Starting phenix.real_space_refine on Wed Aug 5 19:21:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8jpo_36485/08_2026/8jpo_36485.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jpo_36485/08_2026/8jpo_36485.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jpo_36485/08_2026/8jpo_36485.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jpo_36485/08_2026/8jpo_36485.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jpo_36485/08_2026/8jpo_36485.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jpo_36485/08_2026/8jpo_36485.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8jpo_36485/08_2026/8jpo_36485.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8jpo_36485/08_2026/8jpo_36485.cif" } resolution = 3.4 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= 0.004 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: 7 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 70 5.16 5 Cl 4 4.86 5 C 7430 2.51 5 N 1922 2.21 5 O 2042 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: 11476 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 733, 5704 Classifications: {'peptide': 733} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 31, 'TRANS': 701} Chain breaks: 4 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 5, 'PHE:plan': 1, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "B" Number of atoms: 5704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 733, 5704 Classifications: {'peptide': 733} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 31, 'TRANS': 701} Chain breaks: 4 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 5, 'PHE:plan': 1, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' CL': 2, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' CL': 2, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 2.80, per 1000 atoms: 0.24 Number of scatterers: 11476 At special positions: 0 Unit cell: (92.9514, 96.301, 113.886, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 4 17.00 S 70 16.00 P 6 15.00 Mg 2 11.99 O 2042 8.00 N 1922 7.00 C 7430 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 120 " - pdb=" SG CYS A 125 " distance=2.02 Simple disulfide: pdb=" SG CYS A 319 " - pdb=" SG CYS A 326 " distance=2.03 Simple disulfide: pdb=" SG CYS A 399 " - pdb=" SG CYS A 430 " distance=2.03 Simple disulfide: pdb=" SG CYS B 120 " - pdb=" SG CYS B 125 " distance=2.02 Simple disulfide: pdb=" SG CYS B 319 " - pdb=" SG CYS B 326 " distance=2.03 Simple disulfide: pdb=" SG CYS B 399 " - pdb=" SG CYS B 430 " 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: 0.96 Conformation dependent library (CDL) restraints added in 546.9 milliseconds 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2696 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 8 sheets defined 65.4% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 58 through 68 Processing helix chain 'A' and resid 69 through 123 removed outlier: 3.554A pdb=" N LEU A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N THR A 115 " --> pdb=" O GLY A 111 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER A 116 " --> pdb=" O VAL A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 151 removed outlier: 3.605A pdb=" N VAL A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 155 Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 161 through 166 removed outlier: 3.825A pdb=" N TYR A 165 " --> pdb=" O GLU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 191 removed outlier: 3.618A pdb=" N GLY A 186 " --> pdb=" O CYS A 182 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 201 through 214 removed outlier: 4.341A pdb=" N HIS A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 233 removed outlier: 3.549A pdb=" N PHE A 232 " --> pdb=" O PHE A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 255 removed outlier: 4.087A pdb=" N ASP A 240 " --> pdb=" O ARG A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 266 Processing helix chain 'A' and resid 276 through 299 removed outlier: 3.681A pdb=" N PHE A 282 " --> pdb=" O TRP A 278 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN A 292 " --> pdb=" O THR A 288 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE A 293 " --> pdb=" O PHE A 289 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY A 297 " --> pdb=" O PHE A 293 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN A 299 " --> pdb=" O ARG A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 366 removed outlier: 4.217A pdb=" N PHE A 336 " --> pdb=" O MET A 332 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG A 364 " --> pdb=" O LYS A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 395 Processing helix chain 'A' and resid 437 through 443 Processing helix chain 'A' and resid 445 through 456 Processing helix chain 'A' and resid 461 through 480 Processing helix chain 'A' and resid 488 through 511 removed outlier: 3.760A pdb=" N CYS A 495 " --> pdb=" O PRO A 491 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY A 496 " --> pdb=" O SER A 492 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA A 497 " --> pdb=" O LEU A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 534 removed outlier: 3.816A pdb=" N ALA A 522 " --> pdb=" O SER A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 549 Processing helix chain 'A' and resid 550 through 552 No H-bonds generated for 'chain 'A' and resid 550 through 552' Processing helix chain 'A' and resid 553 through 569 removed outlier: 3.852A pdb=" N VAL A 563 " --> pdb=" O VAL A 559 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA A 564 " --> pdb=" O THR A 560 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TRP A 566 " --> pdb=" O MET A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 582 Processing helix chain 'A' and resid 593 through 598 Processing helix chain 'A' and resid 600 through 605 removed outlier: 3.793A pdb=" N ILE A 604 " --> pdb=" O ARG A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 628 Processing helix chain 'A' and resid 650 through 664 removed outlier: 3.605A pdb=" N ILE A 664 " --> pdb=" O LYS A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 677 Processing helix chain 'A' and resid 732 through 736 Processing helix chain 'A' and resid 747 through 756 Processing helix chain 'A' and resid 773 through 779 Processing helix chain 'A' and resid 819 through 830 Processing helix chain 'A' and resid 849 through 853 Processing helix chain 'A' and resid 854 through 869 Processing helix chain 'B' and resid 58 through 68 Processing helix chain 'B' and resid 69 through 123 removed outlier: 3.648A pdb=" N VAL B 113 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N THR B 115 " --> pdb=" O GLY B 111 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER B 116 " --> pdb=" O VAL B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 151 removed outlier: 3.600A pdb=" N VAL B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 155 Processing helix chain 'B' and resid 158 through 160 No H-bonds generated for 'chain 'B' and resid 158 through 160' Processing helix chain 'B' and resid 161 through 166 removed outlier: 3.832A pdb=" N TYR B 165 " --> pdb=" O GLU B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 191 removed outlier: 3.623A pdb=" N GLY B 186 " --> pdb=" O CYS B 182 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 194 No H-bonds generated for 'chain 'B' and resid 192 through 194' Processing helix chain 'B' and resid 199 through 214 removed outlier: 3.558A pdb=" N MET B 203 " --> pdb=" O LYS B 199 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ILE B 204 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N HIS B 205 " --> pdb=" O GLY B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 233 removed outlier: 3.527A pdb=" N PHE B 232 " --> pdb=" O PHE B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 255 removed outlier: 4.067A pdb=" N ASP B 240 " --> pdb=" O ARG B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 266 Processing helix chain 'B' and resid 276 through 299 removed outlier: 3.668A pdb=" N PHE B 282 " --> pdb=" O TRP B 278 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN B 292 " --> pdb=" O THR B 288 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE B 293 " --> pdb=" O PHE B 289 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY B 297 " --> pdb=" O PHE B 293 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN B 299 " --> pdb=" O ARG B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 366 removed outlier: 4.152A pdb=" N PHE B 336 " --> pdb=" O MET B 332 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG B 364 " --> pdb=" O LYS B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 395 removed outlier: 3.636A pdb=" N VAL B 389 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 443 Processing helix chain 'B' and resid 445 through 456 removed outlier: 3.650A pdb=" N GLN B 456 " --> pdb=" O GLN B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 480 Processing helix chain 'B' and resid 488 through 511 removed outlier: 3.751A pdb=" N CYS B 495 " --> pdb=" O PRO B 491 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY B 496 " --> pdb=" O SER B 492 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B 497 " --> pdb=" O LEU B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 534 removed outlier: 3.904A pdb=" N ALA B 522 " --> pdb=" O SER B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 549 Processing helix chain 'B' and resid 550 through 552 No H-bonds generated for 'chain 'B' and resid 550 through 552' Processing helix chain 'B' and resid 553 through 569 removed outlier: 3.811A pdb=" N VAL B 563 " --> pdb=" O VAL B 559 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA B 564 " --> pdb=" O THR B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 582 Processing helix chain 'B' and resid 593 through 598 Processing helix chain 'B' and resid 600 through 605 removed outlier: 3.800A pdb=" N ILE B 604 " --> pdb=" O ARG B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 628 Processing helix chain 'B' and resid 650 through 664 removed outlier: 3.658A pdb=" N ILE B 664 " --> pdb=" O LYS B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 677 Processing helix chain 'B' and resid 732 through 736 Processing helix chain 'B' and resid 747 through 756 Processing helix chain 'B' and resid 773 through 779 Processing helix chain 'B' and resid 819 through 830 Processing helix chain 'B' and resid 854 through 869 Processing sheet with id=AA1, first strand: chain 'A' and resid 399 through 401 Processing sheet with id=AA2, first strand: chain 'A' and resid 616 through 617 Processing sheet with id=AA3, first strand: chain 'A' and resid 632 through 638 removed outlier: 6.546A pdb=" N THR A 637 " --> pdb=" O PHE A 741 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N PHE A 741 " --> pdb=" O THR A 637 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 835 through 838 removed outlier: 6.808A pdb=" N LEU A 835 " --> pdb=" O ILE A 847 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ILE A 847 " --> pdb=" O LEU A 835 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL A 837 " --> pdb=" O VAL A 845 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 399 through 401 Processing sheet with id=AA6, first strand: chain 'B' and resid 616 through 617 Processing sheet with id=AA7, first strand: chain 'B' and resid 632 through 638 removed outlier: 6.546A pdb=" N THR B 637 " --> pdb=" O PHE B 741 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N PHE B 741 " --> pdb=" O THR B 637 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 835 through 838 removed outlier: 6.782A pdb=" N LEU B 835 " --> pdb=" O ILE B 847 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE B 847 " --> pdb=" O LEU B 835 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL B 837 " --> pdb=" O VAL B 845 " (cutoff:3.500A) 655 hydrogen bonds defined for protein. 1941 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: 2.06 Time building geometry restraints manager: 1.29 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: 3614 1.34 - 1.47: 2886 1.47 - 1.59: 5122 1.59 - 1.71: 2 1.71 - 1.83: 110 Bond restraints: 11734 Sorted by residual: bond pdb=" C HIS B 367 " pdb=" N PRO B 368 " ideal model delta sigma weight residual 1.334 1.371 -0.037 2.34e-02 1.83e+03 2.54e+00 bond pdb=" C HIS A 367 " pdb=" N PRO A 368 " ideal model delta sigma weight residual 1.334 1.370 -0.036 2.34e-02 1.83e+03 2.42e+00 bond pdb=" CA GLY B 397 " pdb=" C GLY B 397 " ideal model delta sigma weight residual 1.520 1.512 0.008 7.30e-03 1.88e+04 1.29e+00 bond pdb=" C VAL A 175 " pdb=" O VAL A 175 " ideal model delta sigma weight residual 1.236 1.223 0.013 1.19e-02 7.06e+03 1.16e+00 bond pdb=" CA GLY A 397 " pdb=" C GLY A 397 " ideal model delta sigma weight residual 1.520 1.512 0.008 7.30e-03 1.88e+04 1.13e+00 ... (remaining 11729 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 15186 1.28 - 2.56: 586 2.56 - 3.84: 117 3.84 - 5.12: 30 5.12 - 6.40: 9 Bond angle restraints: 15928 Sorted by residual: angle pdb=" N VAL A 162 " pdb=" CA VAL A 162 " pdb=" C VAL A 162 " ideal model delta sigma weight residual 112.96 107.99 4.97 1.00e+00 1.00e+00 2.47e+01 angle pdb=" N VAL B 162 " pdb=" CA VAL B 162 " pdb=" C VAL B 162 " ideal model delta sigma weight residual 112.96 108.09 4.87 1.00e+00 1.00e+00 2.37e+01 angle pdb=" C GLY A 158 " pdb=" N ILE A 159 " pdb=" CA ILE A 159 " ideal model delta sigma weight residual 120.24 122.96 -2.72 6.30e-01 2.52e+00 1.86e+01 angle pdb=" C GLY B 158 " pdb=" N ILE B 159 " pdb=" CA ILE B 159 " ideal model delta sigma weight residual 120.24 122.94 -2.70 6.30e-01 2.52e+00 1.83e+01 angle pdb=" C ILE A 159 " pdb=" CA ILE A 159 " pdb=" CB ILE A 159 " ideal model delta sigma weight residual 114.35 110.96 3.39 1.06e+00 8.90e-01 1.02e+01 ... (remaining 15923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.64: 6200 14.64 - 29.27: 523 29.27 - 43.91: 130 43.91 - 58.55: 16 58.55 - 73.19: 15 Dihedral angle restraints: 6884 sinusoidal: 2686 harmonic: 4198 Sorted by residual: dihedral pdb=" CB CYS A 120 " pdb=" SG CYS A 120 " pdb=" SG CYS A 125 " pdb=" CB CYS A 125 " ideal model delta sinusoidal sigma weight residual -86.00 -148.19 62.19 1 1.00e+01 1.00e-02 5.12e+01 dihedral pdb=" CB CYS B 120 " pdb=" SG CYS B 120 " pdb=" SG CYS B 125 " pdb=" CB CYS B 125 " ideal model delta sinusoidal sigma weight residual -86.00 -147.05 61.05 1 1.00e+01 1.00e-02 4.95e+01 dihedral pdb=" CA VAL A 171 " pdb=" C VAL A 171 " pdb=" N PRO A 172 " pdb=" CA PRO A 172 " ideal model delta harmonic sigma weight residual 180.00 -158.64 -21.36 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 6881 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1173 0.032 - 0.064: 466 0.064 - 0.096: 132 0.096 - 0.128: 64 0.128 - 0.160: 7 Chirality restraints: 1842 Sorted by residual: chirality pdb=" CA VAL A 171 " pdb=" N VAL A 171 " pdb=" C VAL A 171 " pdb=" CB VAL A 171 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.44e-01 chirality pdb=" CA VAL B 171 " pdb=" N VAL B 171 " pdb=" C VAL B 171 " pdb=" CB VAL B 171 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.19e-01 chirality pdb=" CB VAL B 242 " pdb=" CA VAL B 242 " pdb=" CG1 VAL B 242 " pdb=" CG2 VAL B 242 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.86e-01 ... (remaining 1839 not shown) Planarity restraints: 1990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 769 " -0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO A 770 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 770 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 770 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 769 " 0.026 5.00e-02 4.00e+02 3.98e-02 2.53e+00 pdb=" N PRO B 770 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 770 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 770 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 484 " 0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO B 485 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 485 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 485 " 0.022 5.00e-02 4.00e+02 ... (remaining 1987 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2824 2.79 - 3.32: 11215 3.32 - 3.85: 18893 3.85 - 4.37: 22316 4.37 - 4.90: 39182 Nonbonded interactions: 94430 Sorted by model distance: nonbonded pdb=" O THR B 440 " pdb=" ND2 ASN B 444 " model vdw 2.267 3.120 nonbonded pdb=" O ASP A 603 " pdb=" NH1 ARG A 861 " model vdw 2.272 3.120 nonbonded pdb=" O ASP B 603 " pdb=" NH1 ARG B 861 " model vdw 2.284 3.120 nonbonded pdb=" O THR A 440 " pdb=" ND2 ASN A 444 " model vdw 2.302 3.120 nonbonded pdb=" O PRO B 431 " pdb=" OG1 THR B 434 " model vdw 2.308 3.040 ... (remaining 94425 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 46 through 869 or resid 902 or resid 904)) selection = (chain 'B' and (resid 46 through 869 or resid 902 or resid 904)) } 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: 0.010 Normalize map: mean=0, sd=1: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.040 Find NCS groups from input model: 0.270 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: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 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 11740 Z= 0.166 Angle : 0.630 6.396 15940 Z= 0.373 Chirality : 0.041 0.160 1842 Planarity : 0.005 0.040 1990 Dihedral : 11.922 73.186 4170 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.23), residues: 1446 helix: 1.12 (0.18), residues: 896 sheet: -2.55 (0.85), residues: 24 loop : -0.96 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 626 TYR 0.013 0.001 TYR A 781 PHE 0.014 0.001 PHE A 390 TRP 0.007 0.001 TRP A 478 HIS 0.002 0.001 HIS A 851 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 (11734) covalent geometry : angle 0.62787 / 0.37 (15928) SS BOND : bond 0.00401 / 0.21 ( 6) SS BOND : angle 1.97106 / 1.14 ( 12) hydrogen bonds : bond 0.17280 / 11.33 ( 655) hydrogen bonds : angle 6.01244 / 4.34 ( 1941) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.441 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.0878 time to fit residues: 15.1535 Evaluate side-chains 92 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 ASN ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 ASN B 452 GLN B 515 HIS B 764 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.107883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.082343 restraints weight = 13980.847| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 1.45 r_work: 0.2777 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9178 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 11740 Z= 0.285 Angle : 0.680 7.707 15940 Z= 0.350 Chirality : 0.047 0.160 1842 Planarity : 0.006 0.046 1990 Dihedral : 4.840 22.764 1580 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.72 % Allowed : 6.32 % Favored : 92.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.23), residues: 1446 helix: 1.26 (0.18), residues: 908 sheet: -2.62 (0.82), residues: 24 loop : -0.85 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 103 TYR 0.025 0.002 TYR A 510 PHE 0.020 0.002 PHE A 351 TRP 0.012 0.002 TRP B 303 HIS 0.004 0.001 HIS B 615 Details of bonding type rmsd/Z covalent geometry : bond 0.00725 / 0.29 (11734) covalent geometry : angle 0.67899 / 0.35 (15928) SS BOND : bond 0.00286 / 0.16 ( 6) SS BOND : angle 1.21146 / 0.64 ( 12) hydrogen bonds : bond 0.05733 / 3.77 ( 655) hydrogen bonds : angle 4.12286 / 2.98 ( 1941) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.545 Fit side-chains REVERT: A 72 LYS cc_start: 0.8053 (mtpt) cc_final: 0.7482 (mttp) REVERT: B 72 LYS cc_start: 0.7990 (mtpt) cc_final: 0.7433 (mttp) REVERT: B 332 MET cc_start: 0.8242 (mmt) cc_final: 0.7941 (ptm) outliers start: 9 outliers final: 6 residues processed: 102 average time/residue: 0.1057 time to fit residues: 16.3371 Evaluate side-chains 97 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 394 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 90 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 127 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 47 optimal weight: 0.4980 chunk 39 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 70 optimal weight: 0.3980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 452 GLN ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.114293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.090162 restraints weight = 13695.970| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.33 r_work: 0.2943 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9105 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11740 Z= 0.112 Angle : 0.505 6.593 15940 Z= 0.258 Chirality : 0.038 0.161 1842 Planarity : 0.004 0.039 1990 Dihedral : 4.312 20.584 1580 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.72 % Allowed : 8.16 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.15 (0.23), residues: 1446 helix: 1.77 (0.18), residues: 904 sheet: -2.96 (0.80), residues: 24 loop : -0.87 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 861 TYR 0.016 0.001 TYR A 781 PHE 0.010 0.001 PHE B 351 TRP 0.009 0.001 TRP A 278 HIS 0.003 0.000 HIS B 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (11734) covalent geometry : angle 0.50497 / 0.26 (15928) SS BOND : bond 0.00094 / 0.05 ( 6) SS BOND : angle 0.87505 / 0.44 ( 12) hydrogen bonds : bond 0.03927 / 2.57 ( 655) hydrogen bonds : angle 3.71495 / 2.69 ( 1941) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.415 Fit side-chains REVERT: A 456 GLN cc_start: 0.7782 (mt0) cc_final: 0.7571 (tt0) REVERT: A 670 GLU cc_start: 0.8235 (tp30) cc_final: 0.8006 (tp30) REVERT: A 673 LYS cc_start: 0.8271 (ttpt) cc_final: 0.7927 (tttm) REVERT: B 120 CYS cc_start: 0.7719 (OUTLIER) cc_final: 0.7490 (t) REVERT: B 332 MET cc_start: 0.8197 (mmt) cc_final: 0.7950 (ptm) outliers start: 9 outliers final: 2 residues processed: 109 average time/residue: 0.0798 time to fit residues: 14.1181 Evaluate side-chains 96 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 93 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 732 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 56 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 126 optimal weight: 0.8980 chunk 64 optimal weight: 8.9990 chunk 25 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 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 = 0.3120 r_free = 0.3120 target = 0.111680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.085989 restraints weight = 13909.780| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.46 r_work: 0.2834 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9135 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11740 Z= 0.150 Angle : 0.524 7.246 15940 Z= 0.267 Chirality : 0.040 0.158 1842 Planarity : 0.004 0.038 1990 Dihedral : 4.320 21.094 1580 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.20 % Allowed : 8.72 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.23), residues: 1446 helix: 1.86 (0.18), residues: 900 sheet: -3.07 (0.82), residues: 24 loop : -0.94 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 103 TYR 0.016 0.001 TYR A 781 PHE 0.014 0.001 PHE A 101 TRP 0.007 0.001 TRP B 303 HIS 0.003 0.001 HIS B 615 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.15 (11734) covalent geometry : angle 0.52309 / 0.27 (15928) SS BOND : bond 0.00161 / 0.08 ( 6) SS BOND : angle 1.03898 / 0.51 ( 12) hydrogen bonds : bond 0.04248 / 2.79 ( 655) hydrogen bonds : angle 3.72234 / 2.70 ( 1941) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.436 Fit side-chains REVERT: A 266 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8225 (pm20) REVERT: A 456 GLN cc_start: 0.7808 (mt0) cc_final: 0.7594 (tt0) REVERT: B 75 ARG cc_start: 0.7450 (ttm170) cc_final: 0.6927 (ttt90) REVERT: B 120 CYS cc_start: 0.7680 (OUTLIER) cc_final: 0.7398 (t) REVERT: B 266 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8200 (pm20) REVERT: B 332 MET cc_start: 0.8248 (mmt) cc_final: 0.7988 (ptm) REVERT: B 786 ASP cc_start: 0.8182 (t0) cc_final: 0.7786 (t0) outliers start: 15 outliers final: 6 residues processed: 113 average time/residue: 0.0839 time to fit residues: 14.8902 Evaluate side-chains 104 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 732 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 4 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 97 optimal weight: 7.9990 chunk 116 optimal weight: 9.9990 chunk 92 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 142 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 515 HIS ** 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 = 0.3162 r_free = 0.3162 target = 0.114771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.089328 restraints weight = 13666.103| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.44 r_work: 0.2858 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9099 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11740 Z= 0.106 Angle : 0.489 7.258 15940 Z= 0.246 Chirality : 0.038 0.156 1842 Planarity : 0.004 0.036 1990 Dihedral : 4.101 19.747 1580 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.28 % Allowed : 9.84 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.23), residues: 1446 helix: 2.04 (0.18), residues: 900 sheet: -3.24 (0.84), residues: 24 loop : -0.92 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 295 TYR 0.013 0.001 TYR A 781 PHE 0.012 0.001 PHE A 101 TRP 0.008 0.001 TRP A 278 HIS 0.002 0.000 HIS B 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (11734) covalent geometry : angle 0.48847 / 0.25 (15928) SS BOND : bond 0.00085 / 0.05 ( 6) SS BOND : angle 1.00532 / 0.49 ( 12) hydrogen bonds : bond 0.03650 / 2.39 ( 655) hydrogen bonds : angle 3.57591 / 2.59 ( 1941) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.466 Fit side-chains revert: symmetry clash REVERT: A 360 LYS cc_start: 0.8920 (mttt) cc_final: 0.8632 (mtmm) REVERT: A 786 ASP cc_start: 0.8216 (t0) cc_final: 0.7965 (t0) REVERT: B 120 CYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7516 (t) REVERT: B 332 MET cc_start: 0.8225 (mmt) cc_final: 0.7974 (ptm) REVERT: B 786 ASP cc_start: 0.8199 (t0) cc_final: 0.7968 (t0) outliers start: 16 outliers final: 9 residues processed: 119 average time/residue: 0.0899 time to fit residues: 16.9227 Evaluate side-chains 109 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 732 MET Chi-restraints excluded: chain B residue 761 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 106 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 579 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.110252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.084388 restraints weight = 13930.143| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 1.46 r_work: 0.2856 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9164 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11740 Z= 0.188 Angle : 0.565 9.380 15940 Z= 0.283 Chirality : 0.041 0.156 1842 Planarity : 0.005 0.038 1990 Dihedral : 4.324 21.172 1580 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.60 % Allowed : 10.16 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.23), residues: 1446 helix: 1.87 (0.18), residues: 904 sheet: -3.15 (0.87), residues: 24 loop : -0.96 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 103 TYR 0.016 0.001 TYR A 781 PHE 0.015 0.001 PHE A 351 TRP 0.008 0.001 TRP B 303 HIS 0.003 0.001 HIS A 579 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.19 (11734) covalent geometry : angle 0.56487 / 0.28 (15928) SS BOND : bond 0.00154 / 0.08 ( 6) SS BOND : angle 1.09363 / 0.53 ( 12) hydrogen bonds : bond 0.04482 / 2.95 ( 655) hydrogen bonds : angle 3.71379 / 2.70 ( 1941) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.449 Fit side-chains revert: symmetry clash REVERT: A 120 CYS cc_start: 0.7700 (OUTLIER) cc_final: 0.7367 (t) REVERT: A 786 ASP cc_start: 0.8227 (t0) cc_final: 0.7913 (t0) REVERT: B 75 ARG cc_start: 0.7526 (ttm170) cc_final: 0.6977 (ttt90) REVERT: B 120 CYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7433 (t) REVERT: B 332 MET cc_start: 0.8351 (mmt) cc_final: 0.8035 (ptm) REVERT: B 786 ASP cc_start: 0.8229 (t0) cc_final: 0.7957 (t0) outliers start: 20 outliers final: 11 residues processed: 115 average time/residue: 0.0832 time to fit residues: 15.4278 Evaluate side-chains 105 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 732 MET Chi-restraints excluded: chain B residue 761 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 139 optimal weight: 0.6980 chunk 131 optimal weight: 9.9990 chunk 138 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 114 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 796 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.114948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.089335 restraints weight = 13612.037| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.43 r_work: 0.2862 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9099 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 11740 Z= 0.102 Angle : 0.488 7.886 15940 Z= 0.244 Chirality : 0.038 0.155 1842 Planarity : 0.004 0.036 1990 Dihedral : 4.033 19.580 1580 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.28 % Allowed : 10.96 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.23), residues: 1446 helix: 2.11 (0.18), residues: 902 sheet: -3.26 (0.87), residues: 24 loop : -1.06 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 295 TYR 0.012 0.001 TYR A 781 PHE 0.012 0.001 PHE A 101 TRP 0.008 0.001 TRP B 278 HIS 0.002 0.000 HIS B 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (11734) covalent geometry : angle 0.48775 / 0.24 (15928) SS BOND : bond 0.00128 / 0.05 ( 6) SS BOND : angle 0.99814 / 0.48 ( 12) hydrogen bonds : bond 0.03542 / 2.32 ( 655) hydrogen bonds : angle 3.54199 / 2.57 ( 1941) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.452 Fit side-chains REVERT: A 120 CYS cc_start: 0.7716 (OUTLIER) cc_final: 0.7400 (t) REVERT: A 360 LYS cc_start: 0.8933 (mttt) cc_final: 0.8643 (mtmm) REVERT: A 786 ASP cc_start: 0.8229 (t0) cc_final: 0.8009 (t0) REVERT: B 120 CYS cc_start: 0.7681 (OUTLIER) cc_final: 0.7394 (t) REVERT: B 332 MET cc_start: 0.8309 (mmt) cc_final: 0.8012 (ptm) outliers start: 16 outliers final: 7 residues processed: 111 average time/residue: 0.0849 time to fit residues: 15.2773 Evaluate side-chains 104 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 732 MET Chi-restraints excluded: chain B residue 761 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 49 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 115 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 97 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 515 HIS ** 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 = 0.3080 r_free = 0.3080 target = 0.108821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.083179 restraints weight = 13901.912| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 1.45 r_work: 0.2819 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9171 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 11740 Z= 0.226 Angle : 0.596 8.853 15940 Z= 0.301 Chirality : 0.043 0.158 1842 Planarity : 0.005 0.039 1990 Dihedral : 4.410 21.825 1580 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.60 % Allowed : 11.12 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.23), residues: 1446 helix: 1.79 (0.18), residues: 908 sheet: None (None), residues: 0 loop : -1.15 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 236 TYR 0.016 0.001 TYR A 781 PHE 0.017 0.001 PHE A 351 TRP 0.009 0.001 TRP A 303 HIS 0.003 0.001 HIS B 615 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.23 (11734) covalent geometry : angle 0.59566 / 0.30 (15928) SS BOND : bond 0.00153 / 0.08 ( 6) SS BOND : angle 1.11750 / 0.54 ( 12) hydrogen bonds : bond 0.04802 / 3.16 ( 655) hydrogen bonds : angle 3.79357 / 2.75 ( 1941) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.497 Fit side-chains REVERT: A 120 CYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7662 (t) REVERT: A 786 ASP cc_start: 0.8324 (t0) cc_final: 0.8112 (t0) REVERT: B 75 ARG cc_start: 0.7506 (ttm170) cc_final: 0.6980 (ttt90) REVERT: B 120 CYS cc_start: 0.7858 (OUTLIER) cc_final: 0.7617 (t) REVERT: B 332 MET cc_start: 0.8399 (mmt) cc_final: 0.8077 (ptm) REVERT: B 850 ARG cc_start: 0.9304 (OUTLIER) cc_final: 0.8477 (ttm110) outliers start: 20 outliers final: 9 residues processed: 114 average time/residue: 0.0892 time to fit residues: 16.1290 Evaluate side-chains 106 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 732 MET Chi-restraints excluded: chain B residue 761 SER Chi-restraints excluded: chain B residue 850 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 87 optimal weight: 0.0570 chunk 107 optimal weight: 0.0770 chunk 143 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 64 optimal weight: 40.0000 chunk 112 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 515 HIS B 579 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.116191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.090951 restraints weight = 13523.237| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.42 r_work: 0.2909 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9081 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 11740 Z= 0.095 Angle : 0.486 7.963 15940 Z= 0.245 Chirality : 0.037 0.160 1842 Planarity : 0.004 0.036 1990 Dihedral : 4.009 19.707 1580 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.72 % Allowed : 11.84 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.23), residues: 1446 helix: 2.16 (0.18), residues: 902 sheet: None (None), residues: 0 loop : -1.13 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 861 TYR 0.010 0.001 TYR A 781 PHE 0.012 0.001 PHE B 101 TRP 0.008 0.001 TRP A 278 HIS 0.003 0.000 HIS B 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.09 (11734) covalent geometry : angle 0.48447 / 0.24 (15928) SS BOND : bond 0.00220 / 0.11 ( 6) SS BOND : angle 1.46948 / 0.58 ( 12) hydrogen bonds : bond 0.03374 / 2.21 ( 655) hydrogen bonds : angle 3.54043 / 2.57 ( 1941) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.426 Fit side-chains REVERT: A 120 CYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7481 (t) REVERT: A 360 LYS cc_start: 0.8911 (mttt) cc_final: 0.8631 (mtmm) REVERT: B 120 CYS cc_start: 0.7641 (OUTLIER) cc_final: 0.7402 (t) REVERT: B 332 MET cc_start: 0.8307 (mmt) cc_final: 0.8025 (ptm) outliers start: 9 outliers final: 4 residues processed: 110 average time/residue: 0.0827 time to fit residues: 14.3962 Evaluate side-chains 106 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 100 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 732 MET Chi-restraints excluded: chain B residue 761 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 77 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 chunk 136 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 143 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 515 HIS A 631 HIS B 456 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.113149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.087992 restraints weight = 13753.710| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.42 r_work: 0.2894 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9113 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11740 Z= 0.126 Angle : 0.521 7.896 15940 Z= 0.261 Chirality : 0.039 0.160 1842 Planarity : 0.004 0.037 1990 Dihedral : 4.038 19.660 1580 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.64 % Allowed : 12.56 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.51 (0.23), residues: 1446 helix: 2.19 (0.18), residues: 902 sheet: None (None), residues: 0 loop : -1.13 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 103 TYR 0.013 0.001 TYR A 781 PHE 0.011 0.001 PHE A 101 TRP 0.011 0.001 TRP A 278 HIS 0.002 0.001 HIS B 615 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (11734) covalent geometry : angle 0.52029 / 0.26 (15928) SS BOND : bond 0.00056 / 0.03 ( 6) SS BOND : angle 1.38253 / 0.58 ( 12) hydrogen bonds : bond 0.03796 / 2.50 ( 655) hydrogen bonds : angle 3.58195 / 2.60 ( 1941) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.432 Fit side-chains REVERT: A 120 CYS cc_start: 0.7756 (OUTLIER) cc_final: 0.7523 (t) REVERT: B 120 CYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7465 (t) REVERT: B 332 MET cc_start: 0.8308 (mmt) cc_final: 0.8004 (ptm) REVERT: B 456 GLN cc_start: 0.8097 (tt0) cc_final: 0.7852 (tt0) outliers start: 8 outliers final: 4 residues processed: 106 average time/residue: 0.0804 time to fit residues: 13.6546 Evaluate side-chains 101 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 732 MET Chi-restraints excluded: chain B residue 761 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 15 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 131 optimal weight: 10.0000 chunk 116 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 95 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 115 optimal weight: 0.9990 chunk 57 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 515 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.114138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.088738 restraints weight = 13733.480| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.44 r_work: 0.2919 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9116 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11740 Z= 0.112 Angle : 0.505 7.733 15940 Z= 0.253 Chirality : 0.038 0.158 1842 Planarity : 0.004 0.036 1990 Dihedral : 3.975 19.310 1580 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.80 % Allowed : 12.72 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.23), residues: 1446 helix: 2.22 (0.18), residues: 902 sheet: None (None), residues: 0 loop : -1.09 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 103 TYR 0.012 0.001 TYR A 781 PHE 0.011 0.001 PHE A 101 TRP 0.008 0.001 TRP A 278 HIS 0.002 0.001 HIS B 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (11734) covalent geometry : angle 0.50425 / 0.25 (15928) SS BOND : bond 0.00043 / 0.02 ( 6) SS BOND : angle 1.29838 / 0.55 ( 12) hydrogen bonds : bond 0.03617 / 2.38 ( 655) hydrogen bonds : angle 3.54504 / 2.57 ( 1941) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2332.08 seconds wall clock time: 40 minutes 50.22 seconds (2450.22 seconds total)