Starting phenix.real_space_refine on Wed Aug 5 02:46:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ney_49339/08_2026/9ney_49339.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ney_49339/08_2026/9ney_49339.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ney_49339/08_2026/9ney_49339.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ney_49339/08_2026/9ney_49339.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ney_49339/08_2026/9ney_49339.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ney_49339/08_2026/9ney_49339.map" } resolution = 3.06 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= 0.001 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 5142 2.51 5 N 1323 2.21 5 O 1524 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8015 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 807, 6270 Classifications: {'peptide': 807} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 28, 'TRANS': 778} Chain breaks: 9 Unresolved non-hydrogen bonds: 288 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 16, 'GLU:plan': 11, 'ASN:plan1': 6, 'HIS:plan': 1, 'ARG:plan': 2, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 166 Chain: "C" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 968 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain: "B" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 777 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 19 Time building chain proxies: 1.85, per 1000 atoms: 0.23 Number of scatterers: 8015 At special positions: 0 Unit cell: (98.3654, 107.458, 113.244, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 1524 8.00 N 1323 7.00 C 5142 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 104 " - pdb=" SG CYS C 109 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 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: 0.59 Conformation dependent library (CDL) restraints added in 451.0 milliseconds 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1966 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 10 sheets defined 38.4% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 82 through 100 removed outlier: 3.686A pdb=" N ASN A 86 " --> pdb=" O ASN A 82 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR A 87 " --> pdb=" O GLU A 83 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 113 removed outlier: 3.809A pdb=" N THR A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER A 110 " --> pdb=" O MET A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 132 No H-bonds generated for 'chain 'A' and resid 130 through 132' Processing helix chain 'A' and resid 174 through 178 removed outlier: 3.990A pdb=" N ASN A 178 " --> pdb=" O LEU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 231 removed outlier: 3.602A pdb=" N ARG A 231 " --> pdb=" O HIS A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 267 Processing helix chain 'A' and resid 270 through 274 removed outlier: 3.681A pdb=" N ILE A 274 " --> pdb=" O ALA A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 297 removed outlier: 3.554A pdb=" N LEU A 284 " --> pdb=" O ASN A 280 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR A 287 " --> pdb=" O ARG A 283 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS A 289 " --> pdb=" O TYR A 285 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N PHE A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 319 removed outlier: 3.648A pdb=" N PHE A 317 " --> pdb=" O MET A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 347 removed outlier: 3.530A pdb=" N LYS A 340 " --> pdb=" O LEU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 353 through 358 removed outlier: 3.867A pdb=" N PHE A 357 " --> pdb=" O ASN A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 405 Processing helix chain 'A' and resid 409 through 413 removed outlier: 3.726A pdb=" N PHE A 413 " --> pdb=" O ASN A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 467 through 471 removed outlier: 3.928A pdb=" N PHE A 471 " --> pdb=" O GLU A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 506 removed outlier: 3.618A pdb=" N LEU A 504 " --> pdb=" O GLN A 500 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N THR A 505 " --> pdb=" O GLN A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 557 Processing helix chain 'A' and resid 573 through 578 removed outlier: 3.653A pdb=" N LEU A 577 " --> pdb=" O ASN A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 595 removed outlier: 3.600A pdb=" N ASN A 595 " --> pdb=" O VAL A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 601 No H-bonds generated for 'chain 'A' and resid 599 through 601' Processing helix chain 'A' and resid 602 through 620 removed outlier: 4.388A pdb=" N VAL A 611 " --> pdb=" O VAL A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 642 Processing helix chain 'A' and resid 643 through 646 removed outlier: 3.591A pdb=" N MET A 646 " --> pdb=" O ILE A 643 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 643 through 646' Processing helix chain 'A' and resid 651 through 659 removed outlier: 3.554A pdb=" N ILE A 657 " --> pdb=" O VAL A 653 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE A 658 " --> pdb=" O GLY A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 664 removed outlier: 3.590A pdb=" N ILE A 663 " --> pdb=" O GLY A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 721 Processing helix chain 'A' and resid 721 through 752 removed outlier: 3.544A pdb=" N ALA A 742 " --> pdb=" O ASN A 738 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE A 746 " --> pdb=" O ALA A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 800 removed outlier: 3.685A pdb=" N LEU A 769 " --> pdb=" O ASN A 765 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE A 782 " --> pdb=" O ASN A 778 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASN A 783 " --> pdb=" O LYS A 779 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN A 785 " --> pdb=" O MET A 781 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET A 800 " --> pdb=" O LEU A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 825 removed outlier: 3.691A pdb=" N ARG A 807 " --> pdb=" O TYR A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 847 removed outlier: 4.158A pdb=" N LEU A 845 " --> pdb=" O VAL A 841 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR A 847 " --> pdb=" O ASN A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 857 removed outlier: 4.316A pdb=" N TYR A 856 " --> pdb=" O GLN A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 870 removed outlier: 3.965A pdb=" N THR A 865 " --> pdb=" O ARG A 861 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU A 868 " --> pdb=" O SER A 864 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR A 869 " --> pdb=" O THR A 865 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.633A pdb=" N THR C 91 " --> pdb=" O ALA C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 110 removed outlier: 3.683A pdb=" N PHE C 110 " --> pdb=" O LEU C 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.982A pdb=" N PHE B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 144 through 148 removed outlier: 3.602A pdb=" N GLU A 147 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR A 21 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE A 42 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL A 152 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 126 through 127 Processing sheet with id=AA3, first strand: chain 'A' and resid 192 through 195 Processing sheet with id=AA4, first strand: chain 'A' and resid 455 through 458 removed outlier: 9.154A pdb=" N TYR A 543 " --> pdb=" O TYR A 426 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU A 428 " --> pdb=" O TYR A 543 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N LEU A 545 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N CYS A 430 " --> pdb=" O LEU A 545 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 568 through 570 removed outlier: 6.037A pdb=" N LEU A 568 " --> pdb=" O VAL A 582 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA7, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.797A pdb=" N MET C 34 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N SER C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.793A pdb=" N SER C 115 " --> pdb=" O LYS C 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'B' and resid 53 through 54 removed outlier: 7.185A pdb=" N LEU B 46 " --> pdb=" O GLN B 37 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLN B 37 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA B 84 " --> pdb=" O VAL B 105 " (cutoff:3.500A) 320 hydrogen bonds defined for protein. 882 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: 1.30 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2561 1.34 - 1.46: 1669 1.46 - 1.57: 3912 1.57 - 1.69: 0 1.69 - 1.81: 41 Bond restraints: 8183 Sorted by residual: bond pdb=" CG1 ILE B 21 " pdb=" CD1 ILE B 21 " ideal model delta sigma weight residual 1.513 1.476 0.037 3.90e-02 6.57e+02 8.83e-01 bond pdb=" CG GLU A 252 " pdb=" CD GLU A 252 " ideal model delta sigma weight residual 1.516 1.494 0.022 2.50e-02 1.60e+03 8.02e-01 bond pdb=" CB THR A 569 " pdb=" CG2 THR A 569 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.16e-01 bond pdb=" N GLY A 155 " pdb=" CA GLY A 155 " ideal model delta sigma weight residual 1.443 1.432 0.011 1.37e-02 5.33e+03 6.40e-01 bond pdb=" CB VAL C 53 " pdb=" CG2 VAL C 53 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.13e-01 ... (remaining 8178 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 10807 1.40 - 2.80: 246 2.80 - 4.19: 38 4.19 - 5.59: 10 5.59 - 6.99: 2 Bond angle restraints: 11103 Sorted by residual: angle pdb=" CA GLY B 102 " pdb=" C GLY B 102 " pdb=" O GLY B 102 " ideal model delta sigma weight residual 122.37 120.15 2.22 7.30e-01 1.88e+00 9.26e+00 angle pdb=" CA GLY B 102 " pdb=" C GLY B 102 " pdb=" N THR B 103 " ideal model delta sigma weight residual 114.13 117.27 -3.14 1.11e+00 8.12e-01 8.00e+00 angle pdb=" C GLN A 753 " pdb=" N TYR A 754 " pdb=" CA TYR A 754 " ideal model delta sigma weight residual 121.70 125.84 -4.14 1.80e+00 3.09e-01 5.29e+00 angle pdb=" C ILE B 21 " pdb=" N THR B 22 " pdb=" CA THR B 22 " ideal model delta sigma weight residual 122.62 119.20 3.42 1.56e+00 4.11e-01 4.80e+00 angle pdb=" CA TYR C 103 " pdb=" CB TYR C 103 " pdb=" CG TYR C 103 " ideal model delta sigma weight residual 113.90 117.77 -3.87 1.80e+00 3.09e-01 4.62e+00 ... (remaining 11098 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 4105 17.64 - 35.27: 558 35.27 - 52.91: 141 52.91 - 70.55: 37 70.55 - 88.18: 11 Dihedral angle restraints: 4852 sinusoidal: 1804 harmonic: 3048 Sorted by residual: dihedral pdb=" CB CYS C 104 " pdb=" SG CYS C 104 " pdb=" SG CYS C 109 " pdb=" CB CYS C 109 " ideal model delta sinusoidal sigma weight residual -86.00 -145.60 59.60 1 1.00e+01 1.00e-02 4.74e+01 dihedral pdb=" CA PHE A 357 " pdb=" C PHE A 357 " pdb=" N PHE A 358 " pdb=" CA PHE A 358 " ideal model delta harmonic sigma weight residual 180.00 162.74 17.26 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA CYS C 109 " pdb=" C CYS C 109 " pdb=" N PHE C 110 " pdb=" CA PHE C 110 " ideal model delta harmonic sigma weight residual 180.00 163.04 16.96 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 4849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 882 0.040 - 0.080: 271 0.080 - 0.120: 95 0.120 - 0.160: 10 0.160 - 0.200: 1 Chirality restraints: 1259 Sorted by residual: chirality pdb=" CA ILE B 21 " pdb=" N ILE B 21 " pdb=" C ILE B 21 " pdb=" CB ILE B 21 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.99e-01 chirality pdb=" CA ILE A 115 " pdb=" N ILE A 115 " pdb=" C ILE A 115 " pdb=" CB ILE A 115 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.34e-01 chirality pdb=" CA ILE A 19 " pdb=" N ILE A 19 " pdb=" C ILE A 19 " pdb=" CB ILE A 19 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.60e-01 ... (remaining 1256 not shown) Planarity restraints: 1421 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 801 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.25e+00 pdb=" N PRO A 802 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 802 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 802 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 60 " 0.029 5.00e-02 4.00e+02 4.37e-02 3.05e+00 pdb=" N PRO A 61 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 61 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 61 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 68 " -0.026 5.00e-02 4.00e+02 3.95e-02 2.50e+00 pdb=" N PRO A 69 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 69 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 69 " -0.022 5.00e-02 4.00e+02 ... (remaining 1418 not shown) Histogram of nonbonded interaction distances: 2.59 - 3.05: 4795 3.05 - 3.51: 7868 3.51 - 3.97: 12561 3.97 - 4.44: 15627 4.44 - 4.90: 24797 Nonbonded interactions: 65648 Sorted by model distance: nonbonded pdb=" N ASN A 533 " pdb=" OD1 ASN A 533 " model vdw 2.585 3.120 nonbonded pdb=" O ASN A 507 " pdb=" OD1 ASN A 507 " model vdw 2.604 3.040 nonbonded pdb=" N ILE A 235 " pdb=" N ALA A 236 " model vdw 2.606 2.560 nonbonded pdb=" N THR A 306 " pdb=" OG1 THR A 306 " model vdw 2.612 2.496 nonbonded pdb=" N PHE A 213 " pdb=" O PHE A 213 " model vdw 2.612 2.496 ... (remaining 65643 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: 4.530 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.760 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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: 0.010 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: 14.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8187 Z= 0.153 Angle : 0.528 6.988 11111 Z= 0.284 Chirality : 0.043 0.200 1259 Planarity : 0.004 0.052 1421 Dihedral : 17.983 88.182 2874 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 5.13 % Allowed : 28.52 % Favored : 66.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.25), residues: 1018 helix: -1.44 (0.27), residues: 326 sheet: -1.15 (0.40), residues: 165 loop : -1.01 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 105 TYR 0.018 0.001 TYR C 103 PHE 0.017 0.001 PHE A 369 TRP 0.016 0.001 TRP A 460 HIS 0.002 0.001 HIS A 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.15 ( 8183) covalent geometry : angle 0.52743 / 0.28 (11103) SS BOND : bond 0.00154 / 0.09 ( 4) SS BOND : angle 1.25824 / 0.51 ( 8) hydrogen bonds : bond 0.23703 / 15.96 ( 315) hydrogen bonds : angle 8.93949 / 6.18 ( 882) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 98 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: A 51 PHE cc_start: 0.8455 (OUTLIER) cc_final: 0.7434 (p90) REVERT: A 153 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8173 (mm) REVERT: A 177 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.8073 (mtm-85) REVERT: A 319 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7777 (mt-10) REVERT: A 343 LYS cc_start: 0.8110 (ttpp) cc_final: 0.7687 (ttmm) REVERT: A 364 LYS cc_start: 0.8542 (mmtp) cc_final: 0.8203 (mmtm) REVERT: A 397 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7458 (pp) REVERT: A 407 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7872 (mm-30) REVERT: A 479 GLU cc_start: 0.8249 (tp30) cc_final: 0.7843 (tp30) REVERT: A 524 ILE cc_start: 0.6925 (OUTLIER) cc_final: 0.6280 (mm) REVERT: A 554 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8191 (tp) REVERT: A 596 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7691 (pttp) REVERT: A 734 GLU cc_start: 0.8188 (tt0) cc_final: 0.7661 (mt-10) REVERT: A 796 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8318 (tp) REVERT: A 861 ARG cc_start: 0.7035 (OUTLIER) cc_final: 0.6528 (ttp-170) REVERT: C 17 SER cc_start: 0.8459 (p) cc_final: 0.8195 (m) REVERT: C 118 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.7236 (pt0) REVERT: C 121 ARG cc_start: 0.8256 (ttm-80) cc_final: 0.7833 (ttm-80) REVERT: B 95 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.7136 (mtm110) outliers start: 43 outliers final: 28 residues processed: 131 average time/residue: 0.0876 time to fit residues: 15.9216 Evaluate side-chains 139 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 99 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LYS Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 177 ARG Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 400 ASN Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 861 ARG Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 104 CYS Chi-restraints excluded: chain C residue 118 GLN Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 95 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 223 HIS A 412 ASN A 514 ASN C 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.164019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.136435 restraints weight = 9322.194| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.13 r_work: 0.3469 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.0681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8187 Z= 0.168 Angle : 0.555 6.920 11111 Z= 0.299 Chirality : 0.044 0.181 1259 Planarity : 0.004 0.051 1421 Dihedral : 8.454 69.857 1190 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 7.40 % Allowed : 26.61 % Favored : 65.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.26), residues: 1018 helix: -0.40 (0.28), residues: 335 sheet: -1.00 (0.41), residues: 162 loop : -0.99 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 95 TYR 0.018 0.001 TYR C 103 PHE 0.019 0.001 PHE A 338 TRP 0.015 0.002 TRP A 460 HIS 0.002 0.001 HIS A 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 ( 8183) covalent geometry : angle 0.55409 / 0.30 (11103) SS BOND : bond 0.00158 / 0.08 ( 4) SS BOND : angle 1.22670 / 0.52 ( 8) hydrogen bonds : bond 0.05309 / 3.51 ( 315) hydrogen bonds : angle 5.37529 / 3.67 ( 882) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 102 time to evaluate : 0.294 Fit side-chains REVERT: A 51 PHE cc_start: 0.8445 (OUTLIER) cc_final: 0.7482 (p90) REVERT: A 319 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7889 (mt-10) REVERT: A 343 LYS cc_start: 0.7994 (ttpp) cc_final: 0.7572 (ttmm) REVERT: A 364 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8252 (mmtm) REVERT: A 397 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7357 (pp) REVERT: A 407 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7861 (mm-30) REVERT: A 479 GLU cc_start: 0.8296 (tp30) cc_final: 0.7864 (tp30) REVERT: A 503 TYR cc_start: 0.7466 (t80) cc_final: 0.7246 (t80) REVERT: A 608 GLU cc_start: 0.7781 (tp30) cc_final: 0.7240 (pt0) REVERT: A 732 MET cc_start: 0.7243 (mmm) cc_final: 0.6870 (tpt) REVERT: A 861 ARG cc_start: 0.6831 (tpp-160) cc_final: 0.6175 (ttp-170) REVERT: C 17 SER cc_start: 0.8541 (p) cc_final: 0.8303 (m) REVERT: C 103 TYR cc_start: 0.8242 (OUTLIER) cc_final: 0.6833 (m-80) REVERT: B 42 LYS cc_start: 0.7491 (OUTLIER) cc_final: 0.7252 (mmtp) outliers start: 62 outliers final: 39 residues processed: 154 average time/residue: 0.0768 time to fit residues: 16.8703 Evaluate side-chains 140 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 95 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 364 LYS Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 473 ASN Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 514 ASN Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 581 ARG Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 778 ASN Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 104 CYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 42 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 78 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 64 optimal weight: 10.0000 chunk 89 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 HIS A 280 ASN C 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.163187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.135640 restraints weight = 9191.245| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.11 r_work: 0.3459 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.0838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8187 Z= 0.194 Angle : 0.569 7.703 11111 Z= 0.304 Chirality : 0.045 0.194 1259 Planarity : 0.004 0.049 1421 Dihedral : 7.541 70.024 1148 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 8.11 % Allowed : 25.54 % Favored : 66.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.26), residues: 1018 helix: 0.04 (0.28), residues: 337 sheet: -1.22 (0.39), residues: 179 loop : -0.93 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 95 TYR 0.019 0.002 TYR C 103 PHE 0.019 0.002 PHE A 338 TRP 0.017 0.002 TRP A 460 HIS 0.002 0.001 HIS A 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.19 ( 8183) covalent geometry : angle 0.56775 / 0.30 (11103) SS BOND : bond 0.00195 / 0.10 ( 4) SS BOND : angle 1.33335 / 0.57 ( 8) hydrogen bonds : bond 0.04734 / 3.14 ( 315) hydrogen bonds : angle 5.04680 / 3.43 ( 882) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 98 time to evaluate : 0.292 Fit side-chains REVERT: A 51 PHE cc_start: 0.8482 (OUTLIER) cc_final: 0.7547 (p90) REVERT: A 208 LEU cc_start: 0.6870 (OUTLIER) cc_final: 0.6609 (mp) REVERT: A 319 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7893 (mt-10) REVERT: A 364 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8243 (mmtm) REVERT: A 397 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7385 (pp) REVERT: A 407 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7847 (mm-30) REVERT: A 479 GLU cc_start: 0.8308 (tp30) cc_final: 0.7863 (tp30) REVERT: A 608 GLU cc_start: 0.7807 (tp30) cc_final: 0.7329 (pt0) REVERT: A 732 MET cc_start: 0.7276 (mmm) cc_final: 0.6912 (tpt) REVERT: A 737 GLU cc_start: 0.7692 (tt0) cc_final: 0.7279 (mt-10) REVERT: A 861 ARG cc_start: 0.6818 (tpp-160) cc_final: 0.6180 (ttp-170) REVERT: C 17 SER cc_start: 0.8567 (p) cc_final: 0.8326 (m) REVERT: C 103 TYR cc_start: 0.8272 (OUTLIER) cc_final: 0.6857 (m-80) REVERT: B 42 LYS cc_start: 0.7476 (OUTLIER) cc_final: 0.7254 (mmtp) REVERT: B 95 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.7155 (mtm110) outliers start: 68 outliers final: 47 residues processed: 152 average time/residue: 0.0733 time to fit residues: 15.9956 Evaluate side-chains 151 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 96 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 364 LYS Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 473 ASN Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 581 ARG Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 778 ASN Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 104 CYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 95 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 83 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 20 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 514 ASN C 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.164744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.137381 restraints weight = 9268.575| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.09 r_work: 0.3480 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8187 Z= 0.159 Angle : 0.536 6.845 11111 Z= 0.287 Chirality : 0.044 0.190 1259 Planarity : 0.004 0.050 1421 Dihedral : 7.219 70.252 1146 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 8.00 % Allowed : 26.13 % Favored : 65.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.26), residues: 1018 helix: 0.30 (0.29), residues: 337 sheet: -1.18 (0.38), residues: 179 loop : -0.88 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 95 TYR 0.017 0.001 TYR C 103 PHE 0.019 0.001 PHE A 338 TRP 0.016 0.002 TRP A 460 HIS 0.009 0.001 HIS A 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 ( 8183) covalent geometry : angle 0.53560 / 0.29 (11103) SS BOND : bond 0.00169 / 0.09 ( 4) SS BOND : angle 1.19610 / 0.51 ( 8) hydrogen bonds : bond 0.04269 / 2.84 ( 315) hydrogen bonds : angle 4.81478 / 3.26 ( 882) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 103 time to evaluate : 0.215 Fit side-chains REVERT: A 51 PHE cc_start: 0.8450 (OUTLIER) cc_final: 0.7483 (p90) REVERT: A 208 LEU cc_start: 0.6838 (OUTLIER) cc_final: 0.6572 (mp) REVERT: A 319 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7849 (mt-10) REVERT: A 322 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8101 (mt) REVERT: A 364 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8213 (mmtm) REVERT: A 397 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7364 (pp) REVERT: A 407 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7853 (mm-30) REVERT: A 479 GLU cc_start: 0.8284 (tp30) cc_final: 0.7841 (tp30) REVERT: A 533 ASN cc_start: 0.7872 (p0) cc_final: 0.7654 (p0) REVERT: A 608 GLU cc_start: 0.7761 (tp30) cc_final: 0.7335 (pt0) REVERT: A 737 GLU cc_start: 0.7620 (tt0) cc_final: 0.7235 (mt-10) REVERT: A 861 ARG cc_start: 0.6797 (tpp-160) cc_final: 0.6203 (ttp-170) REVERT: C 17 SER cc_start: 0.8559 (p) cc_final: 0.8317 (m) REVERT: C 103 TYR cc_start: 0.8228 (OUTLIER) cc_final: 0.6777 (m-80) REVERT: C 118 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7294 (pt0) REVERT: B 42 LYS cc_start: 0.7437 (OUTLIER) cc_final: 0.7212 (mmtp) REVERT: B 95 ARG cc_start: 0.7529 (OUTLIER) cc_final: 0.7118 (mtm110) outliers start: 67 outliers final: 49 residues processed: 155 average time/residue: 0.0807 time to fit residues: 17.6019 Evaluate side-chains 158 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 99 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 364 LYS Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 473 ASN Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 514 ASN Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 581 ARG Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 657 ILE Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 778 ASN Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 104 CYS Chi-restraints excluded: chain C residue 118 GLN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 95 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 66 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 64 optimal weight: 0.0970 chunk 47 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 HIS C 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.165432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.137828 restraints weight = 9253.993| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.12 r_work: 0.3485 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8187 Z= 0.145 Angle : 0.524 6.839 11111 Z= 0.281 Chirality : 0.043 0.186 1259 Planarity : 0.004 0.051 1421 Dihedral : 7.065 69.977 1142 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 8.47 % Allowed : 25.66 % Favored : 65.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.26), residues: 1018 helix: 0.55 (0.29), residues: 335 sheet: -1.11 (0.38), residues: 179 loop : -0.86 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 18 TYR 0.017 0.001 TYR C 103 PHE 0.019 0.001 PHE A 338 TRP 0.015 0.002 TRP A 460 HIS 0.002 0.001 HIS A 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 8183) covalent geometry : angle 0.52325 / 0.28 (11103) SS BOND : bond 0.00156 / 0.08 ( 4) SS BOND : angle 1.15287 / 0.48 ( 8) hydrogen bonds : bond 0.04060 / 2.70 ( 315) hydrogen bonds : angle 4.66499 / 3.16 ( 882) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 102 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 208 LEU cc_start: 0.6839 (OUTLIER) cc_final: 0.6573 (mp) REVERT: A 231 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.7843 (mtp-110) REVERT: A 319 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7857 (mt-10) REVERT: A 322 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8102 (mt) REVERT: A 364 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8220 (mmtm) REVERT: A 397 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7358 (pp) REVERT: A 407 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7864 (mm-30) REVERT: A 427 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8242 (tttt) REVERT: A 524 ILE cc_start: 0.6851 (OUTLIER) cc_final: 0.6173 (mm) REVERT: A 533 ASN cc_start: 0.7854 (p0) cc_final: 0.7645 (p0) REVERT: A 608 GLU cc_start: 0.7742 (tp30) cc_final: 0.7342 (pt0) REVERT: A 737 GLU cc_start: 0.7599 (tt0) cc_final: 0.7253 (mt-10) REVERT: A 861 ARG cc_start: 0.6791 (tpp-160) cc_final: 0.6219 (ttp-170) REVERT: C 17 SER cc_start: 0.8545 (p) cc_final: 0.8304 (m) REVERT: C 103 TYR cc_start: 0.8205 (OUTLIER) cc_final: 0.6766 (m-80) REVERT: C 118 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7305 (pt0) REVERT: B 42 LYS cc_start: 0.7465 (OUTLIER) cc_final: 0.7238 (mmtp) REVERT: B 95 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.7117 (mtm110) outliers start: 71 outliers final: 49 residues processed: 157 average time/residue: 0.0850 time to fit residues: 18.6485 Evaluate side-chains 162 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 101 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 364 LYS Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 427 LYS Chi-restraints excluded: chain A residue 473 ASN Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 552 HIS Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 581 ARG Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 104 CYS Chi-restraints excluded: chain C residue 118 GLN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 95 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 30 optimal weight: 6.9990 chunk 92 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 57.3224 > 50:) chunk 95 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 91 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 412 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.166215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.139861 restraints weight = 9319.358| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 1.99 r_work: 0.3537 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8187 Z= 0.176 Angle : 0.551 7.242 11111 Z= 0.293 Chirality : 0.044 0.195 1259 Planarity : 0.004 0.050 1421 Dihedral : 7.045 70.067 1138 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 9.07 % Allowed : 25.06 % Favored : 65.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.26), residues: 1018 helix: 0.52 (0.29), residues: 336 sheet: -1.14 (0.38), residues: 184 loop : -0.85 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 105 TYR 0.018 0.002 TYR C 103 PHE 0.019 0.001 PHE A 338 TRP 0.016 0.002 TRP A 460 HIS 0.002 0.001 HIS A 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.18 ( 8183) covalent geometry : angle 0.54987 / 0.29 (11103) SS BOND : bond 0.00200 / 0.10 ( 4) SS BOND : angle 1.25185 / 0.54 ( 8) hydrogen bonds : bond 0.04153 / 2.76 ( 315) hydrogen bonds : angle 4.67775 / 3.16 ( 882) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 101 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: A 51 PHE cc_start: 0.8463 (OUTLIER) cc_final: 0.7497 (p90) REVERT: A 208 LEU cc_start: 0.6851 (OUTLIER) cc_final: 0.6615 (mp) REVERT: A 231 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.7791 (mtp-110) REVERT: A 319 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7850 (mt-10) REVERT: A 322 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8144 (mt) REVERT: A 364 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8209 (mmtm) REVERT: A 397 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7404 (pp) REVERT: A 407 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7841 (mm-30) REVERT: A 427 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8229 (tttt) REVERT: A 479 GLU cc_start: 0.8253 (tp30) cc_final: 0.7820 (tp30) REVERT: A 524 ILE cc_start: 0.6868 (OUTLIER) cc_final: 0.6191 (mm) REVERT: A 531 MET cc_start: 0.6280 (mmt) cc_final: 0.5994 (mmt) REVERT: A 608 GLU cc_start: 0.7659 (tp30) cc_final: 0.7332 (pt0) REVERT: A 737 GLU cc_start: 0.7616 (tt0) cc_final: 0.7236 (mt-10) REVERT: A 861 ARG cc_start: 0.6840 (tpp-160) cc_final: 0.6321 (ttp-170) REVERT: C 17 SER cc_start: 0.8563 (p) cc_final: 0.8314 (m) REVERT: C 103 TYR cc_start: 0.8264 (OUTLIER) cc_final: 0.6804 (m-80) REVERT: C 118 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.7302 (pt0) REVERT: B 42 LYS cc_start: 0.7520 (OUTLIER) cc_final: 0.7303 (mmtp) REVERT: B 95 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.7098 (mtm110) outliers start: 76 outliers final: 56 residues processed: 159 average time/residue: 0.0855 time to fit residues: 18.9943 Evaluate side-chains 168 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 99 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 364 LYS Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 427 LYS Chi-restraints excluded: chain A residue 473 ASN Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 552 HIS Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 581 ARG Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 104 CYS Chi-restraints excluded: chain C residue 118 GLN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 95 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 14 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 97 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 86 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.167430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.140977 restraints weight = 9338.320| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.01 r_work: 0.3550 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8187 Z= 0.151 Angle : 0.529 6.874 11111 Z= 0.282 Chirality : 0.043 0.194 1259 Planarity : 0.004 0.050 1421 Dihedral : 6.980 69.942 1138 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 8.83 % Allowed : 25.30 % Favored : 65.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.27), residues: 1018 helix: 0.69 (0.29), residues: 334 sheet: -1.09 (0.38), residues: 184 loop : -0.84 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 95 TYR 0.017 0.001 TYR C 103 PHE 0.018 0.001 PHE A 338 TRP 0.016 0.002 TRP A 460 HIS 0.002 0.001 HIS A 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 ( 8183) covalent geometry : angle 0.52829 / 0.28 (11103) SS BOND : bond 0.00172 / 0.09 ( 4) SS BOND : angle 1.19368 / 0.51 ( 8) hydrogen bonds : bond 0.03952 / 2.63 ( 315) hydrogen bonds : angle 4.57641 / 3.09 ( 882) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 102 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: A 51 PHE cc_start: 0.8433 (OUTLIER) cc_final: 0.7451 (p90) REVERT: A 208 LEU cc_start: 0.6802 (OUTLIER) cc_final: 0.6566 (mp) REVERT: A 231 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7769 (mtp-110) REVERT: A 319 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7849 (mt-10) REVERT: A 322 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8127 (mt) REVERT: A 364 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8193 (mmtm) REVERT: A 375 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8219 (tttm) REVERT: A 397 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7371 (pp) REVERT: A 407 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7847 (mm-30) REVERT: A 427 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8221 (tttt) REVERT: A 479 GLU cc_start: 0.8221 (tp30) cc_final: 0.7794 (tp30) REVERT: A 524 ILE cc_start: 0.6872 (OUTLIER) cc_final: 0.6195 (mm) REVERT: A 531 MET cc_start: 0.6283 (mmt) cc_final: 0.6016 (mmt) REVERT: A 608 GLU cc_start: 0.7667 (tp30) cc_final: 0.7342 (pt0) REVERT: A 737 GLU cc_start: 0.7597 (tt0) cc_final: 0.7225 (mt-10) REVERT: A 861 ARG cc_start: 0.6822 (tpp-160) cc_final: 0.6313 (ttp-170) REVERT: C 17 SER cc_start: 0.8547 (p) cc_final: 0.8306 (m) REVERT: C 103 TYR cc_start: 0.8227 (OUTLIER) cc_final: 0.6786 (m-80) REVERT: C 118 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7300 (pt0) REVERT: B 42 LYS cc_start: 0.7481 (OUTLIER) cc_final: 0.7257 (mmtp) REVERT: B 95 ARG cc_start: 0.7490 (OUTLIER) cc_final: 0.7073 (mtm110) outliers start: 74 outliers final: 53 residues processed: 159 average time/residue: 0.0891 time to fit residues: 19.7446 Evaluate side-chains 168 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 101 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 364 LYS Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 427 LYS Chi-restraints excluded: chain A residue 473 ASN Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 552 HIS Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 581 ARG Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 104 CYS Chi-restraints excluded: chain C residue 118 GLN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 95 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 37 optimal weight: 0.0040 chunk 96 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.168830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.142383 restraints weight = 9343.546| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.02 r_work: 0.3564 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8187 Z= 0.130 Angle : 0.512 6.533 11111 Z= 0.272 Chirality : 0.043 0.186 1259 Planarity : 0.004 0.051 1421 Dihedral : 6.893 69.366 1138 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 7.76 % Allowed : 26.25 % Favored : 65.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.27), residues: 1018 helix: 0.83 (0.29), residues: 334 sheet: -1.05 (0.38), residues: 179 loop : -0.85 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 18 TYR 0.016 0.001 TYR C 103 PHE 0.018 0.001 PHE A 338 TRP 0.014 0.001 TRP A 460 HIS 0.002 0.001 HIS A 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 8183) covalent geometry : angle 0.51145 / 0.27 (11103) SS BOND : bond 0.00154 / 0.09 ( 4) SS BOND : angle 1.12596 / 0.47 ( 8) hydrogen bonds : bond 0.03777 / 2.52 ( 315) hydrogen bonds : angle 4.49774 / 3.03 ( 882) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 103 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 51 PHE cc_start: 0.8399 (OUTLIER) cc_final: 0.7330 (p90) REVERT: A 208 LEU cc_start: 0.6796 (OUTLIER) cc_final: 0.6566 (mp) REVERT: A 231 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7735 (mtp-110) REVERT: A 319 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7865 (mt-10) REVERT: A 322 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8124 (mt) REVERT: A 364 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8171 (mmtm) REVERT: A 375 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8190 (tttm) REVERT: A 397 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7346 (pp) REVERT: A 407 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7867 (mm-30) REVERT: A 427 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8160 (tttt) REVERT: A 531 MET cc_start: 0.6273 (mmt) cc_final: 0.6015 (mmt) REVERT: A 608 GLU cc_start: 0.7633 (tp30) cc_final: 0.7311 (pt0) REVERT: A 737 GLU cc_start: 0.7593 (tt0) cc_final: 0.7222 (mt-10) REVERT: A 861 ARG cc_start: 0.6824 (tpp-160) cc_final: 0.6337 (ttp-170) REVERT: C 17 SER cc_start: 0.8530 (p) cc_final: 0.8296 (m) REVERT: C 103 TYR cc_start: 0.8176 (OUTLIER) cc_final: 0.6730 (m-80) REVERT: C 118 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7257 (pt0) REVERT: B 42 LYS cc_start: 0.7486 (OUTLIER) cc_final: 0.7251 (mmtp) REVERT: B 95 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.7036 (mtm110) outliers start: 65 outliers final: 45 residues processed: 153 average time/residue: 0.0918 time to fit residues: 19.3992 Evaluate side-chains 161 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 103 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 364 LYS Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 427 LYS Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 552 HIS Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 581 ARG Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 104 CYS Chi-restraints excluded: chain C residue 118 GLN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 95 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 71 optimal weight: 0.6980 chunk 86 optimal weight: 0.6980 chunk 54 optimal weight: 0.0070 chunk 2 optimal weight: 0.0040 chunk 95 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 overall best weight: 0.4410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.170570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.144436 restraints weight = 9305.566| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.00 r_work: 0.3589 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8187 Z= 0.107 Angle : 0.491 6.301 11111 Z= 0.262 Chirality : 0.042 0.185 1259 Planarity : 0.004 0.052 1421 Dihedral : 6.760 69.163 1137 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 6.92 % Allowed : 26.37 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.27), residues: 1018 helix: 1.05 (0.29), residues: 334 sheet: -0.96 (0.38), residues: 180 loop : -0.80 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 18 TYR 0.015 0.001 TYR C 103 PHE 0.016 0.001 PHE A 338 TRP 0.014 0.001 TRP A 460 HIS 0.001 0.001 HIS B 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 8183) covalent geometry : angle 0.49037 / 0.26 (11103) SS BOND : bond 0.00115 / 0.07 ( 4) SS BOND : angle 1.07759 / 0.45 ( 8) hydrogen bonds : bond 0.03598 / 2.41 ( 315) hydrogen bonds : angle 4.36314 / 2.94 ( 882) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 111 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 PHE cc_start: 0.8317 (OUTLIER) cc_final: 0.7214 (p90) REVERT: A 208 LEU cc_start: 0.6782 (OUTLIER) cc_final: 0.6563 (mp) REVERT: A 231 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.7700 (mtp-110) REVERT: A 319 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7841 (mt-10) REVERT: A 322 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8114 (mt) REVERT: A 364 LYS cc_start: 0.8533 (mmtp) cc_final: 0.8143 (mmtm) REVERT: A 397 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7296 (pp) REVERT: A 407 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7891 (mm-30) REVERT: A 427 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.8134 (tttt) REVERT: A 524 ILE cc_start: 0.6758 (OUTLIER) cc_final: 0.6099 (mm) REVERT: A 531 MET cc_start: 0.6294 (mmt) cc_final: 0.6070 (mmt) REVERT: A 608 GLU cc_start: 0.7585 (tp30) cc_final: 0.7294 (pt0) REVERT: A 737 GLU cc_start: 0.7543 (tt0) cc_final: 0.7189 (mt-10) REVERT: A 861 ARG cc_start: 0.6810 (tpp-160) cc_final: 0.6381 (ttp-170) REVERT: C 17 SER cc_start: 0.8506 (p) cc_final: 0.8287 (m) REVERT: C 103 TYR cc_start: 0.8111 (OUTLIER) cc_final: 0.6613 (m-80) REVERT: C 118 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7260 (pt0) REVERT: B 42 LYS cc_start: 0.7465 (OUTLIER) cc_final: 0.7218 (mmtp) REVERT: B 95 ARG cc_start: 0.7451 (OUTLIER) cc_final: 0.6995 (mtm110) outliers start: 58 outliers final: 43 residues processed: 154 average time/residue: 0.0877 time to fit residues: 18.8301 Evaluate side-chains 158 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 103 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 427 LYS Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 552 HIS Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 581 ARG Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 104 CYS Chi-restraints excluded: chain C residue 118 GLN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 95 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 68 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 80 optimal weight: 0.0870 chunk 76 optimal weight: 0.7980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 223 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.169775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.143568 restraints weight = 9259.458| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 1.99 r_work: 0.3577 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8187 Z= 0.125 Angle : 0.506 6.562 11111 Z= 0.270 Chirality : 0.042 0.186 1259 Planarity : 0.004 0.051 1421 Dihedral : 6.726 68.317 1136 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 6.80 % Allowed : 27.21 % Favored : 65.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.27), residues: 1018 helix: 1.13 (0.29), residues: 334 sheet: -0.96 (0.37), residues: 180 loop : -0.77 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 18 TYR 0.016 0.001 TYR C 103 PHE 0.017 0.001 PHE A 338 TRP 0.014 0.001 TRP A 460 HIS 0.002 0.001 HIS A 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 8183) covalent geometry : angle 0.50563 / 0.27 (11103) SS BOND : bond 0.00135 / 0.07 ( 4) SS BOND : angle 1.10019 / 0.46 ( 8) hydrogen bonds : bond 0.03686 / 2.46 ( 315) hydrogen bonds : angle 4.37073 / 2.94 ( 882) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 102 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 51 PHE cc_start: 0.8328 (OUTLIER) cc_final: 0.7229 (p90) REVERT: A 208 LEU cc_start: 0.6802 (OUTLIER) cc_final: 0.6572 (mp) REVERT: A 231 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.8197 (mtp85) REVERT: A 319 GLU cc_start: 0.8277 (mt-10) cc_final: 0.7866 (mt-10) REVERT: A 322 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8125 (mt) REVERT: A 364 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8164 (mmtm) REVERT: A 375 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.8109 (tttm) REVERT: A 397 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7343 (pp) REVERT: A 407 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7897 (mm-30) REVERT: A 427 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.8181 (tttt) REVERT: A 524 ILE cc_start: 0.6821 (OUTLIER) cc_final: 0.6155 (mm) REVERT: A 531 MET cc_start: 0.6295 (mmt) cc_final: 0.6051 (mmt) REVERT: A 608 GLU cc_start: 0.7520 (tp30) cc_final: 0.7243 (pt0) REVERT: A 737 GLU cc_start: 0.7607 (tt0) cc_final: 0.7237 (mt-10) REVERT: A 861 ARG cc_start: 0.6838 (tpp-160) cc_final: 0.6411 (ttp-170) REVERT: C 17 SER cc_start: 0.8511 (p) cc_final: 0.8296 (m) REVERT: C 103 TYR cc_start: 0.8126 (OUTLIER) cc_final: 0.6643 (m-80) REVERT: C 118 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7282 (pt0) REVERT: B 42 LYS cc_start: 0.7469 (OUTLIER) cc_final: 0.7218 (mmtp) REVERT: B 95 ARG cc_start: 0.7477 (OUTLIER) cc_final: 0.7012 (mtm110) outliers start: 57 outliers final: 41 residues processed: 145 average time/residue: 0.0860 time to fit residues: 17.5707 Evaluate side-chains 157 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 102 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 364 LYS Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 427 LYS Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 552 HIS Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 581 ARG Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 683 SER Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 867 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 62 ASP Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 104 CYS Chi-restraints excluded: chain C residue 118 GLN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 95 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 0.0000 chunk 69 optimal weight: 1.9990 chunk 101 optimal weight: 0.0980 chunk 60 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 311 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.169320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.142974 restraints weight = 9252.371| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.01 r_work: 0.3575 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8187 Z= 0.135 Angle : 0.519 6.614 11111 Z= 0.274 Chirality : 0.043 0.189 1259 Planarity : 0.004 0.050 1421 Dihedral : 6.746 68.019 1136 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 6.68 % Allowed : 27.21 % Favored : 66.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.27), residues: 1018 helix: 1.11 (0.29), residues: 334 sheet: -0.93 (0.38), residues: 180 loop : -0.76 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 18 TYR 0.017 0.001 TYR A 250 PHE 0.017 0.001 PHE A 338 TRP 0.015 0.001 TRP A 460 HIS 0.002 0.001 HIS A 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.13 ( 8183) covalent geometry : angle 0.51791 / 0.27 (11103) SS BOND : bond 0.00145 / 0.08 ( 4) SS BOND : angle 1.11970 / 0.46 ( 8) hydrogen bonds : bond 0.03722 / 2.49 ( 315) hydrogen bonds : angle 4.38903 / 2.95 ( 882) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2350.42 seconds wall clock time: 40 minutes 56.64 seconds (2456.64 seconds total)