646 Evaluate side-chains 61 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain C residue 137 GLN 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 B residue 44 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.6980 chunk 33 optimal weight: 0.0970 chunk 94 optimal weight: 0.9990 chunk 53 optimal weight: 0.4980 chunk 21 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 117 optimal weight: 20.0000 chunk 68 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 238 ASN ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.059416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.039270 restraints weight = 41617.956| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 3.64 r_work: 0.2701 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10405 Z= 0.107 Angle : 0.530 10.404 14059 Z= 0.263 Chirality : 0.040 0.171 1534 Planarity : 0.003 0.033 1792 Dihedral : 7.668 116.024 1428 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 3.85 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: 2.02 (0.25), residues: 1235 helix: 2.18 (0.22), residues: 613 sheet: 0.71 (0.43), residues: 154 loop : 0.55 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 340 HIS 0.003 0.001 HIS A 81 PHE 0.011 0.001 PHE B 16 TYR 0.009 0.001 TYR A 79 ARG 0.003 0.000 ARG A 712 Details of bonding type rmsd link_TRANS : bond 0.00128 ( 2) link_TRANS : angle 0.58757 ( 6) hydrogen bonds : bond 0.03090 ( 512) hydrogen bonds : angle 4.28519 ( 1437) covalent geometry : bond 0.00244 (10403) covalent geometry : angle 0.53008 (14053) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7974.75 seconds wall clock time: 141 minutes 45.13 seconds (8505.13 seconds total)