Starting phenix.real_space_refine on Mon Jul 28 06:16:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ejm_48105/07_2025/9ejm_48105_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ejm_48105/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ejm_48105/07_2025/9ejm_48105.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ejm_48105/07_2025/9ejm_48105.map" model { file = "/net/cci-nas-00/data/ceres_data/9ejm_48105/07_2025/9ejm_48105_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ejm_48105/07_2025/9ejm_48105_neut.cif" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.015 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLU:plan': 15, 'ARG:plan': 7, '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, 'TPO:plan-1': 2, 'TYR:plan': 1, 'ASP:plan': 8, 'GLU:plan': 7, 'ARG:plan': 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: {'GLU:plan': 4, 'ARG:plan': 2, '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: 8.54, per 1000 atoms: 0.85 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: 2.20 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.55 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: 3.83 Time building geometry restraints manager: 2.68 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: 8.310 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: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 28.510 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.380 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.007 0.001 TRP A 100 HIS 0.003 0.001 HIS A 609 PHE 0.014 0.001 PHE A 300 TYR 0.011 0.001 TYR A 225 ARG 0.052 0.001 ARG B 480 Details of bonding type rmsd hydrogen bonds : bond 0.15677 ( 334) hydrogen bonds : angle 6.39210 ( 912) covalent geometry : bond 0.00195 (10303) covalent geometry : angle 0.50340 (14019) *********************** 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 : 1.104 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: 0.2355 time to fit residues: 47.3933 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 : 1.216 ------------------------------------------------------------------------------- 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 108 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 52 optimal weight: 0.1980 chunk 101 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 61 optimal weight: 0.0060 chunk 75 optimal weight: 3.9990 chunk 117 optimal weight: 10.0000 overall best weight: 1.3800 ------------------------------------------------------------------------------- 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 = 0.3542 r_free = 0.3542 target = 0.136453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.100284 restraints weight = 11892.113| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.37 r_work: 0.3066 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10303 Z= 0.163 Angle : 0.556 7.311 14019 Z= 0.281 Chirality : 0.046 0.174 1575 Planarity : 0.004 0.038 1807 Dihedral : 4.386 44.863 1415 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.18 % Allowed : 11.00 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.24), residues: 1273 helix: 0.84 (0.39), residues: 176 sheet: 0.14 (0.26), residues: 405 loop : -0.90 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 450 HIS 0.009 0.001 HIS A 319 PHE 0.018 0.002 PHE A 227 TYR 0.014 0.002 TYR A 911 ARG 0.006 0.000 ARG B 480 Details of bonding type rmsd hydrogen bonds : bond 0.04151 ( 334) hydrogen bonds : angle 5.10395 ( 912) covalent geometry : bond 0.00404 (10303) covalent geometry : angle 0.55622 (14019) *********************** 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 130 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 1.177 Fit side-chains REVERT: A 19 ASP cc_start: 0.8515 (m-30) cc_final: 0.7579 (t0) REVERT: A 85 GLN cc_start: 0.8562 (mt0) cc_final: 0.7741 (mt0) REVERT: A 190 MET cc_start: 0.6590 (mmm) cc_final: 0.6239 (mmt) REVERT: A 244 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8286 (tp) REVERT: A 551 GLN cc_start: 0.6991 (tt0) cc_final: 0.6173 (pm20) REVERT: A 553 GLN cc_start: 0.6699 (mp10) cc_final: 0.6494 (mp10) REVERT: A 886 ARG cc_start: 0.8020 (ttp80) cc_final: 0.7181 (ptm-80) REVERT: B 465 ASN cc_start: 0.7045 (m-40) cc_final: 0.6275 (p0) REVERT: B 532 GLN cc_start: 0.7918 (mm110) cc_final: 0.6519 (pt0) REVERT: B 582 PHE cc_start: 0.7156 (t80) cc_final: 0.6672 (t80) outliers start: 23 outliers final: 15 residues processed: 121 average time/residue: 0.2505 time to fit residues: 42.5122 Evaluate side-chains 109 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 1.114 ------------------------------------------------------------------------------- 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 696 VAL 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 374 ILE 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 109 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 73 optimal weight: 0.3980 chunk 57 optimal weight: 3.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 = 0.3519 r_free = 0.3519 target = 0.134598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.098312 restraints weight = 12037.475| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.37 r_work: 0.3033 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10303 Z= 0.182 Angle : 0.567 8.012 14019 Z= 0.285 Chirality : 0.046 0.179 1575 Planarity : 0.005 0.046 1807 Dihedral : 4.565 45.765 1413 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.94 % Allowed : 12.42 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.24), residues: 1273 helix: 0.91 (0.39), residues: 168 sheet: 0.03 (0.26), residues: 403 loop : -0.93 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 437 HIS 0.005 0.001 HIS A 616 PHE 0.020 0.002 PHE A 227 TYR 0.013 0.002 TYR A 911 ARG 0.003 0.000 ARG A 177 Details of bonding type rmsd hydrogen bonds : bond 0.04152 ( 334) hydrogen bonds : angle 4.98262 ( 912) covalent geometry : bond 0.00457 (10303) covalent geometry : angle 0.56738 (14019) *********************** 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 130 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 99 time to evaluate : 1.163 Fit side-chains REVERT: A 19 ASP cc_start: 0.8539 (m-30) cc_final: 0.7630 (t0) REVERT: A 85 GLN cc_start: 0.8592 (mt0) cc_final: 0.7737 (mt0) REVERT: A 190 MET cc_start: 0.6692 (mmm) cc_final: 0.6317 (mmt) REVERT: A 244 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8318 (tp) REVERT: A 551 GLN cc_start: 0.6997 (tt0) cc_final: 0.6143 (pm20) REVERT: A 553 GLN cc_start: 0.6861 (mp10) cc_final: 0.6575 (mp10) REVERT: A 801 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7513 (ptpp) REVERT: A 886 ARG cc_start: 0.8072 (ttp80) cc_final: 0.7235 (ptm-80) REVERT: B 465 ASN cc_start: 0.7144 (m-40) cc_final: 0.6484 (p0) REVERT: B 532 GLN cc_start: 0.7949 (mm110) cc_final: 0.6553 (pt0) REVERT: B 582 PHE cc_start: 0.7229 (t80) cc_final: 0.6769 (t80) outliers start: 31 outliers final: 16 residues processed: 123 average time/residue: 0.2485 time to fit residues: 42.7996 Evaluate side-chains 107 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 1.169 ------------------------------------------------------------------------------- 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 801 LYS 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 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 57 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.135887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.102437 restraints weight = 11842.729| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.03 r_work: 0.3074 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1440 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= 0.134 Angle : 0.522 7.534 14019 Z= 0.262 Chirality : 0.045 0.165 1575 Planarity : 0.004 0.047 1807 Dihedral : 4.436 46.425 1413 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.22 % Allowed : 13.08 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.24), residues: 1273 helix: 1.05 (0.39), residues: 168 sheet: 0.00 (0.26), residues: 403 loop : -0.92 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 437 HIS 0.003 0.001 HIS A 616 PHE 0.021 0.002 PHE A 227 TYR 0.011 0.001 TYR A 911 ARG 0.003 0.000 ARG A 177 Details of bonding type rmsd hydrogen bonds : bond 0.03664 ( 334) hydrogen bonds : angle 4.83656 ( 912) covalent geometry : bond 0.00330 (10303) covalent geometry : angle 0.52190 (14019) *********************** 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 128 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 94 time to evaluate : 1.092 Fit side-chains revert: symmetry clash REVERT: A 19 ASP cc_start: 0.8439 (m-30) cc_final: 0.7751 (t0) REVERT: A 85 GLN cc_start: 0.8605 (mt0) cc_final: 0.7850 (mt0) REVERT: A 190 MET cc_start: 0.6892 (mmm) cc_final: 0.6610 (mmt) REVERT: A 244 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8551 (tp) REVERT: A 551 GLN cc_start: 0.7188 (tt0) cc_final: 0.6369 (pm20) REVERT: A 801 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7783 (ptpp) REVERT: B 465 ASN cc_start: 0.7402 (m-40) cc_final: 0.6873 (p0) REVERT: B 532 GLN cc_start: 0.8123 (mm110) cc_final: 0.6770 (pt0) REVERT: B 582 PHE cc_start: 0.7368 (t80) cc_final: 0.7054 (t80) outliers start: 34 outliers final: 20 residues processed: 119 average time/residue: 0.2365 time to fit residues: 40.1748 Evaluate side-chains 110 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 1.240 ------------------------------------------------------------------------------- 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 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 696 VAL Chi-restraints excluded: chain A residue 749 VAL Chi-restraints excluded: chain A residue 786 SER Chi-restraints excluded: chain A residue 801 LYS 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 305 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 56 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 70 optimal weight: 0.0000 chunk 93 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.3590 ------------------------------------------------------------------------------- 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 = 0.3519 r_free = 0.3519 target = 0.134655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.098461 restraints weight = 12002.376| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.37 r_work: 0.3118 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1567 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= 0.156 Angle : 0.541 7.944 14019 Z= 0.271 Chirality : 0.045 0.168 1575 Planarity : 0.004 0.048 1807 Dihedral : 4.513 47.106 1413 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.32 % Allowed : 13.18 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.24), residues: 1273 helix: 0.75 (0.39), residues: 175 sheet: -0.06 (0.26), residues: 404 loop : -1.00 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 437 HIS 0.004 0.001 HIS A 616 PHE 0.021 0.002 PHE A 227 TYR 0.012 0.002 TYR A 911 ARG 0.004 0.000 ARG A 177 Details of bonding type rmsd hydrogen bonds : bond 0.03854 ( 334) hydrogen bonds : angle 4.82914 ( 912) covalent geometry : bond 0.00390 (10303) covalent geometry : angle 0.54131 (14019) *********************** 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 127 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 92 time to evaluate : 1.034 Fit side-chains revert: symmetry clash REVERT: A 19 ASP cc_start: 0.8530 (m-30) cc_final: 0.7645 (t0) REVERT: A 85 GLN cc_start: 0.8587 (mt0) cc_final: 0.7724 (mt0) REVERT: A 190 MET cc_start: 0.6611 (mmm) cc_final: 0.6235 (mmt) REVERT: A 244 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8321 (tp) REVERT: A 551 GLN cc_start: 0.7013 (tt0) cc_final: 0.6142 (pm20) REVERT: A 608 SER cc_start: 0.6427 (t) cc_final: 0.6214 (m) REVERT: A 801 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7462 (ptpp) REVERT: B 465 ASN cc_start: 0.7199 (m-40) cc_final: 0.6623 (p0) REVERT: B 532 GLN cc_start: 0.7900 (mm110) cc_final: 0.6489 (pt0) REVERT: B 582 PHE cc_start: 0.7174 (t80) cc_final: 0.6741 (t80) outliers start: 35 outliers final: 22 residues processed: 118 average time/residue: 0.2240 time to fit residues: 37.7134 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 : 1.038 ------------------------------------------------------------------------------- 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 405 ILE 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 801 LYS 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 410 THR Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 561 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 67 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 125 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3537 r_free = 0.3537 target = 0.136270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.100189 restraints weight = 12008.742| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.36 r_work: 0.3139 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10303 Z= 0.110 Angle : 0.505 7.221 14019 Z= 0.253 Chirality : 0.044 0.159 1575 Planarity : 0.004 0.048 1807 Dihedral : 4.356 47.594 1413 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.75 % Allowed : 13.84 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.24), residues: 1273 helix: 0.90 (0.39), residues: 175 sheet: -0.01 (0.26), residues: 404 loop : -0.92 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 216 HIS 0.003 0.001 HIS A 383 PHE 0.020 0.001 PHE B 329 TYR 0.010 0.001 TYR B 430 ARG 0.004 0.000 ARG A 177 Details of bonding type rmsd hydrogen bonds : bond 0.03441 ( 334) hydrogen bonds : angle 4.71822 ( 912) covalent geometry : bond 0.00266 (10303) covalent geometry : angle 0.50451 (14019) *********************** 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 125 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 1.072 Fit side-chains REVERT: A 19 ASP cc_start: 0.8536 (m-30) cc_final: 0.7652 (t0) REVERT: A 85 GLN cc_start: 0.8529 (mt0) cc_final: 0.7718 (mt0) REVERT: A 190 MET cc_start: 0.6626 (mmm) cc_final: 0.6260 (mmt) REVERT: A 551 GLN cc_start: 0.6998 (tt0) cc_final: 0.6139 (pm20) REVERT: A 801 LYS cc_start: 0.7696 (OUTLIER) cc_final: 0.7421 (ptpp) REVERT: A 886 ARG cc_start: 0.7999 (ttp80) cc_final: 0.7134 (ptm-80) REVERT: A 902 VAL cc_start: 0.7928 (p) cc_final: 0.7678 (m) REVERT: B 465 ASN cc_start: 0.7171 (m-40) cc_final: 0.6640 (p0) REVERT: B 532 GLN cc_start: 0.7878 (mm110) cc_final: 0.6471 (pt0) REVERT: B 582 PHE cc_start: 0.7179 (t80) cc_final: 0.6763 (t80) outliers start: 29 outliers final: 19 residues processed: 118 average time/residue: 0.2243 time to fit residues: 37.7482 Evaluate side-chains 110 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 1.042 ------------------------------------------------------------------------------- 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 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 801 LYS 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 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 103 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3537 r_free = 0.3537 target = 0.136119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.099875 restraints weight = 12064.059| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.37 r_work: 0.3129 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10303 Z= 0.119 Angle : 0.507 7.229 14019 Z= 0.254 Chirality : 0.044 0.160 1575 Planarity : 0.004 0.047 1807 Dihedral : 4.352 48.019 1413 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.03 % Allowed : 14.22 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.24), residues: 1273 helix: 0.93 (0.39), residues: 177 sheet: 0.01 (0.26), residues: 404 loop : -0.89 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 437 HIS 0.003 0.001 HIS A 616 PHE 0.023 0.001 PHE A 227 TYR 0.010 0.001 TYR B 430 ARG 0.004 0.000 ARG A 177 Details of bonding type rmsd hydrogen bonds : bond 0.03466 ( 334) hydrogen bonds : angle 4.67915 ( 912) covalent geometry : bond 0.00292 (10303) covalent geometry : angle 0.50730 (14019) *********************** 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 125 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 93 time to evaluate : 1.169 Fit side-chains REVERT: A 19 ASP cc_start: 0.8515 (m-30) cc_final: 0.7662 (t0) REVERT: A 85 GLN cc_start: 0.8542 (mt0) cc_final: 0.7736 (mt0) REVERT: A 190 MET cc_start: 0.6699 (mmm) cc_final: 0.6326 (mmt) REVERT: A 551 GLN cc_start: 0.7003 (tt0) cc_final: 0.6149 (pm20) REVERT: A 553 GLN cc_start: 0.6996 (mp10) cc_final: 0.6319 (mp10) REVERT: A 608 SER cc_start: 0.6454 (t) cc_final: 0.6237 (m) REVERT: A 886 ARG cc_start: 0.8010 (ttp80) cc_final: 0.7150 (ptm-80) REVERT: A 902 VAL cc_start: 0.7994 (p) cc_final: 0.7742 (m) REVERT: B 443 MET cc_start: 0.7992 (mtp) cc_final: 0.7790 (mtp) REVERT: B 465 ASN cc_start: 0.7184 (m-40) cc_final: 0.6680 (p0) REVERT: B 532 GLN cc_start: 0.7895 (mm110) cc_final: 0.6492 (pt0) REVERT: B 582 PHE cc_start: 0.7205 (t80) cc_final: 0.6817 (t80) outliers start: 32 outliers final: 24 residues processed: 119 average time/residue: 0.2435 time to fit residues: 41.6970 Evaluate side-chains 115 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE 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 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 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 279 ILE 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 28 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 92 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 50 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 47 optimal weight: 0.0670 overall best weight: 0.9520 ------------------------------------------------------------------------------- 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 = 0.3539 r_free = 0.3539 target = 0.136147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.099887 restraints weight = 12000.905| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.37 r_work: 0.2958 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10303 Z= 0.122 Angle : 0.512 7.281 14019 Z= 0.257 Chirality : 0.044 0.160 1575 Planarity : 0.004 0.048 1807 Dihedral : 4.350 48.259 1413 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.84 % Allowed : 14.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.24), residues: 1273 helix: 0.88 (0.39), residues: 178 sheet: -0.00 (0.26), residues: 404 loop : -0.88 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 437 HIS 0.003 0.001 HIS A 616 PHE 0.018 0.001 PHE A 347 TYR 0.011 0.001 TYR B 430 ARG 0.005 0.000 ARG A 177 Details of bonding type rmsd hydrogen bonds : bond 0.03474 ( 334) hydrogen bonds : angle 4.66100 ( 912) covalent geometry : bond 0.00299 (10303) covalent geometry : angle 0.51178 (14019) *********************** 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 128 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 98 time to evaluate : 0.913 Fit side-chains REVERT: A 19 ASP cc_start: 0.8548 (m-30) cc_final: 0.7681 (t0) REVERT: A 85 GLN cc_start: 0.8542 (mt0) cc_final: 0.7735 (mt0) REVERT: A 190 MET cc_start: 0.6708 (mmm) cc_final: 0.6327 (mmt) REVERT: A 244 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8370 (tp) REVERT: A 551 GLN cc_start: 0.7010 (tt0) cc_final: 0.6147 (pm20) REVERT: A 608 SER cc_start: 0.6497 (t) cc_final: 0.6280 (m) REVERT: A 886 ARG cc_start: 0.7979 (ttp80) cc_final: 0.7088 (ptm-80) REVERT: A 902 VAL cc_start: 0.8061 (p) cc_final: 0.7795 (m) REVERT: B 336 ASN cc_start: 0.7313 (p0) cc_final: 0.7097 (p0) REVERT: B 364 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7410 (tt) REVERT: B 447 MET cc_start: 0.8439 (mtm) cc_final: 0.8219 (mtp) REVERT: B 465 ASN cc_start: 0.7222 (m-40) cc_final: 0.6719 (p0) REVERT: B 532 GLN cc_start: 0.7864 (mm110) cc_final: 0.6443 (pt0) REVERT: B 582 PHE cc_start: 0.7214 (t80) cc_final: 0.6792 (t80) outliers start: 30 outliers final: 23 residues processed: 122 average time/residue: 0.2686 time to fit residues: 46.7562 Evaluate side-chains 118 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE 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 426 THR Chi-restraints excluded: chain A residue 548 ASP 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 876 VAL Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 933 CYS Chi-restraints excluded: chain B residue 279 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 126 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 81 optimal weight: 0.3980 chunk 20 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 46 optimal weight: 0.0000 chunk 55 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.2790 ------------------------------------------------------------------------------- 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 = 0.3529 r_free = 0.3529 target = 0.135181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.099002 restraints weight = 12029.224| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.38 r_work: 0.3075 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 10303 Z= 0.150 Angle : 0.536 7.823 14019 Z= 0.269 Chirality : 0.045 0.165 1575 Planarity : 0.004 0.047 1807 Dihedral : 4.459 48.788 1413 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.46 % Allowed : 14.98 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.24), residues: 1273 helix: 0.82 (0.39), residues: 178 sheet: -0.06 (0.26), residues: 404 loop : -0.94 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 437 HIS 0.004 0.001 HIS A 616 PHE 0.025 0.002 PHE A 227 TYR 0.026 0.002 TYR B 368 ARG 0.004 0.000 ARG A 177 Details of bonding type rmsd hydrogen bonds : bond 0.03698 ( 334) hydrogen bonds : angle 4.69898 ( 912) covalent geometry : bond 0.00374 (10303) covalent geometry : angle 0.53650 (14019) *********************** 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 118 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 1.036 Fit side-chains REVERT: A 19 ASP cc_start: 0.8552 (m-30) cc_final: 0.7667 (t0) REVERT: A 85 GLN cc_start: 0.8531 (mt0) cc_final: 0.7703 (mt0) REVERT: A 190 MET cc_start: 0.6624 (mmm) cc_final: 0.6226 (mmt) REVERT: A 244 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8327 (tp) REVERT: A 551 GLN cc_start: 0.6953 (tt0) cc_final: 0.6099 (pm20) REVERT: A 608 SER cc_start: 0.6499 (t) cc_final: 0.6260 (m) REVERT: A 886 ARG cc_start: 0.8012 (ttp80) cc_final: 0.7111 (ptm-80) REVERT: A 902 VAL cc_start: 0.8006 (p) cc_final: 0.7717 (m) REVERT: B 336 ASN cc_start: 0.7375 (p0) cc_final: 0.7153 (p0) REVERT: B 447 MET cc_start: 0.8449 (mtm) cc_final: 0.8196 (mtp) REVERT: B 465 ASN cc_start: 0.7185 (m-40) cc_final: 0.6693 (p0) REVERT: B 532 GLN cc_start: 0.7857 (mm110) cc_final: 0.6415 (pt0) REVERT: B 582 PHE cc_start: 0.7172 (t80) cc_final: 0.6724 (t80) outliers start: 26 outliers final: 22 residues processed: 112 average time/residue: 0.2212 time to fit residues: 35.2856 Evaluate side-chains 113 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE 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 426 THR 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 876 VAL Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 933 CYS Chi-restraints excluded: chain B residue 279 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 119 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 6 optimal weight: 0.3980 chunk 107 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 98 optimal weight: 0.5980 chunk 3 optimal weight: 4.9990 chunk 115 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3573 r_free = 0.3573 target = 0.137985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.102936 restraints weight = 11857.316| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.24 r_work: 0.3185 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10303 Z= 0.103 Angle : 0.499 6.924 14019 Z= 0.251 Chirality : 0.044 0.157 1575 Planarity : 0.004 0.048 1807 Dihedral : 4.309 49.159 1413 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.24), residues: 1273 helix: 0.95 (0.39), residues: 178 sheet: -0.04 (0.26), residues: 398 loop : -0.81 (0.25), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 216 HIS 0.003 0.001 HIS A 383 PHE 0.024 0.001 PHE A 227 TYR 0.023 0.001 TYR B 368 ARG 0.005 0.000 ARG B 258 Details of bonding type rmsd hydrogen bonds : bond 0.03315 ( 334) hydrogen bonds : angle 4.62675 ( 912) covalent geometry : bond 0.00246 (10303) covalent geometry : angle 0.49901 (14019) ********************** 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 118 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 1.178 Fit side-chains revert: symmetry clash REVERT: A 19 ASP cc_start: 0.8470 (m-30) cc_final: 0.7774 (t0) REVERT: A 85 GLN cc_start: 0.8560 (mt0) cc_final: 0.7855 (mt0) REVERT: A 190 MET cc_start: 0.6889 (mmm) cc_final: 0.6601 (mmt) REVERT: A 551 GLN cc_start: 0.7158 (tt0) cc_final: 0.6341 (pm20) REVERT: A 886 ARG cc_start: 0.8062 (ttp80) cc_final: 0.7355 (ptm-80) REVERT: B 258 ARG cc_start: 0.6475 (ttm170) cc_final: 0.5822 (ttp-110) REVERT: B 465 ASN cc_start: 0.7382 (m-40) cc_final: 0.6982 (p0) REVERT: B 532 GLN cc_start: 0.8092 (mm110) cc_final: 0.6660 (pt0) REVERT: B 582 PHE cc_start: 0.7318 (t80) cc_final: 0.7018 (t80) outliers start: 21 outliers final: 19 residues processed: 112 average time/residue: 0.2155 time to fit residues: 35.2647 Evaluate side-chains 110 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 49 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 126 optimal weight: 0.5980 chunk 92 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3565 r_free = 0.3565 target = 0.137528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.104099 restraints weight = 11864.621| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.05 r_work: 0.3128 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10303 Z= 0.106 Angle : 0.500 6.781 14019 Z= 0.252 Chirality : 0.044 0.157 1575 Planarity : 0.004 0.048 1807 Dihedral : 4.279 49.103 1413 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.46 % Allowed : 15.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.24), residues: 1273 helix: 0.97 (0.39), residues: 178 sheet: -0.02 (0.26), residues: 398 loop : -0.81 (0.24), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 437 HIS 0.003 0.001 HIS A 383 PHE 0.024 0.001 PHE B 329 TYR 0.023 0.001 TYR B 368 ARG 0.004 0.000 ARG A 177 Details of bonding type rmsd hydrogen bonds : bond 0.03312 ( 334) hydrogen bonds : angle 4.55371 ( 912) covalent geometry : bond 0.00255 (10303) covalent geometry : angle 0.50047 (14019) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5708.51 seconds wall clock time: 101 minutes 15.54 seconds (6075.54 seconds total)