Starting phenix.real_space_refine on Wed Sep 17 17:32:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ejm_48105/09_2025/9ejm_48105_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ejm_48105/09_2025/9ejm_48105.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ejm_48105/09_2025/9ejm_48105_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ejm_48105/09_2025/9ejm_48105_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ejm_48105/09_2025/9ejm_48105.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ejm_48105/09_2025/9ejm_48105.map" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.015 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 4 5.49 5 Mg 1 5.21 5 S 40 5.16 5 C 6428 2.51 5 N 1765 2.21 5 O 1818 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10056 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 869, 6730 Classifications: {'peptide': 869} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PCIS': 5, 'PTRANS': 52, 'TRANS': 811} Chain breaks: 3 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 104 Planarities with less than four sites: {'ARG:plan': 7, 'GLU:plan': 15, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 107 Chain: "B" Number of atoms: 2520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2520 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 17, 'TRANS': 304} Chain breaks: 2 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASP:plan': 8, 'GLU:plan': 7, 'ARG:plan': 2, 'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 83 Chain: "C" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 778 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain breaks: 3 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 38 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.62, per 1000 atoms: 0.26 Number of scatterers: 10056 At special positions: 0 Unit cell: (91.102, 108.878, 118.321, 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 40 16.00 P 4 15.00 Mg 1 11.99 O 1818 8.00 N 1765 7.00 C 6428 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: 0.96 Conformation dependent library (CDL) restraints added in 436.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2416 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 23 sheets defined 17.7% alpha, 28.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 13 through 20 Processing helix chain 'A' and resid 126 through 131 removed outlier: 3.587A pdb=" N THR A 130 " --> pdb=" O PRO A 127 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLN A 131 " --> pdb=" O SER A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 177 removed outlier: 3.661A pdb=" N ARG A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 183 removed outlier: 3.637A pdb=" N ARG A 183 " --> pdb=" O GLU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 410 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 633 through 637 removed outlier: 3.686A pdb=" N LEU A 636 " --> pdb=" O GLN A 633 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU A 637 " --> pdb=" O LEU A 634 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 633 through 637' Processing helix chain 'A' and resid 651 through 655 Processing helix chain 'A' and resid 751 through 755 removed outlier: 3.704A pdb=" N ARG A 755 " --> pdb=" O ALA A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 798 Processing helix chain 'A' and resid 835 through 840 Processing helix chain 'A' and resid 894 through 900 removed outlier: 3.793A pdb=" N ILE A 898 " --> pdb=" O ASP A 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 252 No H-bonds generated for 'chain 'B' and resid 250 through 252' Processing helix chain 'B' and resid 298 through 309 Processing helix chain 'B' and resid 310 through 312 No H-bonds generated for 'chain 'B' and resid 310 through 312' Processing helix chain 'B' and resid 339 through 348 Processing helix chain 'B' and resid 351 through 372 removed outlier: 3.558A pdb=" N ARG B 372 " --> pdb=" O TYR B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 427 removed outlier: 3.625A pdb=" N LEU B 425 " --> pdb=" O ALA B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 449 removed outlier: 3.889A pdb=" N TRP B 436 " --> pdb=" O PHE B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 457 removed outlier: 3.668A pdb=" N VAL B 456 " --> pdb=" O PHE B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 477 removed outlier: 3.833A pdb=" N LEU B 470 " --> pdb=" O THR B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 497 Processing helix chain 'B' and resid 511 through 518 Processing helix chain 'B' and resid 526 through 531 Processing helix chain 'B' and resid 545 through 552 removed outlier: 6.028A pdb=" N ASP B 550 " --> pdb=" O PHE B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 558 Processing helix chain 'C' and resid 201 through 207 removed outlier: 3.508A pdb=" N GLY C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 238 Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 25 removed outlier: 3.790A pdb=" N LEU A 923 " --> pdb=" O GLN A 22 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ASN A 24 " --> pdb=" O PHE A 921 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N PHE A 921 " --> pdb=" O ASN A 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 41 removed outlier: 6.529A pdb=" N GLY A 50 " --> pdb=" O SER A 36 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU A 38 " --> pdb=" O ALA A 48 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA A 48 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N TYR A 40 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE A 46 " --> pdb=" O TYR A 40 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ALA A 55 " --> pdb=" O THR A 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 81 removed outlier: 3.507A pdb=" N GLN A 78 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N SER A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU A 97 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N SER A 116 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU A 99 " --> pdb=" O ASP A 114 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 135 through 137 removed outlier: 3.706A pdb=" N ARG A 162 " --> pdb=" O GLN A 157 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 191 through 196 removed outlier: 4.094A pdb=" N TYR A 225 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ASP A 217 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL A 223 " --> pdb=" O ASP A 217 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 233 through 238 removed outlier: 3.785A pdb=" N TYR A 254 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU A 272 " --> pdb=" O TYR A 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 285 through 289 removed outlier: 4.084A pdb=" N ARG A 285 " --> pdb=" O GLN A 301 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 334 through 338 removed outlier: 3.628A pdb=" N GLY A 334 " --> pdb=" O LEU A 356 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA A 352 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 387 through 393 removed outlier: 3.713A pdb=" N CYS A 389 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR A 446 " --> pdb=" O HIS A 442 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL A 447 " --> pdb=" O LYS A 462 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LYS A 462 " --> pdb=" O VAL A 447 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N PHE A 449 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG A 458 " --> pdb=" O ASP A 451 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 426 through 427 Processing sheet with id=AB2, first strand: chain 'A' and resid 507 through 513 removed outlier: 3.711A pdb=" N TYR A 518 " --> pdb=" O CYS A 513 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLN A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL A 528 " --> pdb=" O LEU A 582 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU A 582 " --> pdb=" O VAL A 528 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL A 530 " --> pdb=" O PHE A 580 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 538 through 540 Processing sheet with id=AB4, first strand: chain 'A' and resid 593 through 597 removed outlier: 3.748A pdb=" N PHE A 623 " --> pdb=" O LEU A 613 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASP A 615 " --> pdb=" O GLN A 621 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N GLN A 621 " --> pdb=" O ASP A 615 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 697 through 699 removed outlier: 6.629A pdb=" N TYR C 172 " --> pdb=" O SER C 195 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER C 195 " --> pdb=" O TYR C 172 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ILE C 192 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N VAL C 215 " --> pdb=" O ARG C 247 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ARG C 247 " --> pdb=" O VAL C 215 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 697 through 699 removed outlier: 6.629A pdb=" N TYR C 172 " --> pdb=" O SER C 195 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER C 195 " --> pdb=" O TYR C 172 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ILE C 192 " --> pdb=" O VAL C 215 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 713 through 721 removed outlier: 3.575A pdb=" N THR A 715 " --> pdb=" O GLY A 736 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 719 " --> pdb=" O SER A 732 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR A 721 " --> pdb=" O CYS A 730 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR A 741 " --> pdb=" O THR A 737 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE A 742 " --> pdb=" O GLU A 767 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLU A 767 " --> pdb=" O ILE A 742 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ALA A 744 " --> pdb=" O ALA A 765 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG A 761 " --> pdb=" O ARG A 748 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE C 296 " --> pdb=" O GLN A 769 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 776 through 781 removed outlier: 3.536A pdb=" N GLY A 778 " --> pdb=" O VAL A 814 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN A 818 " --> pdb=" O SER A 815 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N THR A 823 " --> pdb=" O ALA A 829 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ALA A 829 " --> pdb=" O THR A 823 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 843 through 852 removed outlier: 4.697A pdb=" N ASP A 872 " --> pdb=" O THR A 868 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL A 885 " --> pdb=" O VAL A 875 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 902 through 903 Processing sheet with id=AC2, first strand: chain 'A' and resid 912 through 914 removed outlier: 3.656A pdb=" N ILE A 913 " --> pdb=" O GLU A 917 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLU A 917 " --> pdb=" O ILE A 913 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 254 through 262 removed outlier: 6.724A pdb=" N LEU B 270 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N VAL B 259 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL B 268 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N GLY B 261 " --> pdb=" O ALA B 266 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ALA B 266 " --> pdb=" O GLY B 261 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 384 through 385 Processing sheet with id=AC5, first strand: chain 'C' and resid 177 through 180 339 hydrogen bonds defined for protein. 912 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: 1.73 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3304 1.34 - 1.46: 2335 1.46 - 1.58: 4600 1.58 - 1.70: 3 1.70 - 1.81: 61 Bond restraints: 10303 Sorted by residual: bond pdb=" CD ARG B 480 " pdb=" NE ARG B 480 " ideal model delta sigma weight residual 1.458 1.442 0.016 1.40e-02 5.10e+03 1.32e+00 bond pdb=" C4 ADP B 601 " pdb=" C5 ADP B 601 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.03e+00 bond pdb=" CG LEU A 780 " pdb=" CD2 LEU A 780 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.35e-01 bond pdb=" CB PRO B 406 " pdb=" CG PRO B 406 " ideal model delta sigma weight residual 1.492 1.532 -0.040 5.00e-02 4.00e+02 6.31e-01 bond pdb=" CB ASP A 783 " pdb=" CG ASP A 783 " ideal model delta sigma weight residual 1.516 1.536 -0.020 2.50e-02 1.60e+03 6.20e-01 ... (remaining 10298 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 13759 1.53 - 3.05: 215 3.05 - 4.58: 29 4.58 - 6.11: 14 6.11 - 7.64: 2 Bond angle restraints: 14019 Sorted by residual: angle pdb=" N SER B 544 " pdb=" CA SER B 544 " pdb=" C SER B 544 " ideal model delta sigma weight residual 108.75 104.02 4.73 1.71e+00 3.42e-01 7.64e+00 angle pdb=" N GLY B 545 " pdb=" CA GLY B 545 " pdb=" C GLY B 545 " ideal model delta sigma weight residual 113.18 107.01 6.17 2.37e+00 1.78e-01 6.78e+00 angle pdb=" CD ARG B 480 " pdb=" NE ARG B 480 " pdb=" CZ ARG B 480 " ideal model delta sigma weight residual 124.40 128.02 -3.62 1.40e+00 5.10e-01 6.69e+00 angle pdb=" C SER B 544 " pdb=" N GLY B 545 " pdb=" CA GLY B 545 " ideal model delta sigma weight residual 121.41 116.61 4.80 1.96e+00 2.60e-01 6.01e+00 angle pdb=" CA LEU A 650 " pdb=" CB LEU A 650 " pdb=" CG LEU A 650 " ideal model delta sigma weight residual 116.30 123.94 -7.64 3.50e+00 8.16e-02 4.76e+00 ... (remaining 14014 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 5626 17.61 - 35.22: 368 35.22 - 52.83: 99 52.83 - 70.43: 18 70.43 - 88.04: 8 Dihedral angle restraints: 6119 sinusoidal: 2380 harmonic: 3739 Sorted by residual: dihedral pdb=" CD ARG B 480 " pdb=" NE ARG B 480 " pdb=" CZ ARG B 480 " pdb=" NH1 ARG B 480 " ideal model delta sinusoidal sigma weight residual 0.00 -88.04 88.04 1 1.00e+01 1.00e-02 9.27e+01 dihedral pdb=" CA CYS A 384 " pdb=" C CYS A 384 " pdb=" N SER A 385 " pdb=" CA SER A 385 " ideal model delta harmonic sigma weight residual 180.00 160.98 19.02 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CB GLU B 333 " pdb=" CG GLU B 333 " pdb=" CD GLU B 333 " pdb=" OE1 GLU B 333 " ideal model delta sinusoidal sigma weight residual 0.00 -87.28 87.28 1 3.00e+01 1.11e-03 1.02e+01 ... (remaining 6116 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1054 0.035 - 0.070: 347 0.070 - 0.105: 119 0.105 - 0.140: 50 0.140 - 0.175: 5 Chirality restraints: 1575 Sorted by residual: chirality pdb=" CA ILE A 315 " pdb=" N ILE A 315 " pdb=" C ILE A 315 " pdb=" CB ILE A 315 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.66e-01 chirality pdb=" CG LEU A 782 " pdb=" CB LEU A 782 " pdb=" CD1 LEU A 782 " pdb=" CD2 LEU A 782 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.97e-01 chirality pdb=" CA ILE A 318 " pdb=" N ILE A 318 " pdb=" C ILE A 318 " pdb=" CB ILE A 318 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.98e-01 ... (remaining 1572 not shown) Planarity restraints: 1807 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 480 " -0.964 9.50e-02 1.11e+02 4.33e-01 1.22e+02 pdb=" NE ARG B 480 " 0.078 2.00e-02 2.50e+03 pdb=" CZ ARG B 480 " -0.041 2.00e-02 2.50e+03 pdb=" NH1 ARG B 480 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 480 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 270 " 0.169 9.50e-02 1.11e+02 7.62e-02 4.61e+00 pdb=" NE ARG A 270 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 270 " 0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG A 270 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 270 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 844 " 0.133 9.50e-02 1.11e+02 6.02e-02 2.91e+00 pdb=" NE ARG A 844 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 844 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 844 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 844 " -0.000 2.00e-02 2.50e+03 ... (remaining 1804 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 87 2.64 - 3.20: 8228 3.20 - 3.77: 14159 3.77 - 4.33: 19786 4.33 - 4.90: 34685 Nonbonded interactions: 76945 Sorted by model distance: nonbonded pdb=" O1B ADP B 601 " pdb="MG MG B 602 " model vdw 2.071 2.170 nonbonded pdb=" OD1 ASN B 383 " pdb="MG MG B 602 " model vdw 2.088 2.170 nonbonded pdb=" OG1 THR A 291 " pdb=" O LEU A 295 " model vdw 2.207 3.040 nonbonded pdb=" OH TYR B 376 " pdb=" O THR B 395 " model vdw 2.209 3.040 nonbonded pdb=" OG1 THR A 388 " pdb=" O ILE A 507 " model vdw 2.299 3.040 ... (remaining 76940 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: 10.210 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: 0.310 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.050 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 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 : 0.002 0.040 10303 Z= 0.088 Angle : 0.503 7.636 14019 Z= 0.250 Chirality : 0.043 0.175 1575 Planarity : 0.011 0.433 1807 Dihedral : 13.255 88.043 3703 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.85 % Allowed : 10.62 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: -0.46 (0.24), residues: 1273 helix: 0.77 (0.40), residues: 174 sheet: 0.19 (0.27), residues: 389 loop : -0.85 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.052 0.001 ARG B 480 TYR 0.011 0.001 TYR A 225 PHE 0.014 0.001 PHE A 300 TRP 0.007 0.001 TRP A 100 HIS 0.003 0.001 HIS A 609 Details of bonding type rmsd covalent geometry : bond 0.00195 (10303) covalent geometry : angle 0.50340 (14019) hydrogen bonds : bond 0.15677 ( 334) hydrogen bonds : angle 6.39210 ( 912) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 139 time to evaluate : 0.368 Fit side-chains REVERT: A 19 ASP cc_start: 0.8301 (m-30) cc_final: 0.7561 (t0) REVERT: A 85 GLN cc_start: 0.8569 (mt0) cc_final: 0.7906 (mt0) REVERT: A 144 LEU cc_start: 0.8101 (mt) cc_final: 0.7681 (tp) REVERT: A 161 PHE cc_start: 0.7919 (OUTLIER) cc_final: 0.7238 (m-80) REVERT: A 551 GLN cc_start: 0.7193 (tt0) cc_final: 0.6446 (pm20) REVERT: A 886 ARG cc_start: 0.8110 (ttp80) cc_final: 0.7515 (ptm-80) REVERT: B 465 ASN cc_start: 0.7250 (m-40) cc_final: 0.6583 (p0) REVERT: B 532 GLN cc_start: 0.8140 (mm110) cc_final: 0.6793 (pt0) REVERT: B 582 PHE cc_start: 0.7267 (t80) cc_final: 0.6927 (t80) outliers start: 9 outliers final: 1 residues processed: 144 average time/residue: 0.1107 time to fit residues: 22.1047 Evaluate side-chains 97 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 95 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 PHE Chi-restraints excluded: chain B residue 340 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 124 optimal weight: 0.0870 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.2980 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.0764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.137481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.101309 restraints weight = 11880.873| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.34 r_work: 0.3137 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10303 Z= 0.138 Angle : 0.536 6.810 14019 Z= 0.271 Chirality : 0.045 0.169 1575 Planarity : 0.004 0.040 1807 Dihedral : 4.281 44.606 1415 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.09 % Allowed : 10.90 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: -0.40 (0.24), residues: 1273 helix: 1.14 (0.39), residues: 170 sheet: 0.14 (0.26), residues: 399 loop : -0.84 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 480 TYR 0.012 0.001 TYR A 911 PHE 0.019 0.002 PHE A 227 TRP 0.009 0.001 TRP A 450 HIS 0.010 0.001 HIS A 319 Details of bonding type rmsd covalent geometry : bond 0.00336 (10303) covalent geometry : angle 0.53571 (14019) hydrogen bonds : bond 0.03770 ( 334) hydrogen bonds : angle 5.05230 ( 912) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.408 Fit side-chains REVERT: A 18 ARG cc_start: 0.8217 (ttm110) cc_final: 0.8011 (ttm110) REVERT: A 19 ASP cc_start: 0.8501 (m-30) cc_final: 0.7574 (t0) REVERT: A 85 GLN cc_start: 0.8558 (mt0) cc_final: 0.7766 (mt0) REVERT: A 161 PHE cc_start: 0.7645 (OUTLIER) cc_final: 0.7106 (m-80) REVERT: A 190 MET cc_start: 0.6562 (mmm) cc_final: 0.6253 (mmt) REVERT: A 244 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8339 (tp) REVERT: A 551 GLN cc_start: 0.7018 (tt0) cc_final: 0.6213 (pm20) REVERT: A 886 ARG cc_start: 0.8015 (ttp80) cc_final: 0.7212 (ptm-80) REVERT: B 465 ASN cc_start: 0.7086 (m-40) cc_final: 0.6332 (p0) REVERT: B 532 GLN cc_start: 0.7919 (mm110) cc_final: 0.6530 (pt0) REVERT: B 582 PHE cc_start: 0.7140 (t80) cc_final: 0.6676 (t80) outliers start: 22 outliers final: 12 residues processed: 120 average time/residue: 0.1133 time to fit residues: 18.9832 Evaluate side-chains 105 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 161 PHE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain A residue 808 SER Chi-restraints excluded: chain A residue 933 CYS Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 561 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 71 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.134215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.097929 restraints weight = 12049.024| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.38 r_work: 0.3018 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 10303 Z= 0.218 Angle : 0.597 8.390 14019 Z= 0.300 Chirality : 0.047 0.184 1575 Planarity : 0.005 0.047 1807 Dihedral : 4.617 45.861 1413 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.03 % Allowed : 11.94 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: -0.56 (0.24), residues: 1273 helix: 0.89 (0.40), residues: 168 sheet: 0.07 (0.26), residues: 403 loop : -0.94 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 177 TYR 0.015 0.002 TYR A 911 PHE 0.020 0.002 PHE A 300 TRP 0.014 0.001 TRP B 437 HIS 0.006 0.001 HIS A 616 Details of bonding type rmsd covalent geometry : bond 0.00551 (10303) covalent geometry : angle 0.59669 (14019) hydrogen bonds : bond 0.04353 ( 334) hydrogen bonds : angle 5.03598 ( 912) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 0.467 Fit side-chains REVERT: A 19 ASP cc_start: 0.8548 (m-30) cc_final: 0.7611 (t0) REVERT: A 85 GLN cc_start: 0.8593 (mt0) cc_final: 0.7729 (mt0) REVERT: A 190 MET cc_start: 0.6646 (mmm) cc_final: 0.6249 (mmt) REVERT: A 244 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8256 (tp) REVERT: A 551 GLN cc_start: 0.7006 (tt0) cc_final: 0.6156 (pm20) REVERT: A 838 LEU cc_start: 0.8961 (mt) cc_final: 0.8756 (mt) REVERT: A 886 ARG cc_start: 0.8053 (ttp80) cc_final: 0.7184 (ptm-80) REVERT: B 465 ASN cc_start: 0.7109 (m-40) cc_final: 0.6429 (p0) REVERT: B 532 GLN cc_start: 0.7918 (mm110) cc_final: 0.6529 (pt0) REVERT: B 582 PHE cc_start: 0.7188 (t80) cc_final: 0.6705 (t80) outliers start: 32 outliers final: 17 residues processed: 122 average time/residue: 0.1097 time to fit residues: 18.7126 Evaluate side-chains 109 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 161 PHE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain A residue 808 SER Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 933 CYS Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 561 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 40 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 81 optimal weight: 0.1980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 434 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.137682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.103809 restraints weight = 11953.322| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.07 r_work: 0.3077 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10303 Z= 0.107 Angle : 0.504 7.036 14019 Z= 0.254 Chirality : 0.044 0.159 1575 Planarity : 0.004 0.048 1807 Dihedral : 4.333 46.141 1413 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.56 % Allowed : 13.36 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: -0.45 (0.24), residues: 1273 helix: 1.10 (0.40), residues: 168 sheet: 0.08 (0.26), residues: 403 loop : -0.86 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 177 TYR 0.009 0.001 TYR B 430 PHE 0.020 0.001 PHE A 227 TRP 0.007 0.001 TRP A 216 HIS 0.004 0.001 HIS A 319 Details of bonding type rmsd covalent geometry : bond 0.00255 (10303) covalent geometry : angle 0.50440 (14019) hydrogen bonds : bond 0.03477 ( 334) hydrogen bonds : angle 4.79896 ( 912) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 0.390 Fit side-chains REVERT: A 19 ASP cc_start: 0.8430 (m-30) cc_final: 0.7737 (t0) REVERT: A 85 GLN cc_start: 0.8602 (mt0) cc_final: 0.7869 (mt0) REVERT: A 190 MET cc_start: 0.6876 (mmm) cc_final: 0.6642 (mmt) REVERT: A 551 GLN cc_start: 0.7189 (tt0) cc_final: 0.6421 (pm20) REVERT: A 886 ARG cc_start: 0.8062 (ttp80) cc_final: 0.7416 (ptm-80) REVERT: B 465 ASN cc_start: 0.7405 (m-40) cc_final: 0.6875 (p0) REVERT: B 532 GLN cc_start: 0.8117 (mm110) cc_final: 0.6764 (pt0) REVERT: B 582 PHE cc_start: 0.7358 (t80) cc_final: 0.7052 (t80) outliers start: 27 outliers final: 16 residues processed: 121 average time/residue: 0.1091 time to fit residues: 18.6498 Evaluate side-chains 107 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 161 PHE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain A residue 808 SER Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 933 CYS Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 561 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 123 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 86 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 434 GLN A 908 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.134963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.098773 restraints weight = 12033.761| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.36 r_work: 0.2945 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 10303 Z= 0.155 Angle : 0.540 7.601 14019 Z= 0.270 Chirality : 0.045 0.166 1575 Planarity : 0.004 0.048 1807 Dihedral : 4.455 46.912 1413 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.84 % Allowed : 13.27 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: -0.60 (0.24), residues: 1273 helix: 0.83 (0.39), residues: 174 sheet: 0.02 (0.26), residues: 404 loop : -0.96 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 177 TYR 0.020 0.002 TYR B 368 PHE 0.016 0.002 PHE A 300 TRP 0.010 0.001 TRP B 437 HIS 0.004 0.001 HIS A 616 Details of bonding type rmsd covalent geometry : bond 0.00386 (10303) covalent geometry : angle 0.53973 (14019) hydrogen bonds : bond 0.03819 ( 334) hydrogen bonds : angle 4.79920 ( 912) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 90 time to evaluate : 0.391 Fit side-chains REVERT: A 19 ASP cc_start: 0.8558 (m-30) cc_final: 0.7670 (t0) REVERT: A 85 GLN cc_start: 0.8593 (mt0) cc_final: 0.7748 (mt0) REVERT: A 190 MET cc_start: 0.6668 (mmm) cc_final: 0.6311 (mmt) REVERT: A 244 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8342 (tp) REVERT: A 551 GLN cc_start: 0.7001 (tt0) cc_final: 0.6189 (pm20) REVERT: A 553 GLN cc_start: 0.6640 (mp10) cc_final: 0.6219 (mp10) REVERT: A 608 SER cc_start: 0.6471 (t) cc_final: 0.6263 (m) REVERT: A 886 ARG cc_start: 0.7987 (ttp80) cc_final: 0.7131 (ptm-80) REVERT: B 465 ASN cc_start: 0.7203 (m-40) cc_final: 0.6623 (p0) REVERT: B 532 GLN cc_start: 0.7923 (mm110) cc_final: 0.6540 (pt0) REVERT: B 582 PHE cc_start: 0.7216 (t80) cc_final: 0.6792 (t80) outliers start: 30 outliers final: 19 residues processed: 112 average time/residue: 0.1040 time to fit residues: 16.8624 Evaluate side-chains 108 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 161 PHE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 322 GLN Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain A residue 808 SER Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 933 CYS Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain C residue 295 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 126 optimal weight: 8.9990 chunk 78 optimal weight: 4.9990 chunk 120 optimal weight: 8.9990 chunk 5 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 125 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 434 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.136688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.100442 restraints weight = 11983.290| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.37 r_work: 0.3140 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10303 Z= 0.107 Angle : 0.504 6.929 14019 Z= 0.252 Chirality : 0.044 0.158 1575 Planarity : 0.004 0.048 1807 Dihedral : 4.324 47.293 1413 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.65 % Allowed : 13.55 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: -0.49 (0.24), residues: 1273 helix: 0.95 (0.39), residues: 174 sheet: 0.05 (0.26), residues: 404 loop : -0.87 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 177 TYR 0.017 0.001 TYR B 368 PHE 0.023 0.001 PHE A 227 TRP 0.007 0.001 TRP B 437 HIS 0.003 0.001 HIS A 383 Details of bonding type rmsd covalent geometry : bond 0.00256 (10303) covalent geometry : angle 0.50371 (14019) hydrogen bonds : bond 0.03407 ( 334) hydrogen bonds : angle 4.69542 ( 912) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 95 time to evaluate : 0.402 Fit side-chains REVERT: A 19 ASP cc_start: 0.8528 (m-30) cc_final: 0.7644 (t0) REVERT: A 85 GLN cc_start: 0.8525 (mt0) cc_final: 0.7712 (mt0) REVERT: A 190 MET cc_start: 0.6637 (mmm) cc_final: 0.6284 (mmt) REVERT: A 551 GLN cc_start: 0.7001 (tt0) cc_final: 0.6184 (pm20) REVERT: A 553 GLN cc_start: 0.6712 (mp10) cc_final: 0.6482 (mp10) REVERT: A 886 ARG cc_start: 0.7993 (ttp80) cc_final: 0.7093 (ptm-80) REVERT: A 902 VAL cc_start: 0.7899 (p) cc_final: 0.7660 (m) REVERT: B 443 MET cc_start: 0.7976 (mtp) cc_final: 0.7743 (mtp) REVERT: B 465 ASN cc_start: 0.7188 (m-40) cc_final: 0.6638 (p0) REVERT: B 532 GLN cc_start: 0.7889 (mm110) cc_final: 0.6481 (pt0) REVERT: B 582 PHE cc_start: 0.7177 (t80) cc_final: 0.6767 (t80) outliers start: 28 outliers final: 19 residues processed: 115 average time/residue: 0.1021 time to fit residues: 16.8290 Evaluate side-chains 108 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 161 PHE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 322 GLN Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain A residue 808 SER Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 933 CYS Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 561 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 2.9990 chunk 68 optimal weight: 0.4980 chunk 85 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 113 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 434 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.134041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.097973 restraints weight = 12069.194| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.36 r_work: 0.3101 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10303 Z= 0.170 Angle : 0.560 8.165 14019 Z= 0.279 Chirality : 0.046 0.167 1575 Planarity : 0.004 0.048 1807 Dihedral : 4.570 48.259 1413 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 3.13 % Allowed : 13.55 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: -0.65 (0.24), residues: 1273 helix: 0.74 (0.39), residues: 176 sheet: -0.01 (0.26), residues: 404 loop : -0.98 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 177 TYR 0.015 0.002 TYR B 368 PHE 0.019 0.002 PHE A 347 TRP 0.012 0.001 TRP B 437 HIS 0.005 0.001 HIS A 616 Details of bonding type rmsd covalent geometry : bond 0.00426 (10303) covalent geometry : angle 0.55980 (14019) hydrogen bonds : bond 0.03934 ( 334) hydrogen bonds : angle 4.80814 ( 912) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 91 time to evaluate : 0.408 Fit side-chains REVERT: A 19 ASP cc_start: 0.8524 (m-30) cc_final: 0.7642 (t0) REVERT: A 85 GLN cc_start: 0.8585 (mt0) cc_final: 0.7866 (mt0) REVERT: A 190 MET cc_start: 0.6677 (mmm) cc_final: 0.6282 (mmt) REVERT: A 244 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8366 (tp) REVERT: A 551 GLN cc_start: 0.7030 (tt0) cc_final: 0.6157 (pm20) REVERT: A 553 GLN cc_start: 0.6797 (mp10) cc_final: 0.6276 (mp10) REVERT: A 608 SER cc_start: 0.6506 (t) cc_final: 0.6302 (m) REVERT: A 886 ARG cc_start: 0.8036 (ttp80) cc_final: 0.7178 (ptm-80) REVERT: B 465 ASN cc_start: 0.7214 (m-40) cc_final: 0.6698 (p0) REVERT: B 532 GLN cc_start: 0.7870 (mm110) cc_final: 0.6430 (pt0) REVERT: B 582 PHE cc_start: 0.7217 (t80) cc_final: 0.6784 (t80) outliers start: 33 outliers final: 23 residues processed: 117 average time/residue: 0.1002 time to fit residues: 16.6907 Evaluate side-chains 112 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 161 PHE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 322 GLN Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain A residue 808 SER Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 933 CYS Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 561 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 4 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 118 optimal weight: 0.0000 chunk 46 optimal weight: 2.9990 chunk 114 optimal weight: 0.0060 chunk 54 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN A 434 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.134934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.098936 restraints weight = 12019.180| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.36 r_work: 0.3106 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 10303 Z= 0.142 Angle : 0.529 7.760 14019 Z= 0.265 Chirality : 0.045 0.164 1575 Planarity : 0.004 0.049 1807 Dihedral : 4.503 49.167 1413 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.94 % Allowed : 14.12 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: -0.61 (0.24), residues: 1273 helix: 0.82 (0.39), residues: 177 sheet: -0.02 (0.26), residues: 404 loop : -0.95 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 177 TYR 0.013 0.001 TYR B 368 PHE 0.026 0.002 PHE A 227 TRP 0.009 0.001 TRP B 437 HIS 0.004 0.001 HIS A 616 Details of bonding type rmsd covalent geometry : bond 0.00353 (10303) covalent geometry : angle 0.52891 (14019) hydrogen bonds : bond 0.03653 ( 334) hydrogen bonds : angle 4.75861 ( 912) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 88 time to evaluate : 0.410 Fit side-chains REVERT: A 19 ASP cc_start: 0.8522 (m-30) cc_final: 0.7679 (t0) REVERT: A 85 GLN cc_start: 0.8558 (mt0) cc_final: 0.7714 (mt0) REVERT: A 190 MET cc_start: 0.6665 (mmm) cc_final: 0.6283 (mmt) REVERT: A 244 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8361 (tp) REVERT: A 551 GLN cc_start: 0.7026 (tt0) cc_final: 0.6156 (pm20) REVERT: A 553 GLN cc_start: 0.6873 (mp10) cc_final: 0.6612 (mp10) REVERT: A 886 ARG cc_start: 0.8015 (ttp80) cc_final: 0.7140 (ptm-80) REVERT: B 465 ASN cc_start: 0.7197 (m-40) cc_final: 0.6714 (p0) REVERT: B 532 GLN cc_start: 0.7912 (mm110) cc_final: 0.6478 (pt0) REVERT: B 582 PHE cc_start: 0.7213 (t80) cc_final: 0.6797 (t80) outliers start: 31 outliers final: 20 residues processed: 112 average time/residue: 0.1063 time to fit residues: 16.9204 Evaluate side-chains 107 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 161 PHE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 322 GLN Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain A residue 808 SER Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 933 CYS Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 561 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 112 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 chunk 54 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.136633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.101476 restraints weight = 11931.669| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.25 r_work: 0.3150 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10303 Z= 0.124 Angle : 0.517 7.405 14019 Z= 0.259 Chirality : 0.045 0.161 1575 Planarity : 0.004 0.050 1807 Dihedral : 4.430 49.194 1413 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.37 % Allowed : 14.79 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: -0.58 (0.24), residues: 1273 helix: 0.85 (0.39), residues: 178 sheet: -0.00 (0.26), residues: 404 loop : -0.94 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 258 TYR 0.013 0.001 TYR B 368 PHE 0.023 0.001 PHE A 227 TRP 0.008 0.001 TRP B 437 HIS 0.003 0.001 HIS A 616 Details of bonding type rmsd covalent geometry : bond 0.00304 (10303) covalent geometry : angle 0.51677 (14019) hydrogen bonds : bond 0.03524 ( 334) hydrogen bonds : angle 4.68815 ( 912) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.417 Fit side-chains REVERT: A 19 ASP cc_start: 0.8470 (m-30) cc_final: 0.7767 (t0) REVERT: A 85 GLN cc_start: 0.8582 (mt0) cc_final: 0.7841 (mt0) REVERT: A 190 MET cc_start: 0.6961 (mmm) cc_final: 0.6633 (mmt) REVERT: A 244 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8571 (tp) REVERT: A 551 GLN cc_start: 0.7193 (tt0) cc_final: 0.6359 (pm20) REVERT: A 886 ARG cc_start: 0.8084 (ttp80) cc_final: 0.7405 (ptm-80) REVERT: B 258 ARG cc_start: 0.6555 (ttm170) cc_final: 0.5916 (ttp-110) REVERT: B 465 ASN cc_start: 0.7402 (m-40) cc_final: 0.6970 (p0) REVERT: B 532 GLN cc_start: 0.8128 (mm110) cc_final: 0.6711 (pt0) REVERT: B 582 PHE cc_start: 0.7359 (t80) cc_final: 0.7043 (t80) outliers start: 25 outliers final: 20 residues processed: 112 average time/residue: 0.1076 time to fit residues: 17.1972 Evaluate side-chains 108 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 161 PHE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 322 GLN Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain A residue 808 SER Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 933 CYS Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 561 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 70 optimal weight: 0.0370 chunk 61 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 115 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.137937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.102894 restraints weight = 11811.328| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.22 r_work: 0.3191 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10303 Z= 0.102 Angle : 0.497 6.657 14019 Z= 0.249 Chirality : 0.044 0.157 1575 Planarity : 0.004 0.051 1807 Dihedral : 4.289 49.200 1413 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.99 % Allowed : 15.36 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: -0.48 (0.24), residues: 1273 helix: 0.98 (0.39), residues: 177 sheet: 0.04 (0.27), residues: 390 loop : -0.84 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 177 TYR 0.013 0.001 TYR B 368 PHE 0.023 0.001 PHE B 329 TRP 0.007 0.001 TRP A 216 HIS 0.003 0.001 HIS A 383 Details of bonding type rmsd covalent geometry : bond 0.00244 (10303) covalent geometry : angle 0.49686 (14019) hydrogen bonds : bond 0.03260 ( 334) hydrogen bonds : angle 4.59508 ( 912) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: A 19 ASP cc_start: 0.8430 (m-30) cc_final: 0.7784 (t0) REVERT: A 85 GLN cc_start: 0.8562 (mt0) cc_final: 0.7848 (mt0) REVERT: A 190 MET cc_start: 0.6916 (mmm) cc_final: 0.6646 (mmt) REVERT: A 551 GLN cc_start: 0.7199 (tt0) cc_final: 0.6391 (pm20) REVERT: A 553 GLN cc_start: 0.7157 (mp10) cc_final: 0.6870 (mp10) REVERT: A 886 ARG cc_start: 0.8052 (ttp80) cc_final: 0.7340 (ptm-80) REVERT: B 465 ASN cc_start: 0.7382 (m-40) cc_final: 0.7001 (p0) REVERT: B 532 GLN cc_start: 0.8138 (mm110) cc_final: 0.6717 (pt0) REVERT: B 582 PHE cc_start: 0.7318 (t80) cc_final: 0.7040 (t80) outliers start: 21 outliers final: 20 residues processed: 112 average time/residue: 0.0999 time to fit residues: 16.1882 Evaluate side-chains 112 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 161 PHE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 322 GLN Chi-restraints excluded: chain A residue 378 TYR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain A residue 808 SER Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 933 CYS Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 561 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 6 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.136185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.102342 restraints weight = 12007.781| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.09 r_work: 0.3086 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10303 Z= 0.134 Angle : 0.524 7.304 14019 Z= 0.263 Chirality : 0.045 0.163 1575 Planarity : 0.004 0.050 1807 Dihedral : 4.388 49.421 1413 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.90 % Allowed : 15.64 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: -0.56 (0.24), residues: 1273 helix: 0.88 (0.39), residues: 178 sheet: -0.01 (0.26), residues: 404 loop : -0.91 (0.25), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 177 TYR 0.012 0.001 TYR B 430 PHE 0.026 0.002 PHE B 329 TRP 0.009 0.001 TRP B 437 HIS 0.003 0.001 HIS A 616 Details of bonding type rmsd covalent geometry : bond 0.00332 (10303) covalent geometry : angle 0.52449 (14019) hydrogen bonds : bond 0.03553 ( 334) hydrogen bonds : angle 4.62075 ( 912) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2740.94 seconds wall clock time: 47 minutes 40.80 seconds (2860.80 seconds total)