Starting phenix.real_space_refine on Thu Jul 2 05:47:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yg4_72912/07_2026/9yg4_72912.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yg4_72912/07_2026/9yg4_72912.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yg4_72912/07_2026/9yg4_72912.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yg4_72912/07_2026/9yg4_72912.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yg4_72912/07_2026/9yg4_72912.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yg4_72912/07_2026/9yg4_72912.map" } resolution = 3.38 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= 1.000 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: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 4318 2.51 5 N 1119 2.21 5 O 1276 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6741 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1156 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain: "B" Number of atoms: 5585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5585 Classifications: {'peptide': 684} Link IDs: {'PTRANS': 34, 'TRANS': 649} Chain breaks: 4 Time building chain proxies: 1.72, per 1000 atoms: 0.26 Number of scatterers: 6741 At special positions: 0 Unit cell: (91.52, 114.816, 99.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 1276 8.00 N 1119 7.00 C 4318 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 Time building additional restraints: 0.52 Conformation dependent library (CDL) restraints added in 419.6 milliseconds 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1602 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 2 sheets defined 39.6% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'C' and resid 6 through 20 removed outlier: 3.522A pdb=" N ILE C 10 " --> pdb=" O THR C 6 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE C 20 " --> pdb=" O ALA C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 41 Processing helix chain 'C' and resid 45 through 57 removed outlier: 4.217A pdb=" N ASP C 57 " --> pdb=" O ILE C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 77 Processing helix chain 'C' and resid 81 through 94 Processing helix chain 'C' and resid 102 through 114 Processing helix chain 'C' and resid 118 through 130 Processing helix chain 'C' and resid 138 through 147 removed outlier: 3.608A pdb=" N THR C 147 " --> pdb=" O VAL C 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 127 removed outlier: 3.741A pdb=" N GLU B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 150 removed outlier: 3.630A pdb=" N ASN B 150 " --> pdb=" O GLN B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 237 Processing helix chain 'B' and resid 292 through 312 Processing helix chain 'B' and resid 313 through 318 removed outlier: 4.616A pdb=" N LYS B 316 " --> pdb=" O PRO B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 342 Processing helix chain 'B' and resid 342 through 349 removed outlier: 4.270A pdb=" N ARG B 346 " --> pdb=" O ASN B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 374 Processing helix chain 'B' and resid 379 through 393 Processing helix chain 'B' and resid 394 through 413 Processing helix chain 'B' and resid 459 through 470 removed outlier: 3.591A pdb=" N LYS B 463 " --> pdb=" O THR B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 605 Processing helix chain 'B' and resid 632 through 635 removed outlier: 3.900A pdb=" N LEU B 635 " --> pdb=" O ALA B 632 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 632 through 635' Processing helix chain 'B' and resid 636 through 641 Processing helix chain 'B' and resid 661 through 663 No H-bonds generated for 'chain 'B' and resid 661 through 663' Processing helix chain 'B' and resid 684 through 688 removed outlier: 3.852A pdb=" N GLU B 687 " --> pdb=" O SER B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 704 Processing helix chain 'B' and resid 726 through 731 Processing helix chain 'B' and resid 778 through 791 Processing sheet with id=AA1, first strand: chain 'C' and resid 27 through 29 Processing sheet with id=AA2, first strand: chain 'B' and resid 35 through 42 removed outlier: 7.026A pdb=" N GLY B 63 " --> pdb=" O ASN B 40 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N GLN B 42 " --> pdb=" O HIS B 61 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N HIS B 61 " --> pdb=" O GLN B 42 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LYS B 58 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ILE B 90 " --> pdb=" O LYS B 58 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLY B 60 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU B 88 " --> pdb=" O GLY B 60 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE B 62 " --> pdb=" O ILE B 86 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ILE B 86 " --> pdb=" O ILE B 62 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N GLU B 80 " --> pdb=" O VAL B 153 " (cutoff:3.500A) removed outlier: 10.127A pdb=" N ILE B 155 " --> pdb=" O GLU B 80 " (cutoff:3.500A) removed outlier: 8.804A pdb=" N VAL B 82 " --> pdb=" O ILE B 155 " (cutoff:3.500A) removed outlier: 10.450A pdb=" N SER B 157 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLU B 84 " --> pdb=" O SER B 157 " (cutoff:3.500A) removed outlier: 8.943A pdb=" N HIS B 159 " --> pdb=" O GLU B 84 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ILE B 86 " --> pdb=" O HIS B 159 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N ARG B 161 " --> pdb=" O ILE B 86 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU B 88 " --> pdb=" O ARG B 161 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N GLU B 163 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE B 90 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N LEU B 151 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR B 186 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN B 180 " --> pdb=" O SER B 157 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N HIS B 159 " --> pdb=" O SER B 178 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N SER B 178 " --> pdb=" O HIS B 159 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ARG B 161 " --> pdb=" O GLY B 176 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLY B 176 " --> pdb=" O ARG B 161 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLU B 163 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N SER B 174 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ASN B 211 " --> pdb=" O GLN B 180 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU B 182 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU B 209 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N MET B 184 " --> pdb=" O ILE B 207 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE B 207 " --> pdb=" O MET B 184 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N THR B 186 " --> pdb=" O LYS B 205 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LYS B 205 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ILE B 256 " --> pdb=" O ASN B 211 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 277 through 283 current: chain 'B' and resid 488 through 502 removed outlier: 6.833A pdb=" N LYS B 489 " --> pdb=" O VAL B 523 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL B 523 " --> pdb=" O LYS B 489 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N PHE B 491 " --> pdb=" O LEU B 521 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU B 521 " --> pdb=" O PHE B 491 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N HIS B 493 " --> pdb=" O SER B 519 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N SER B 519 " --> pdb=" O HIS B 493 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LYS B 495 " --> pdb=" O GLU B 517 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL B 511 " --> pdb=" O LEU B 501 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N PHE B 518 " --> pdb=" O ILE B 537 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE B 537 " --> pdb=" O PHE B 518 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR B 520 " --> pdb=" O THR B 535 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N THR B 535 " --> pdb=" O THR B 520 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE B 522 " --> pdb=" O PHE B 533 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N PHE B 533 " --> pdb=" O ILE B 522 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLN B 524 " --> pdb=" O ILE B 531 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE B 531 " --> pdb=" O GLN B 524 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 553 through 556 current: chain 'B' and resid 582 through 585 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 582 through 585 current: chain 'B' and resid 648 through 659 removed outlier: 6.507A pdb=" N LYS B 648 " --> pdb=" O THR B 681 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR B 681 " --> pdb=" O LYS B 648 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASN B 650 " --> pdb=" O LYS B 679 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LYS B 679 " --> pdb=" O ASN B 650 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LYS B 652 " --> pdb=" O HIS B 677 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N SER B 654 " --> pdb=" O LEU B 675 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLY B 676 " --> pdb=" O SER B 715 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N SER B 715 " --> pdb=" O GLY B 676 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LEU B 678 " --> pdb=" O LEU B 713 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LEU B 713 " --> pdb=" O LEU B 678 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL B 680 " --> pdb=" O ILE B 711 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE B 711 " --> pdb=" O VAL B 680 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N SER B 682 " --> pdb=" O PHE B 709 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N PHE B 709 " --> pdb=" O SER B 682 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER B 715 " --> pdb=" O MET B 744 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N MET B 744 " --> pdb=" O SER B 715 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLN B 717 " --> pdb=" O VAL B 742 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL B 742 " --> pdb=" O GLN B 717 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LEU B 719 " --> pdb=" O ILE B 740 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N ILE B 740 " --> pdb=" O LEU B 719 " (cutoff:3.500A) 294 hydrogen bonds defined for protein. 867 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: 1.06 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2196 1.35 - 1.46: 1449 1.46 - 1.58: 3169 1.58 - 1.70: 0 1.70 - 1.82: 53 Bond restraints: 6867 Sorted by residual: bond pdb=" CA GLN C 42 " pdb=" C GLN C 42 " ideal model delta sigma weight residual 1.522 1.505 0.017 1.23e-02 6.61e+03 1.86e+00 bond pdb=" CA PHE B 756 " pdb=" CB PHE B 756 " ideal model delta sigma weight residual 1.528 1.544 -0.016 1.39e-02 5.18e+03 1.37e+00 bond pdb=" CB LEU B 636 " pdb=" CG LEU B 636 " ideal model delta sigma weight residual 1.530 1.510 0.020 2.00e-02 2.50e+03 1.02e+00 bond pdb=" CB LYS B 318 " pdb=" CG LYS B 318 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.01e+00 bond pdb=" N GLN C 42 " pdb=" CA GLN C 42 " ideal model delta sigma weight residual 1.454 1.441 0.013 1.29e-02 6.01e+03 9.66e-01 ... (remaining 6862 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 9107 2.22 - 4.45: 137 4.45 - 6.67: 20 6.67 - 8.89: 4 8.89 - 11.12: 2 Bond angle restraints: 9270 Sorted by residual: angle pdb=" N GLN C 42 " pdb=" CA GLN C 42 " pdb=" C GLN C 42 " ideal model delta sigma weight residual 109.52 117.16 -7.64 1.55e+00 4.16e-01 2.43e+01 angle pdb=" N ASN C 43 " pdb=" CA ASN C 43 " pdb=" CB ASN C 43 " ideal model delta sigma weight residual 110.99 117.29 -6.30 1.58e+00 4.01e-01 1.59e+01 angle pdb=" N GLN C 42 " pdb=" CA GLN C 42 " pdb=" CB GLN C 42 " ideal model delta sigma weight residual 111.55 105.06 6.49 1.74e+00 3.30e-01 1.39e+01 angle pdb=" CB MET C 145 " pdb=" CG MET C 145 " pdb=" SD MET C 145 " ideal model delta sigma weight residual 112.70 123.82 -11.12 3.00e+00 1.11e-01 1.37e+01 angle pdb=" N MET B 757 " pdb=" CA MET B 757 " pdb=" C MET B 757 " ideal model delta sigma weight residual 114.62 110.47 4.15 1.14e+00 7.69e-01 1.32e+01 ... (remaining 9265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.05: 3637 18.05 - 36.09: 468 36.09 - 54.14: 94 54.14 - 72.19: 26 72.19 - 90.24: 10 Dihedral angle restraints: 4235 sinusoidal: 1783 harmonic: 2452 Sorted by residual: dihedral pdb=" CA GLU C 55 " pdb=" C GLU C 55 " pdb=" N VAL C 56 " pdb=" CA VAL C 56 " ideal model delta harmonic sigma weight residual -180.00 -156.37 -23.63 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA TYR B 215 " pdb=" C TYR B 215 " pdb=" N TRP B 216 " pdb=" CA TRP B 216 " ideal model delta harmonic sigma weight residual 180.00 162.68 17.32 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA ASP B 227 " pdb=" CB ASP B 227 " pdb=" CG ASP B 227 " pdb=" OD1 ASP B 227 " ideal model delta sinusoidal sigma weight residual -30.00 -88.58 58.58 1 2.00e+01 2.50e-03 1.15e+01 ... (remaining 4232 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 734 0.042 - 0.084: 218 0.084 - 0.127: 85 0.127 - 0.169: 12 0.169 - 0.211: 2 Chirality restraints: 1051 Sorted by residual: chirality pdb=" CB THR C 30 " pdb=" CA THR C 30 " pdb=" OG1 THR C 30 " pdb=" CG2 THR C 30 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CB ILE B 335 " pdb=" CA ILE B 335 " pdb=" CG1 ILE B 335 " pdb=" CG2 ILE B 335 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.18e-01 chirality pdb=" CB THR C 71 " pdb=" CA THR C 71 " pdb=" OG1 THR C 71 " pdb=" CG2 THR C 71 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.78e-01 ... (remaining 1048 not shown) Planarity restraints: 1183 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 756 " 0.015 2.00e-02 2.50e+03 2.06e-02 7.45e+00 pdb=" CG PHE B 756 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE B 756 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE B 756 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE B 756 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 756 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 756 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 756 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.37e+00 pdb=" C PHE B 756 " 0.036 2.00e-02 2.50e+03 pdb=" O PHE B 756 " -0.014 2.00e-02 2.50e+03 pdb=" N MET B 757 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 587 " -0.033 5.00e-02 4.00e+02 4.97e-02 3.95e+00 pdb=" N PRO B 588 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 588 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 588 " -0.028 5.00e-02 4.00e+02 ... (remaining 1180 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 9 2.45 - 3.06: 4562 3.06 - 3.68: 10427 3.68 - 4.29: 14548 4.29 - 4.90: 24246 Nonbonded interactions: 53792 Sorted by model distance: nonbonded pdb=" NE2 GLN C 42 " pdb=" O MET B 349 " model vdw 1.841 3.120 nonbonded pdb=" O ASP B 271 " pdb=" OD1 ASP B 271 " model vdw 1.984 3.040 nonbonded pdb=" NH2 ARG C 107 " pdb=" OD1 ASP C 119 " model vdw 2.060 3.120 nonbonded pdb=" OG1 THR B 681 " pdb=" OD1 ASP B 710 " model vdw 2.102 3.040 nonbonded pdb=" CG2 THR C 27 " pdb=" OG1 THR C 63 " model vdw 2.107 3.460 ... (remaining 53787 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: 27.250 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: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.970 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: 0.010 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 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 : 0.004 0.032 6867 Z= 0.159 Angle : 0.684 11.116 9270 Z= 0.361 Chirality : 0.047 0.211 1051 Planarity : 0.004 0.050 1183 Dihedral : 17.196 90.236 2633 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.79 % Allowed : 20.24 % Favored : 78.97 % 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: 0.02 (0.31), residues: 819 helix: 1.53 (0.31), residues: 308 sheet: -0.87 (0.35), residues: 229 loop : -0.79 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 760 TYR 0.018 0.001 TYR B 706 PHE 0.047 0.002 PHE B 756 TRP 0.013 0.001 TRP B 330 HIS 0.003 0.001 HIS B 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 ( 6867) covalent geometry : angle 0.68431 / 0.36 ( 9270) hydrogen bonds : bond 0.10499 / 6.15 ( 294) hydrogen bonds : angle 6.18544 / 3.99 ( 867) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 132 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 9 GLN cc_start: 0.7571 (mm-40) cc_final: 0.7251 (mm-40) REVERT: C 55 GLU cc_start: 0.8290 (tm-30) cc_final: 0.7944 (tm-30) REVERT: C 65 ASP cc_start: 0.8472 (p0) cc_final: 0.8089 (p0) REVERT: C 87 ARG cc_start: 0.8554 (ttm110) cc_final: 0.8004 (ttm110) REVERT: C 88 GLU cc_start: 0.8522 (tp30) cc_final: 0.7074 (tp30) REVERT: C 91 ARG cc_start: 0.8818 (mtt-85) cc_final: 0.8473 (mpp80) REVERT: C 95 LYS cc_start: 0.8625 (mptt) cc_final: 0.8369 (tptt) REVERT: C 108 HIS cc_start: 0.7923 (t-170) cc_final: 0.7656 (t70) REVERT: C 110 MET cc_start: 0.8136 (mmm) cc_final: 0.7589 (mmm) REVERT: C 112 ASN cc_start: 0.7913 (m-40) cc_final: 0.7405 (m-40) REVERT: B 106 GLN cc_start: 0.8981 (mt0) cc_final: 0.8678 (mt0) REVERT: B 346 ARG cc_start: 0.8170 (mtm110) cc_final: 0.7920 (mtm-85) REVERT: B 408 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8063 (tm-30) REVERT: B 637 TYR cc_start: 0.5201 (p90) cc_final: 0.4908 (p90) REVERT: B 642 GLN cc_start: 0.8133 (tp-100) cc_final: 0.7821 (tp40) REVERT: B 670 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8439 (pp) REVERT: B 756 PHE cc_start: 0.7653 (p90) cc_final: 0.7281 (p90) outliers start: 6 outliers final: 3 residues processed: 135 average time/residue: 0.0972 time to fit residues: 16.9211 Evaluate side-chains 107 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 103 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 670 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.0470 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 403 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 = 0.4115 r_free = 0.4115 target = 0.132089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.096482 restraints weight = 12440.824| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.70 r_work: 0.3507 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6867 Z= 0.134 Angle : 0.573 7.241 9270 Z= 0.293 Chirality : 0.045 0.175 1051 Planarity : 0.004 0.052 1183 Dihedral : 4.944 40.327 893 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.65 % Allowed : 20.11 % Favored : 77.25 % 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: 0.09 (0.32), residues: 819 helix: 1.60 (0.31), residues: 310 sheet: -1.00 (0.35), residues: 231 loop : -0.61 (0.41), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 760 TYR 0.016 0.001 TYR B 333 PHE 0.016 0.002 PHE C 20 TRP 0.009 0.001 TRP B 330 HIS 0.002 0.001 HIS B 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 6867) covalent geometry : angle 0.57293 / 0.29 ( 9270) hydrogen bonds : bond 0.03031 / 2.01 ( 294) hydrogen bonds : angle 5.14423 / 3.40 ( 867) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 9 GLN cc_start: 0.7684 (mm-40) cc_final: 0.7404 (mm-40) REVERT: C 65 ASP cc_start: 0.8451 (p0) cc_final: 0.7951 (p0) REVERT: C 95 LYS cc_start: 0.8672 (mptt) cc_final: 0.8393 (tptt) REVERT: C 110 MET cc_start: 0.8294 (mmm) cc_final: 0.7661 (mmm) REVERT: B 106 GLN cc_start: 0.9017 (mt0) cc_final: 0.8735 (mt0) REVERT: B 201 LYS cc_start: 0.7624 (ttpt) cc_final: 0.7193 (tmtt) REVERT: B 346 ARG cc_start: 0.8342 (mtm110) cc_final: 0.7882 (mtm180) REVERT: B 391 LYS cc_start: 0.8640 (mptt) cc_final: 0.8381 (tptp) REVERT: B 642 GLN cc_start: 0.8329 (tp-100) cc_final: 0.8062 (tp40) outliers start: 20 outliers final: 12 residues processed: 124 average time/residue: 0.0848 time to fit residues: 13.9636 Evaluate side-chains 117 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 759 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 74 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 77 optimal weight: 0.4980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 108 HIS ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 403 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 = 0.4087 r_free = 0.4087 target = 0.129480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.094266 restraints weight = 12522.451| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.68 r_work: 0.3444 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6867 Z= 0.161 Angle : 0.588 7.030 9270 Z= 0.301 Chirality : 0.045 0.134 1051 Planarity : 0.004 0.051 1183 Dihedral : 4.650 42.756 887 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 4.37 % Allowed : 19.84 % Favored : 75.79 % 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: 0.03 (0.32), residues: 819 helix: 1.65 (0.31), residues: 305 sheet: -1.07 (0.35), residues: 235 loop : -0.67 (0.41), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 760 TYR 0.032 0.002 TYR B 333 PHE 0.018 0.002 PHE C 20 TRP 0.009 0.001 TRP B 330 HIS 0.002 0.001 HIS B 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 6867) covalent geometry : angle 0.58795 / 0.30 ( 9270) hydrogen bonds : bond 0.03104 / 2.05 ( 294) hydrogen bonds : angle 5.03236 / 3.36 ( 867) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 116 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 9 GLN cc_start: 0.7734 (mm-40) cc_final: 0.7499 (mm-40) REVERT: C 87 ARG cc_start: 0.8452 (ttm110) cc_final: 0.8029 (ttm110) REVERT: C 95 LYS cc_start: 0.8724 (mptt) cc_final: 0.8428 (tptt) REVERT: C 110 MET cc_start: 0.8335 (mmm) cc_final: 0.7708 (tpp) REVERT: B 106 GLN cc_start: 0.9012 (mt0) cc_final: 0.8732 (mt0) REVERT: B 108 MET cc_start: 0.8307 (mmm) cc_final: 0.8074 (mmm) REVERT: B 299 MET cc_start: 0.8823 (mtp) cc_final: 0.8451 (mtp) REVERT: B 391 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8456 (tptp) REVERT: B 754 MET cc_start: 0.7202 (pmm) cc_final: 0.6796 (ptp) REVERT: B 757 MET cc_start: 0.6897 (ttt) cc_final: 0.6504 (ptm) outliers start: 33 outliers final: 20 residues processed: 137 average time/residue: 0.0929 time to fit residues: 16.8126 Evaluate side-chains 127 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 213 PHE Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain B residue 391 LYS Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 772 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 75 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 108 HIS C 112 ASN B 336 HIS ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.129960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.096924 restraints weight = 12634.130| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.73 r_work: 0.3465 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6867 Z= 0.147 Angle : 0.578 7.846 9270 Z= 0.295 Chirality : 0.045 0.163 1051 Planarity : 0.004 0.049 1183 Dihedral : 4.499 37.345 887 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 4.23 % Allowed : 21.16 % Favored : 74.60 % 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: -0.00 (0.32), residues: 819 helix: 1.64 (0.30), residues: 305 sheet: -1.12 (0.35), residues: 235 loop : -0.67 (0.41), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 760 TYR 0.039 0.002 TYR B 333 PHE 0.024 0.002 PHE B 756 TRP 0.008 0.001 TRP B 330 HIS 0.002 0.001 HIS B 677 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 6867) covalent geometry : angle 0.57813 / 0.30 ( 9270) hydrogen bonds : bond 0.02983 / 1.98 ( 294) hydrogen bonds : angle 4.97729 / 3.34 ( 867) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 9 GLN cc_start: 0.7677 (mm-40) cc_final: 0.7414 (mm-40) REVERT: C 22 LYS cc_start: 0.8500 (mmmm) cc_final: 0.8224 (mmmm) REVERT: C 87 ARG cc_start: 0.8404 (ttm110) cc_final: 0.8010 (ttm110) REVERT: C 95 LYS cc_start: 0.8767 (mptt) cc_final: 0.8434 (tptt) REVERT: C 110 MET cc_start: 0.8291 (mmm) cc_final: 0.7526 (mmm) REVERT: B 108 MET cc_start: 0.8311 (mmm) cc_final: 0.8059 (mmm) REVERT: B 391 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8355 (tptp) REVERT: B 411 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8374 (pttm) REVERT: B 754 MET cc_start: 0.7492 (OUTLIER) cc_final: 0.7085 (ptp) outliers start: 32 outliers final: 23 residues processed: 130 average time/residue: 0.0792 time to fit residues: 13.9492 Evaluate side-chains 132 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 213 PHE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 336 HIS Chi-restraints excluded: chain B residue 391 LYS Chi-restraints excluded: chain B residue 411 LYS Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 661 ASP Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 754 MET Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 772 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 81 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 36 optimal weight: 0.0060 chunk 43 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 108 HIS C 112 ASN ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.130239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.097392 restraints weight = 12644.931| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.72 r_work: 0.3473 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6867 Z= 0.131 Angle : 0.572 8.573 9270 Z= 0.290 Chirality : 0.044 0.131 1051 Planarity : 0.004 0.049 1183 Dihedral : 4.420 35.756 887 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.57 % Allowed : 23.15 % Favored : 73.28 % 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: 0.08 (0.32), residues: 819 helix: 1.66 (0.31), residues: 305 sheet: -1.06 (0.35), residues: 231 loop : -0.61 (0.41), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 728 TYR 0.027 0.001 TYR B 333 PHE 0.016 0.002 PHE C 17 TRP 0.007 0.001 TRP B 331 HIS 0.012 0.001 HIS B 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 6867) covalent geometry : angle 0.57182 / 0.29 ( 9270) hydrogen bonds : bond 0.02919 / 1.94 ( 294) hydrogen bonds : angle 4.92401 / 3.31 ( 867) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 9 GLN cc_start: 0.7742 (mm-40) cc_final: 0.7331 (mp10) REVERT: C 22 LYS cc_start: 0.8488 (mmmm) cc_final: 0.8194 (mmmm) REVERT: C 87 ARG cc_start: 0.8413 (ttm110) cc_final: 0.8036 (ttm110) REVERT: C 95 LYS cc_start: 0.8776 (mptt) cc_final: 0.8445 (tptt) REVERT: C 110 MET cc_start: 0.8304 (mmm) cc_final: 0.7524 (mmm) REVERT: B 106 GLN cc_start: 0.8981 (mt0) cc_final: 0.8692 (mt0) REVERT: B 329 GLU cc_start: 0.7410 (mp0) cc_final: 0.7192 (mp0) REVERT: B 391 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8387 (tptp) REVERT: B 670 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8505 (pp) REVERT: B 754 MET cc_start: 0.7512 (OUTLIER) cc_final: 0.7072 (ptp) REVERT: B 757 MET cc_start: 0.6716 (ttt) cc_final: 0.6297 (ptm) outliers start: 27 outliers final: 17 residues processed: 126 average time/residue: 0.0664 time to fit residues: 11.5415 Evaluate side-chains 124 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 213 PHE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain B residue 391 LYS Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 754 MET Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 759 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 11 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 34 optimal weight: 0.0020 chunk 81 optimal weight: 1.9990 chunk 67 optimal weight: 0.1980 chunk 1 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 108 HIS ** B 403 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 = 0.4109 r_free = 0.4109 target = 0.130826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.095534 restraints weight = 12602.448| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.67 r_work: 0.3470 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6867 Z= 0.120 Angle : 0.570 9.098 9270 Z= 0.285 Chirality : 0.045 0.172 1051 Planarity : 0.004 0.049 1183 Dihedral : 4.179 22.792 885 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.70 % Allowed : 23.15 % Favored : 73.15 % 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: 0.15 (0.32), residues: 819 helix: 1.65 (0.31), residues: 305 sheet: -1.02 (0.36), residues: 231 loop : -0.47 (0.41), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 728 TYR 0.011 0.001 TYR B 333 PHE 0.019 0.001 PHE C 17 TRP 0.006 0.001 TRP B 331 HIS 0.002 0.001 HIS B 677 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 6867) covalent geometry : angle 0.56960 / 0.28 ( 9270) hydrogen bonds : bond 0.02802 / 1.86 ( 294) hydrogen bonds : angle 4.86304 / 3.27 ( 867) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 9 GLN cc_start: 0.7724 (mm-40) cc_final: 0.7507 (mm-40) REVERT: C 87 ARG cc_start: 0.8413 (ttm110) cc_final: 0.8042 (ttm110) REVERT: C 95 LYS cc_start: 0.8788 (mptt) cc_final: 0.8384 (tptt) REVERT: B 106 GLN cc_start: 0.8979 (mt0) cc_final: 0.8701 (mt0) REVERT: B 299 MET cc_start: 0.8833 (mtp) cc_final: 0.8474 (mtp) REVERT: B 391 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8448 (tptp) REVERT: B 642 GLN cc_start: 0.8310 (tp-100) cc_final: 0.8075 (tp40) REVERT: B 670 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8506 (pp) REVERT: B 744 MET cc_start: 0.8985 (ptm) cc_final: 0.8740 (ptt) REVERT: B 754 MET cc_start: 0.7483 (OUTLIER) cc_final: 0.7024 (ptp) REVERT: B 757 MET cc_start: 0.6549 (ttt) cc_final: 0.6199 (ptm) outliers start: 28 outliers final: 16 residues processed: 126 average time/residue: 0.0729 time to fit residues: 12.6741 Evaluate side-chains 120 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 213 PHE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 391 LYS Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 754 MET Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 772 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 71 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 62 optimal weight: 0.0270 chunk 3 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 32 optimal weight: 0.2980 chunk 39 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 108 HIS C 112 ASN ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 336 HIS ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.130576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.095464 restraints weight = 12513.933| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.66 r_work: 0.3470 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6867 Z= 0.129 Angle : 0.590 9.918 9270 Z= 0.293 Chirality : 0.045 0.155 1051 Planarity : 0.004 0.049 1183 Dihedral : 4.161 22.494 885 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.44 % Allowed : 23.41 % Favored : 73.15 % 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: 0.11 (0.32), residues: 819 helix: 1.62 (0.31), residues: 305 sheet: -1.05 (0.35), residues: 231 loop : -0.50 (0.41), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 728 TYR 0.009 0.001 TYR B 706 PHE 0.020 0.002 PHE B 756 TRP 0.007 0.001 TRP B 350 HIS 0.002 0.001 HIS B 677 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 6867) covalent geometry : angle 0.58961 / 0.29 ( 9270) hydrogen bonds : bond 0.02818 / 1.87 ( 294) hydrogen bonds : angle 4.85551 / 3.27 ( 867) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 9 GLN cc_start: 0.7734 (mm-40) cc_final: 0.7185 (mt0) REVERT: C 87 ARG cc_start: 0.8412 (ttm110) cc_final: 0.8030 (ttm110) REVERT: C 110 MET cc_start: 0.8255 (mmm) cc_final: 0.7653 (mmm) REVERT: B 299 MET cc_start: 0.8839 (mtp) cc_final: 0.8466 (mtp) REVERT: B 391 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8475 (tptp) REVERT: B 642 GLN cc_start: 0.8313 (tp-100) cc_final: 0.8069 (tp40) REVERT: B 744 MET cc_start: 0.8972 (ptm) cc_final: 0.8710 (ptt) REVERT: B 754 MET cc_start: 0.7499 (OUTLIER) cc_final: 0.7068 (ptp) outliers start: 26 outliers final: 20 residues processed: 120 average time/residue: 0.0713 time to fit residues: 11.7582 Evaluate side-chains 121 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 213 PHE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 336 HIS Chi-restraints excluded: chain B residue 391 LYS Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 754 MET Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 772 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 60 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 108 HIS C 112 ASN ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 336 HIS ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.129965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.094893 restraints weight = 12602.533| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.66 r_work: 0.3457 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6867 Z= 0.144 Angle : 0.616 10.645 9270 Z= 0.306 Chirality : 0.045 0.163 1051 Planarity : 0.004 0.049 1183 Dihedral : 4.186 22.917 885 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.97 % Allowed : 23.54 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.09 (0.32), residues: 819 helix: 1.65 (0.31), residues: 305 sheet: -1.10 (0.35), residues: 231 loop : -0.53 (0.41), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 107 TYR 0.010 0.001 TYR B 706 PHE 0.017 0.002 PHE C 20 TRP 0.005 0.001 TRP B 352 HIS 0.002 0.001 HIS B 677 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 6867) covalent geometry : angle 0.61642 / 0.31 ( 9270) hydrogen bonds : bond 0.02856 / 1.88 ( 294) hydrogen bonds : angle 4.88441 / 3.29 ( 867) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 103 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 9 GLN cc_start: 0.7719 (mm-40) cc_final: 0.7216 (mt0) REVERT: C 87 ARG cc_start: 0.8399 (ttm110) cc_final: 0.8009 (ttm110) REVERT: C 116 LYS cc_start: 0.7835 (ptmt) cc_final: 0.7583 (ptmt) REVERT: B 391 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8393 (tptp) REVERT: B 642 GLN cc_start: 0.8317 (tp-100) cc_final: 0.8079 (tp40) REVERT: B 670 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8521 (pp) REVERT: B 744 MET cc_start: 0.8992 (ptm) cc_final: 0.8727 (ptt) REVERT: B 754 MET cc_start: 0.7557 (OUTLIER) cc_final: 0.7109 (ptp) outliers start: 30 outliers final: 22 residues processed: 121 average time/residue: 0.0642 time to fit residues: 10.9807 Evaluate side-chains 128 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 213 PHE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 336 HIS Chi-restraints excluded: chain B residue 391 LYS Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 661 ASP Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 754 MET Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 772 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 35 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 108 HIS ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.129227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.094098 restraints weight = 12601.373| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.65 r_work: 0.3445 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6867 Z= 0.166 Angle : 0.630 10.844 9270 Z= 0.313 Chirality : 0.046 0.155 1051 Planarity : 0.004 0.049 1183 Dihedral : 4.282 23.217 885 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.31 % Allowed : 23.94 % Favored : 72.75 % 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: 0.02 (0.32), residues: 819 helix: 1.62 (0.31), residues: 304 sheet: -1.12 (0.35), residues: 230 loop : -0.61 (0.41), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 107 TYR 0.014 0.001 TYR B 333 PHE 0.019 0.002 PHE C 20 TRP 0.007 0.001 TRP B 331 HIS 0.002 0.001 HIS B 677 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 ( 6867) covalent geometry : angle 0.62964 / 0.31 ( 9270) hydrogen bonds : bond 0.02978 / 1.98 ( 294) hydrogen bonds : angle 4.99867 / 3.37 ( 867) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 9 GLN cc_start: 0.7714 (mm-40) cc_final: 0.7259 (mt0) REVERT: C 87 ARG cc_start: 0.8396 (ttm110) cc_final: 0.8063 (ttm110) REVERT: C 110 MET cc_start: 0.8242 (mmm) cc_final: 0.7623 (mmm) REVERT: C 116 LYS cc_start: 0.7806 (ptmt) cc_final: 0.7468 (ptmt) REVERT: B 670 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8523 (pp) REVERT: B 744 MET cc_start: 0.9055 (ptm) cc_final: 0.8777 (ptt) REVERT: B 754 MET cc_start: 0.7626 (OUTLIER) cc_final: 0.7167 (ptp) outliers start: 25 outliers final: 21 residues processed: 120 average time/residue: 0.0710 time to fit residues: 11.8676 Evaluate side-chains 123 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 213 PHE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 661 ASP Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 754 MET Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 772 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 1 optimal weight: 0.7980 chunk 71 optimal weight: 0.0970 chunk 28 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 43 optimal weight: 0.1980 chunk 68 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 108 HIS B 336 HIS ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.130227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.095225 restraints weight = 12469.169| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.65 r_work: 0.3463 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6867 Z= 0.136 Angle : 0.644 11.609 9270 Z= 0.319 Chirality : 0.046 0.173 1051 Planarity : 0.004 0.048 1183 Dihedral : 4.245 22.764 885 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.04 % Allowed : 24.60 % Favored : 72.35 % 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: 0.02 (0.32), residues: 819 helix: 1.57 (0.31), residues: 303 sheet: -1.12 (0.35), residues: 230 loop : -0.53 (0.41), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 728 TYR 0.009 0.001 TYR B 706 PHE 0.015 0.001 PHE C 20 TRP 0.009 0.001 TRP B 330 HIS 0.003 0.001 HIS B 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 6867) covalent geometry : angle 0.64377 / 0.32 ( 9270) hydrogen bonds : bond 0.02832 / 1.88 ( 294) hydrogen bonds : angle 5.03291 / 3.38 ( 867) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 9 GLN cc_start: 0.7709 (mm-40) cc_final: 0.7266 (mt0) REVERT: C 87 ARG cc_start: 0.8387 (ttm110) cc_final: 0.7983 (ttm110) REVERT: C 110 MET cc_start: 0.8230 (mmm) cc_final: 0.7642 (mmm) REVERT: B 642 GLN cc_start: 0.8314 (tp-100) cc_final: 0.8064 (tp40) REVERT: B 670 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8512 (pp) REVERT: B 744 MET cc_start: 0.9049 (ptm) cc_final: 0.8761 (ptt) REVERT: B 754 MET cc_start: 0.7559 (OUTLIER) cc_final: 0.7100 (ptp) outliers start: 23 outliers final: 20 residues processed: 120 average time/residue: 0.0601 time to fit residues: 10.1802 Evaluate side-chains 122 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 213 PHE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 336 HIS Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 505 HIS Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 661 ASP Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 754 MET Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 772 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 5 optimal weight: 0.0770 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 60 optimal weight: 0.0970 chunk 53 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 108 HIS B 336 HIS ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.130792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.095787 restraints weight = 12381.626| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.65 r_work: 0.3471 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6867 Z= 0.125 Angle : 0.633 11.586 9270 Z= 0.314 Chirality : 0.045 0.164 1051 Planarity : 0.004 0.048 1183 Dihedral : 4.187 22.534 885 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.91 % Allowed : 24.87 % Favored : 72.22 % 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: -0.03 (0.32), residues: 819 helix: 1.50 (0.31), residues: 305 sheet: -1.14 (0.35), residues: 229 loop : -0.54 (0.41), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 107 TYR 0.008 0.001 TYR B 706 PHE 0.014 0.001 PHE C 20 TRP 0.010 0.001 TRP B 350 HIS 0.004 0.001 HIS B 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 6867) covalent geometry : angle 0.63349 / 0.31 ( 9270) hydrogen bonds : bond 0.02747 / 1.81 ( 294) hydrogen bonds : angle 4.99610 / 3.35 ( 867) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2489.82 seconds wall clock time: 43 minutes 23.52 seconds (2603.52 seconds total)