Starting phenix.real_space_refine on Sat Aug 23 10:12:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jpo_36485/08_2025/8jpo_36485.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jpo_36485/08_2025/8jpo_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_2025/8jpo_36485.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jpo_36485/08_2025/8jpo_36485.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jpo_36485/08_2025/8jpo_36485.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jpo_36485/08_2025/8jpo_36485.map" } 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-2.0-5787/lib/python3.9/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: 2.34, per 1000 atoms: 0.20 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: 0.77 Conformation dependent library (CDL) restraints added in 398.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.31 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: 1.86 Time building geometry restraints manager: 1.08 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: 6212 14.64 - 29.27: 527 29.27 - 43.91: 140 43.91 - 58.55: 46 58.55 - 73.19: 21 Dihedral angle restraints: 6946 sinusoidal: 2748 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 6943 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: 0.000 Normalize map: mean=0, sd=1: 0.890 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: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.210 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 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 : 12.938 73.186 4232 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 aren 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 covalent geometry : bond 0.00375 (11734) covalent geometry : angle 0.62787 (15928) SS BOND : bond 0.00401 ( 6) SS BOND : angle 1.97106 ( 12) hydrogen bonds : bond 0.17280 ( 655) hydrogen bonds : angle 6.01244 ( 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 : 0.695 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.0769 time to fit residues: 13.2743 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 : 0.462 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 515 HIS B 764 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.108090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.082655 restraints weight = 13984.954| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 1.44 r_work: 0.2811 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 11740 Z= 0.287 Angle : 0.683 7.789 15940 Z= 0.353 Chirality : 0.047 0.159 1842 Planarity : 0.006 0.046 1990 Dihedral : 8.083 59.625 1642 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.72 % Allowed : 6.48 % Favored : 92.80 % 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 aren not related in a simple way. whole: 0.66 (0.23), residues: 1446 helix: 1.27 (0.18), residues: 906 sheet: -2.62 (0.82), residues: 24 loop : -0.85 (0.28), residues: 516 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 covalent geometry : bond 0.00731 (11734) covalent geometry : angle 0.68218 (15928) SS BOND : bond 0.00275 ( 6) SS BOND : angle 1.26992 ( 12) hydrogen bonds : bond 0.05731 ( 655) hydrogen bonds : angle 4.11395 ( 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 109 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.287 Fit side-chains REVERT: A 72 LYS cc_start: 0.8056 (mtpt) cc_final: 0.7487 (mttp) REVERT: B 72 LYS cc_start: 0.7992 (mtpt) cc_final: 0.7435 (mttp) REVERT: B 332 MET cc_start: 0.8251 (mmt) cc_final: 0.7946 (ptm) outliers start: 9 outliers final: 6 residues processed: 103 average time/residue: 0.0899 time to fit residues: 13.5720 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 : 0.442 ------------------------------------------------------------------------------- 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: 2.9990 chunk 49 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 47 optimal weight: 0.1980 chunk 39 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 ASN B 452 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.111206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.086828 restraints weight = 13804.365| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 1.35 r_work: 0.2897 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.1255 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= 0.157 Angle : 0.549 6.515 15940 Z= 0.282 Chirality : 0.040 0.159 1842 Planarity : 0.005 0.042 1990 Dihedral : 7.324 52.041 1642 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.12 % Allowed : 8.00 % Favored : 90.88 % 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 aren not related in a simple way. whole: 0.98 (0.23), residues: 1446 helix: 1.59 (0.18), residues: 906 sheet: -2.85 (0.81), residues: 24 loop : -0.86 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 861 TYR 0.018 0.001 TYR A 781 PHE 0.013 0.001 PHE B 351 TRP 0.009 0.001 TRP A 278 HIS 0.003 0.001 HIS B 851 Details of bonding type rmsd covalent geometry : bond 0.00389 (11734) covalent geometry : angle 0.54824 (15928) SS BOND : bond 0.00137 ( 6) SS BOND : angle 1.01578 ( 12) hydrogen bonds : bond 0.04497 ( 655) hydrogen bonds : angle 3.82918 ( 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 111 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.463 Fit side-chains REVERT: B 75 ARG cc_start: 0.7477 (ttm170) cc_final: 0.7000 (ttt90) REVERT: B 120 CYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7467 (t) REVERT: B 332 MET cc_start: 0.8251 (mmt) cc_final: 0.7992 (ptm) outliers start: 14 outliers final: 7 residues processed: 106 average time/residue: 0.0848 time to fit residues: 14.1400 Evaluate side-chains 96 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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 394 MET 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 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: 7.9990 chunk 126 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 chunk 25 optimal weight: 0.1980 chunk 32 optimal weight: 5.9990 chunk 35 optimal weight: 0.0020 chunk 44 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 119 optimal weight: 0.8980 overall best weight: 1.2192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3150 r_free = 0.3150 target = 0.113764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.088294 restraints weight = 13875.348| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.44 r_work: 0.2864 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11740 Z= 0.122 Angle : 0.503 7.285 15940 Z= 0.257 Chirality : 0.038 0.158 1842 Planarity : 0.004 0.037 1990 Dihedral : 6.787 53.337 1642 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.36 % Allowed : 9.12 % Favored : 89.52 % 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 aren not related in a simple way. whole: 1.24 (0.23), residues: 1446 helix: 1.91 (0.18), residues: 900 sheet: -3.08 (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 295 TYR 0.015 0.001 TYR A 781 PHE 0.010 0.001 PHE A 351 TRP 0.006 0.001 TRP A 278 HIS 0.002 0.001 HIS B 615 Details of bonding type rmsd covalent geometry : bond 0.00288 (11734) covalent geometry : angle 0.50271 (15928) SS BOND : bond 0.00109 ( 6) SS BOND : angle 0.97643 ( 12) hydrogen bonds : bond 0.03916 ( 655) hydrogen bonds : angle 3.67404 ( 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 116 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: A 456 GLN cc_start: 0.7811 (mt0) cc_final: 0.7561 (tt0) REVERT: A 786 ASP cc_start: 0.8222 (t0) cc_final: 0.7936 (t0) REVERT: B 120 CYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7490 (t) REVERT: B 266 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8153 (pm20) REVERT: B 332 MET cc_start: 0.8227 (mmt) cc_final: 0.7969 (ptm) REVERT: B 786 ASP cc_start: 0.8199 (t0) cc_final: 0.7926 (t0) outliers start: 17 outliers final: 6 residues processed: 113 average time/residue: 0.0853 time to fit residues: 15.6842 Evaluate side-chains 103 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL 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 266 GLU Chi-restraints excluded: chain B residue 381 VAL 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: 6.9990 chunk 38 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 87 optimal weight: 0.4980 chunk 56 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 chunk 116 optimal weight: 10.0000 chunk 92 optimal weight: 7.9990 chunk 110 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 34 optimal weight: 0.0020 overall best weight: 3.0994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.108601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.082809 restraints weight = 13986.000| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.46 r_work: 0.2830 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 11740 Z= 0.233 Angle : 0.607 8.523 15940 Z= 0.308 Chirality : 0.043 0.155 1842 Planarity : 0.005 0.042 1990 Dihedral : 7.066 55.640 1642 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.44 % Allowed : 10.40 % Favored : 88.16 % 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 aren not related in a simple way. whole: 1.00 (0.23), residues: 1446 helix: 1.65 (0.18), residues: 902 sheet: None (None), residues: 0 loop : -1.05 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 236 TYR 0.018 0.001 TYR A 781 PHE 0.017 0.001 PHE A 351 TRP 0.010 0.001 TRP B 303 HIS 0.003 0.001 HIS B 615 Details of bonding type rmsd covalent geometry : bond 0.00590 (11734) covalent geometry : angle 0.60615 (15928) SS BOND : bond 0.00183 ( 6) SS BOND : angle 1.10921 ( 12) hydrogen bonds : bond 0.04977 ( 655) hydrogen bonds : angle 3.87470 ( 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 111 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: A 456 GLN cc_start: 0.7868 (mt0) cc_final: 0.7639 (tt0) REVERT: A 786 ASP cc_start: 0.8255 (t0) cc_final: 0.7947 (t0) REVERT: B 75 ARG cc_start: 0.7536 (ttm170) cc_final: 0.7009 (ttt90) REVERT: B 120 CYS cc_start: 0.7782 (OUTLIER) cc_final: 0.7507 (t) REVERT: B 266 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8254 (pm20) REVERT: B 332 MET cc_start: 0.8436 (mmt) cc_final: 0.8085 (ptm) REVERT: B 786 ASP cc_start: 0.8193 (t0) cc_final: 0.7895 (t0) outliers start: 18 outliers final: 12 residues processed: 107 average time/residue: 0.0850 time to fit residues: 14.6296 Evaluate side-chains 104 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 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 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 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: 6.9990 chunk 117 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 7 optimal weight: 20.0000 chunk 14 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3141 r_free = 0.3141 target = 0.113234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.087735 restraints weight = 13756.169| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 1.44 r_work: 0.2861 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 11740 Z= 0.112 Angle : 0.499 7.155 15940 Z= 0.253 Chirality : 0.038 0.158 1842 Planarity : 0.004 0.038 1990 Dihedral : 6.508 58.157 1642 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.20 % Allowed : 11.28 % Favored : 87.52 % 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 aren not related in a simple way. whole: 1.27 (0.23), residues: 1446 helix: 1.96 (0.18), residues: 900 sheet: None (None), residues: 0 loop : -1.11 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 861 TYR 0.015 0.001 TYR A 781 PHE 0.010 0.001 PHE A 351 TRP 0.009 0.001 TRP A 278 HIS 0.002 0.001 HIS B 615 Details of bonding type rmsd covalent geometry : bond 0.00256 (11734) covalent geometry : angle 0.49807 (15928) SS BOND : bond 0.00182 ( 6) SS BOND : angle 1.03675 ( 12) hydrogen bonds : bond 0.03771 ( 655) hydrogen bonds : angle 3.63713 ( 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 113 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 786 ASP cc_start: 0.8256 (t0) cc_final: 0.7989 (t0) REVERT: B 120 CYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7440 (t) REVERT: B 332 MET cc_start: 0.8352 (mmt) cc_final: 0.8038 (ptm) REVERT: B 570 PHE cc_start: 0.7961 (m-10) cc_final: 0.7757 (t80) REVERT: B 786 ASP cc_start: 0.8202 (t0) cc_final: 0.7943 (t0) outliers start: 15 outliers final: 7 residues processed: 110 average time/residue: 0.0804 time to fit residues: 14.2321 Evaluate side-chains 102 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.9990 chunk 131 optimal weight: 9.9990 chunk 138 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 114 optimal weight: 0.5980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3145 r_free = 0.3145 target = 0.113523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.088094 restraints weight = 13709.427| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 1.43 r_work: 0.2862 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11740 Z= 0.115 Angle : 0.505 8.479 15940 Z= 0.253 Chirality : 0.038 0.157 1842 Planarity : 0.004 0.037 1990 Dihedral : 6.445 61.032 1642 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.68 % Allowed : 10.80 % Favored : 87.52 % 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 aren not related in a simple way. whole: 1.38 (0.23), residues: 1446 helix: 2.06 (0.18), residues: 900 sheet: None (None), residues: 0 loop : -1.10 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 861 TYR 0.014 0.001 TYR A 781 PHE 0.010 0.001 PHE B 97 TRP 0.007 0.001 TRP B 278 HIS 0.002 0.001 HIS B 515 Details of bonding type rmsd covalent geometry : bond 0.00268 (11734) covalent geometry : angle 0.50476 (15928) SS BOND : bond 0.00085 ( 6) SS BOND : angle 0.98181 ( 12) hydrogen bonds : bond 0.03744 ( 655) hydrogen bonds : angle 3.60342 ( 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 120 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: A 120 CYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7372 (t) REVERT: A 786 ASP cc_start: 0.8269 (t0) cc_final: 0.8020 (t0) REVERT: B 120 CYS cc_start: 0.7782 (OUTLIER) cc_final: 0.7524 (t) REVERT: B 332 MET cc_start: 0.8352 (mmt) cc_final: 0.8050 (ptm) REVERT: B 850 ARG cc_start: 0.9246 (OUTLIER) cc_final: 0.8436 (ttm110) outliers start: 21 outliers final: 11 residues processed: 116 average time/residue: 0.0886 time to fit residues: 16.4148 Evaluate side-chains 109 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.445 ------------------------------------------------------------------------------- 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 119 GLU 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 Chi-restraints excluded: chain B residue 850 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 49 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 115 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 630 HIS B 579 HIS B 630 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.109990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.084615 restraints weight = 13809.944| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 1.43 r_work: 0.2838 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.1758 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= 0.175 Angle : 0.561 9.027 15940 Z= 0.283 Chirality : 0.041 0.157 1842 Planarity : 0.005 0.039 1990 Dihedral : 6.740 59.210 1642 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.76 % Allowed : 11.28 % Favored : 86.96 % 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 aren not related in a simple way. whole: 1.25 (0.23), residues: 1446 helix: 1.90 (0.18), residues: 900 sheet: None (None), residues: 0 loop : -1.05 (0.26), residues: 546 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 351 TRP 0.008 0.001 TRP A 303 HIS 0.003 0.001 HIS B 579 Details of bonding type rmsd covalent geometry : bond 0.00436 (11734) covalent geometry : angle 0.56006 (15928) SS BOND : bond 0.00139 ( 6) SS BOND : angle 1.06912 ( 12) hydrogen bonds : bond 0.04419 ( 655) hydrogen bonds : angle 3.72349 ( 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 120 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: A 120 CYS cc_start: 0.7648 (OUTLIER) cc_final: 0.7329 (t) REVERT: A 266 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8029 (pm20) REVERT: A 786 ASP cc_start: 0.8303 (t0) cc_final: 0.8089 (t0) REVERT: A 850 ARG cc_start: 0.9156 (OUTLIER) cc_final: 0.8342 (ttm110) REVERT: B 75 ARG cc_start: 0.7505 (ttm170) cc_final: 0.6973 (ttt90) REVERT: B 120 CYS cc_start: 0.7834 (OUTLIER) cc_final: 0.7562 (t) REVERT: B 850 ARG cc_start: 0.9294 (OUTLIER) cc_final: 0.8449 (ttm110) outliers start: 22 outliers final: 10 residues processed: 116 average time/residue: 0.1012 time to fit residues: 17.9178 Evaluate side-chains 108 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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 266 GLU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 850 ARG Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 117 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: 1.9990 chunk 23 optimal weight: 3.9990 chunk 65 optimal weight: 0.1980 chunk 87 optimal weight: 0.4980 chunk 107 optimal weight: 0.0020 chunk 143 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.116586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.091280 restraints weight = 13494.867| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.42 r_work: 0.2908 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.1914 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 : 0.491 8.077 15940 Z= 0.248 Chirality : 0.037 0.156 1842 Planarity : 0.004 0.036 1990 Dihedral : 6.244 66.249 1642 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.80 % Allowed : 12.48 % Favored : 86.72 % 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 aren not related in a simple way. whole: 1.48 (0.23), residues: 1446 helix: 2.17 (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 A 400 TYR 0.011 0.001 TYR A 781 PHE 0.011 0.001 PHE B 97 TRP 0.007 0.001 TRP B 278 HIS 0.003 0.000 HIS B 515 Details of bonding type rmsd covalent geometry : bond 0.00201 (11734) covalent geometry : angle 0.49012 (15928) SS BOND : bond 0.00054 ( 6) SS BOND : angle 1.24061 ( 12) hydrogen bonds : bond 0.03350 ( 655) hydrogen bonds : angle 3.53138 ( 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 111 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: A 120 CYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7535 (t) REVERT: A 360 LYS cc_start: 0.8921 (mttt) cc_final: 0.8642 (mtmm) REVERT: B 120 CYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7404 (t) outliers start: 10 outliers final: 5 residues processed: 109 average time/residue: 0.0856 time to fit residues: 15.0685 Evaluate side-chains 103 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain B residue 84 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: 0.7980 chunk 136 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 125 optimal weight: 0.0370 chunk 106 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 143 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 overall best weight: 1.0860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 HIS B 455 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 = 0.3153 r_free = 0.3153 target = 0.114235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.089009 restraints weight = 13710.706| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.42 r_work: 0.2904 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 11740 Z= 0.115 Angle : 0.510 8.291 15940 Z= 0.256 Chirality : 0.038 0.156 1842 Planarity : 0.004 0.037 1990 Dihedral : 6.358 64.965 1642 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.64 % Allowed : 12.96 % Favored : 86.40 % 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 aren not related in a simple way. whole: 1.54 (0.23), residues: 1446 helix: 2.21 (0.18), residues: 902 sheet: None (None), residues: 0 loop : -1.09 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 103 TYR 0.015 0.001 TYR A 781 PHE 0.011 0.001 PHE A 101 TRP 0.014 0.001 TRP B 278 HIS 0.002 0.001 HIS B 515 Details of bonding type rmsd covalent geometry : bond 0.00268 (11734) covalent geometry : angle 0.50879 (15928) SS BOND : bond 0.00056 ( 6) SS BOND : angle 1.39127 ( 12) hydrogen bonds : bond 0.03637 ( 655) hydrogen bonds : angle 3.54928 ( 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 107 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.497 Fit side-chains REVERT: A 120 CYS cc_start: 0.7832 (OUTLIER) cc_final: 0.7560 (t) REVERT: A 360 LYS cc_start: 0.8947 (mttt) cc_final: 0.8653 (mtmm) REVERT: A 401 GLN cc_start: 0.8315 (mt0) cc_final: 0.7984 (mm-40) REVERT: B 120 CYS cc_start: 0.7685 (OUTLIER) cc_final: 0.7453 (t) REVERT: B 456 GLN cc_start: 0.8093 (tt0) cc_final: 0.7834 (tt0) outliers start: 8 outliers final: 5 residues processed: 106 average time/residue: 0.0866 time to fit residues: 14.7629 Evaluate side-chains 101 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain B residue 84 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: 5.9990 chunk 0 optimal weight: 8.9990 chunk 131 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 95 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 57 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.111513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.086027 restraints weight = 13889.348| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 1.44 r_work: 0.2854 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11740 Z= 0.160 Angle : 0.547 8.733 15940 Z= 0.276 Chirality : 0.040 0.156 1842 Planarity : 0.004 0.038 1990 Dihedral : 6.567 62.427 1642 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.88 % Allowed : 12.72 % Favored : 86.40 % 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 aren not related in a simple way. whole: 1.36 (0.23), residues: 1446 helix: 2.02 (0.18), residues: 906 sheet: None (None), residues: 0 loop : -1.09 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 103 TYR 0.017 0.001 TYR A 781 PHE 0.013 0.001 PHE B 351 TRP 0.007 0.001 TRP A 303 HIS 0.003 0.001 HIS B 615 Details of bonding type rmsd covalent geometry : bond 0.00397 (11734) covalent geometry : angle 0.54617 (15928) SS BOND : bond 0.00076 ( 6) SS BOND : angle 1.38175 ( 12) hydrogen bonds : bond 0.04167 ( 655) hydrogen bonds : angle 3.65600 ( 1941) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2269.21 seconds wall clock time: 39 minutes 51.02 seconds (2391.02 seconds total)