Starting phenix.real_space_refine on Sat Oct 11 02:16:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xfp_38307/10_2025/8xfp_38307.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xfp_38307/10_2025/8xfp_38307.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xfp_38307/10_2025/8xfp_38307.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xfp_38307/10_2025/8xfp_38307.map" model { file = "/net/cci-nas-00/data/ceres_data/8xfp_38307/10_2025/8xfp_38307.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xfp_38307/10_2025/8xfp_38307.cif" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 81 5.16 5 C 6865 2.51 5 N 1814 2.21 5 O 1982 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10742 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 5733 Classifications: {'peptide': 734} Link IDs: {'PTRANS': 36, 'TRANS': 697} Chain breaks: 3 Chain: "E" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 876 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain breaks: 1 Chain: "C" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1400 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 171} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 781 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1171 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 8, 'TRANS': 143} Chain: "J" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 781 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 2.62, per 1000 atoms: 0.24 Number of scatterers: 10742 At special positions: 0 Unit cell: (103.887, 109.242, 159.579, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 81 16.00 O 1982 8.00 N 1814 7.00 C 6865 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS A 33 " - pdb=" SG CYS A 43 " distance=2.03 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 364 " distance=2.03 Simple disulfide: pdb=" SG CYS A 618 " - pdb=" SG CYS A 693 " distance=2.03 Simple disulfide: pdb=" SG CYS E 447 " - pdb=" SG CYS E 520 " distance=2.03 Simple disulfide: pdb=" SG CYS C 107 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS G 46 " - pdb=" SG CYS G 52 " distance=2.03 Simple disulfide: pdb=" SG CYS G 55 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 78 " - pdb=" SG CYS G 93 " distance=2.03 Simple disulfide: pdb=" SG CYS G 101 " - pdb=" SG CYS G 110 " distance=2.03 Simple disulfide: pdb=" SG CYS G 113 " - pdb=" SG CYS G 124 " distance=2.03 Simple disulfide: pdb=" SG CYS G 128 " - pdb=" SG CYS G 141 " distance=2.03 Simple disulfide: pdb=" SG CYS H 107 " - pdb=" SG CYS H 136 " distance=2.03 Simple disulfide: pdb=" SG CYS J 43 " - pdb=" SG CYS J 74 " distance=2.03 Simple disulfide: pdb=" SG CYS J 46 " - pdb=" SG CYS J 52 " distance=2.03 Simple disulfide: pdb=" SG CYS J 55 " - pdb=" SG CYS J 74 " distance=2.03 Simple disulfide: pdb=" SG CYS J 78 " - pdb=" SG CYS J 93 " distance=2.03 Simple disulfide: pdb=" SG CYS J 101 " - pdb=" SG CYS J 110 " distance=2.03 Simple disulfide: pdb=" SG CYS J 113 " - pdb=" SG CYS J 124 " distance=2.03 Simple disulfide: pdb=" SG CYS J 128 " - pdb=" SG CYS J 141 " 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: 1.02 Conformation dependent library (CDL) restraints added in 537.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2576 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 16 sheets defined 28.5% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 169 through 174 Processing helix chain 'A' and resid 242 through 247 removed outlier: 3.521A pdb=" N LYS A 245 " --> pdb=" O GLN A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 339 removed outlier: 4.368A pdb=" N CYS A 339 " --> pdb=" O ASN A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 472 removed outlier: 4.278A pdb=" N ALA A 472 " --> pdb=" O GLN A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 567 removed outlier: 4.243A pdb=" N SER A 566 " --> pdb=" O THR A 562 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N CYS A 567 " --> pdb=" O THR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 601 removed outlier: 3.553A pdb=" N PHE A 586 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N MET A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 615 removed outlier: 3.728A pdb=" N PHE A 608 " --> pdb=" O ARG A 604 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ILE A 610 " --> pdb=" O ALA A 606 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N TRP A 611 " --> pdb=" O GLU A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 649 removed outlier: 4.230A pdb=" N LYS A 619 " --> pdb=" O GLY A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 683 Proline residue: A 680 - end of helix Processing helix chain 'A' and resid 686 through 690 removed outlier: 3.746A pdb=" N ALA A 689 " --> pdb=" O GLU A 686 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER A 690 " --> pdb=" O TYR A 687 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 686 through 690' Processing helix chain 'A' and resid 694 through 699 removed outlier: 3.813A pdb=" N THR A 698 " --> pdb=" O LEU A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 732 Processing helix chain 'A' and resid 743 through 769 Proline residue: A 762 - end of helix Processing helix chain 'A' and resid 778 through 790 Processing helix chain 'A' and resid 791 through 804 removed outlier: 3.611A pdb=" N CYS A 795 " --> pdb=" O PRO A 791 " (cutoff:3.500A) Proline residue: A 798 - end of helix Processing helix chain 'A' and resid 805 through 820 removed outlier: 4.109A pdb=" N LYS A 809 " --> pdb=" O ASN A 805 " (cutoff:3.500A) Processing helix chain 'E' and resid 511 through 515 removed outlier: 3.910A pdb=" N THR E 515 " --> pdb=" O PRO E 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 106 Processing helix chain 'C' and resid 138 through 149 Processing helix chain 'C' and resid 162 through 171 removed outlier: 3.978A pdb=" N ASP C 166 " --> pdb=" O PRO C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 185 through 198 Processing helix chain 'C' and resid 213 through 220 removed outlier: 4.146A pdb=" N PHE C 217 " --> pdb=" O PRO C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 227 removed outlier: 3.881A pdb=" N PHE C 225 " --> pdb=" O ILE C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 239 removed outlier: 3.612A pdb=" N LEU C 231 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL C 238 " --> pdb=" O LEU C 234 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 106 removed outlier: 3.787A pdb=" N LEU H 106 " --> pdb=" O PRO H 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 132 Processing helix chain 'H' and resid 138 through 149 Processing helix chain 'H' and resid 162 through 171 removed outlier: 3.969A pdb=" N ASP H 166 " --> pdb=" O PRO H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 174 No H-bonds generated for 'chain 'H' and resid 172 through 174' Processing helix chain 'H' and resid 185 through 198 Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 42 removed outlier: 6.928A pdb=" N VAL A 41 " --> pdb=" O ASP A 63 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 191 through 192 removed outlier: 3.814A pdb=" N ILE A 192 " --> pdb=" O SER A 215 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 300 through 303 removed outlier: 6.468A pdb=" N LEU A 324 " --> pdb=" O ASP A 349 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU A 348 " --> pdb=" O SER A 371 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE A 370 " --> pdb=" O ASP A 395 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LEU A 394 " --> pdb=" O ASP A 419 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LEU A 418 " --> pdb=" O LYS A 440 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 379 through 380 Processing sheet with id=AA5, first strand: chain 'E' and resid 24 through 26 Processing sheet with id=AA6, first strand: chain 'E' and resid 482 through 484 removed outlier: 5.424A pdb=" N GLY E 472 " --> pdb=" O ARG E 463 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ARG E 463 " --> pdb=" O GLY E 472 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA E 474 " --> pdb=" O TRP E 461 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N CYS E 458 " --> pdb=" O ARG E 523 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ARG E 523 " --> pdb=" O CYS E 458 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 482 through 484 removed outlier: 5.424A pdb=" N GLY E 472 " --> pdb=" O ARG E 463 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ARG E 463 " --> pdb=" O GLY E 472 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA E 474 " --> pdb=" O TRP E 461 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N CYS E 458 " --> pdb=" O ARG E 523 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ARG E 523 " --> pdb=" O CYS E 458 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 58 through 66 removed outlier: 8.778A pdb=" N VAL C 181 " --> pdb=" O THR C 152 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N VAL C 154 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N VAL C 183 " --> pdb=" O VAL C 154 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N PHE C 156 " --> pdb=" O VAL C 183 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TRP C 120 " --> pdb=" O ALA C 153 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ILE C 155 " --> pdb=" O TRP C 120 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLY C 122 " --> pdb=" O ILE C 155 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ASP C 157 " --> pdb=" O GLY C 122 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL C 124 " --> pdb=" O ASP C 157 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 60 through 66 removed outlier: 3.553A pdb=" N ARG G 69 " --> pdb=" O GLU G 66 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 82 through 85 Processing sheet with id=AB2, first strand: chain 'G' and resid 101 through 103 Processing sheet with id=AB3, first strand: chain 'G' and resid 118 through 119 Processing sheet with id=AB4, first strand: chain 'H' and resid 58 through 66 removed outlier: 5.926A pdb=" N VAL H 154 " --> pdb=" O VAL H 181 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N VAL H 183 " --> pdb=" O VAL H 154 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N PHE H 156 " --> pdb=" O VAL H 183 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLY H 122 " --> pdb=" O ILE H 155 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ASP H 157 " --> pdb=" O GLY H 122 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N VAL H 124 " --> pdb=" O ASP H 157 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LYS H 125 " --> pdb=" O MET H 101 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 69 through 75 removed outlier: 5.532A pdb=" N LEU J 63 " --> pdb=" O CYS J 93 " (cutoff:3.500A) removed outlier: 9.210A pdb=" N ARG J 95 " --> pdb=" O LEU J 63 " (cutoff:3.500A) removed outlier: 14.442A pdb=" N ARG J 65 " --> pdb=" O ARG J 95 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 101 through 106 removed outlier: 6.600A pdb=" N CYS J 101 " --> pdb=" O CYS J 113 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N CYS J 113 " --> pdb=" O CYS J 101 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N SER J 103 " --> pdb=" O THR J 111 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N PHE J 109 " --> pdb=" O PHE J 105 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 118 through 119 393 hydrogen bonds defined for protein. 1098 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: 2.15 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3479 1.35 - 1.46: 2555 1.46 - 1.58: 4837 1.58 - 1.70: 0 1.70 - 1.82: 104 Bond restraints: 10975 Sorted by residual: bond pdb=" CA CYS A 761 " pdb=" C CYS A 761 " ideal model delta sigma weight residual 1.520 1.530 -0.010 1.23e-02 6.61e+03 6.02e-01 bond pdb=" C GLU C 62 " pdb=" N VAL C 63 " ideal model delta sigma weight residual 1.330 1.316 0.014 1.97e-02 2.58e+03 4.82e-01 bond pdb=" CA PHE A 696 " pdb=" C PHE A 696 " ideal model delta sigma weight residual 1.524 1.532 -0.008 1.26e-02 6.30e+03 4.02e-01 bond pdb=" CB PRO A 697 " pdb=" CG PRO A 697 " ideal model delta sigma weight residual 1.492 1.461 0.031 5.00e-02 4.00e+02 3.84e-01 bond pdb=" C THR A 523 " pdb=" N PRO A 524 " ideal model delta sigma weight residual 1.334 1.348 -0.014 2.34e-02 1.83e+03 3.83e-01 ... (remaining 10970 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 14586 1.41 - 2.81: 197 2.81 - 4.22: 68 4.22 - 5.63: 11 5.63 - 7.04: 4 Bond angle restraints: 14866 Sorted by residual: angle pdb=" N GLN A 113 " pdb=" CA GLN A 113 " pdb=" C GLN A 113 " ideal model delta sigma weight residual 110.97 114.60 -3.63 1.09e+00 8.42e-01 1.11e+01 angle pdb=" C HIS A 209 " pdb=" N ASN A 210 " pdb=" CA ASN A 210 " ideal model delta sigma weight residual 122.31 116.41 5.90 2.00e+00 2.50e-01 8.72e+00 angle pdb=" N HIS A 209 " pdb=" CA HIS A 209 " pdb=" C HIS A 209 " ideal model delta sigma weight residual 110.97 113.54 -2.57 1.09e+00 8.42e-01 5.56e+00 angle pdb=" N PHE A 696 " pdb=" CA PHE A 696 " pdb=" C PHE A 696 " ideal model delta sigma weight residual 109.81 114.97 -5.16 2.21e+00 2.05e-01 5.46e+00 angle pdb=" N SER A 65 " pdb=" CA SER A 65 " pdb=" C SER A 65 " ideal model delta sigma weight residual 110.80 115.14 -4.34 2.13e+00 2.20e-01 4.16e+00 ... (remaining 14861 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.08: 5980 12.08 - 24.17: 447 24.17 - 36.25: 129 36.25 - 48.34: 36 48.34 - 60.42: 15 Dihedral angle restraints: 6607 sinusoidal: 2624 harmonic: 3983 Sorted by residual: dihedral pdb=" CB CYS J 78 " pdb=" SG CYS J 78 " pdb=" SG CYS J 93 " pdb=" CB CYS J 93 " ideal model delta sinusoidal sigma weight residual 93.00 145.68 -52.68 1 1.00e+01 1.00e-02 3.78e+01 dihedral pdb=" CB CYS G 78 " pdb=" SG CYS G 78 " pdb=" SG CYS G 93 " pdb=" CB CYS G 93 " ideal model delta sinusoidal sigma weight residual 93.00 138.78 -45.78 1 1.00e+01 1.00e-02 2.91e+01 dihedral pdb=" CB CYS J 43 " pdb=" SG CYS J 43 " pdb=" SG CYS J 74 " pdb=" CB CYS J 74 " ideal model delta sinusoidal sigma weight residual 93.00 133.51 -40.51 1 1.00e+01 1.00e-02 2.30e+01 ... (remaining 6604 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1007 0.027 - 0.055: 402 0.055 - 0.082: 159 0.082 - 0.109: 81 0.109 - 0.136: 35 Chirality restraints: 1684 Sorted by residual: chirality pdb=" CA PHE A 696 " pdb=" N PHE A 696 " pdb=" C PHE A 696 " pdb=" CB PHE A 696 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.66e-01 chirality pdb=" CA CYS A 761 " pdb=" N CYS A 761 " pdb=" C CYS A 761 " pdb=" CB CYS A 761 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.28e-01 chirality pdb=" CA ILE A 277 " pdb=" N ILE A 277 " pdb=" C ILE A 277 " pdb=" CB ILE A 277 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 1681 not shown) Planarity restraints: 1907 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 623 " -0.008 2.00e-02 2.50e+03 1.57e-02 2.46e+00 pdb=" C PHE A 623 " 0.027 2.00e-02 2.50e+03 pdb=" O PHE A 623 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU A 624 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 69 " -0.020 5.00e-02 4.00e+02 3.01e-02 1.44e+00 pdb=" N PRO C 70 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO C 70 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 70 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER H 69 " 0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO H 70 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO H 70 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO H 70 " 0.016 5.00e-02 4.00e+02 ... (remaining 1904 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 173 2.66 - 3.22: 10291 3.22 - 3.78: 16360 3.78 - 4.34: 22013 4.34 - 4.90: 36743 Nonbonded interactions: 85580 Sorted by model distance: nonbonded pdb=" OG1 THR A 329 " pdb=" OD1 ASN A 353 " model vdw 2.101 3.040 nonbonded pdb=" OG SER H 69 " pdb=" O GLY H 72 " model vdw 2.129 3.040 nonbonded pdb=" OD1 ASP A 161 " pdb=" N ASP A 162 " model vdw 2.250 3.120 nonbonded pdb=" OH TYR C 74 " pdb=" O TYR H 116 " model vdw 2.255 3.040 nonbonded pdb=" O TYR C 116 " pdb=" OH TYR H 74 " model vdw 2.268 3.040 ... (remaining 85575 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.950 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: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.380 Find NCS groups from input model: 0.060 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:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10994 Z= 0.101 Angle : 0.492 7.036 14904 Z= 0.252 Chirality : 0.041 0.136 1684 Planarity : 0.003 0.030 1907 Dihedral : 10.037 60.424 3974 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.76 % Favored : 94.17 % Rotamer: Outliers : 2.10 % Allowed : 6.22 % Favored : 91.67 % 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: -0.41 (0.24), residues: 1355 helix: 1.99 (0.30), residues: 336 sheet: -1.11 (0.32), residues: 277 loop : -1.00 (0.23), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 202 TYR 0.011 0.001 TYR A 590 PHE 0.009 0.001 PHE A 696 TRP 0.016 0.001 TRP A 546 HIS 0.003 0.000 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00214 (10975) covalent geometry : angle 0.49153 (14866) SS BOND : bond 0.00153 ( 19) SS BOND : angle 0.58498 ( 38) hydrogen bonds : bond 0.07775 ( 382) hydrogen bonds : angle 4.54563 ( 1098) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 261 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 GLU cc_start: 0.7470 (tt0) cc_final: 0.7233 (tp30) REVERT: A 596 PHE cc_start: 0.8261 (m-80) cc_final: 0.7628 (m-10) REVERT: A 633 ILE cc_start: 0.7312 (mm) cc_final: 0.7012 (mt) REVERT: A 643 ARG cc_start: 0.4993 (mmp-170) cc_final: 0.4734 (tpp80) REVERT: A 670 PHE cc_start: 0.5094 (OUTLIER) cc_final: 0.4239 (m-80) REVERT: A 696 PHE cc_start: 0.8611 (p90) cc_final: 0.8301 (p90) REVERT: E 454 TYR cc_start: 0.8534 (p90) cc_final: 0.8227 (p90) REVERT: E 503 LEU cc_start: 0.8081 (tp) cc_final: 0.7846 (tp) REVERT: E 517 MET cc_start: 0.8348 (tpp) cc_final: 0.8063 (mmm) REVERT: E 539 TYR cc_start: 0.7729 (m-80) cc_final: 0.7479 (m-80) REVERT: G 83 TYR cc_start: 0.7823 (p90) cc_final: 0.6726 (p90) REVERT: G 117 PHE cc_start: 0.8770 (m-80) cc_final: 0.8397 (m-80) REVERT: H 97 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7376 (tp30) REVERT: H 116 TYR cc_start: 0.8377 (m-80) cc_final: 0.8171 (m-80) REVERT: H 148 GLN cc_start: 0.9033 (mt0) cc_final: 0.8666 (mt0) REVERT: J 102 ASP cc_start: 0.8154 (m-30) cc_final: 0.7616 (m-30) outliers start: 25 outliers final: 9 residues processed: 282 average time/residue: 0.1331 time to fit residues: 49.9461 Evaluate side-chains 175 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 164 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 85 PHE Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 200 VAL Chi-restraints excluded: chain J residue 136 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.0470 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.4980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 overall best weight: 1.4882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN A 258 ASN A 386 GLN A 423 ASN A 658 HIS A 714 ASN A 742 GLN E 496 GLN E 508 ASN G 50 ASN G 120 HIS H 108 ASN ** H 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 207 HIS J 91 ASN J 120 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.111971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.079908 restraints weight = 28747.625| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 4.66 r_work: 0.3183 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10994 Z= 0.186 Angle : 0.647 8.675 14904 Z= 0.325 Chirality : 0.045 0.146 1684 Planarity : 0.004 0.031 1907 Dihedral : 5.926 59.689 1487 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.98 % Favored : 93.95 % Rotamer: Outliers : 3.87 % Allowed : 12.36 % Favored : 83.77 % 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: -0.54 (0.24), residues: 1355 helix: 1.71 (0.29), residues: 344 sheet: -1.15 (0.34), residues: 257 loop : -1.06 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 523 TYR 0.019 0.002 TYR A 725 PHE 0.029 0.001 PHE A 662 TRP 0.015 0.001 TRP A 546 HIS 0.006 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00427 (10975) covalent geometry : angle 0.64578 (14866) SS BOND : bond 0.00650 ( 19) SS BOND : angle 0.93756 ( 38) hydrogen bonds : bond 0.03490 ( 382) hydrogen bonds : angle 4.49391 ( 1098) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 191 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 GLU cc_start: 0.8365 (tt0) cc_final: 0.7631 (tp30) REVERT: A 344 MET cc_start: 0.7922 (tpt) cc_final: 0.7687 (tpt) REVERT: A 596 PHE cc_start: 0.8831 (m-80) cc_final: 0.8253 (m-10) REVERT: A 643 ARG cc_start: 0.4583 (mmp-170) cc_final: 0.4195 (tpp-160) REVERT: A 670 PHE cc_start: 0.3432 (OUTLIER) cc_final: 0.2891 (m-80) REVERT: A 687 TYR cc_start: 0.7336 (m-10) cc_final: 0.7039 (m-10) REVERT: E 459 MET cc_start: 0.7110 (mtm) cc_final: 0.6815 (ttp) REVERT: E 517 MET cc_start: 0.8442 (tpp) cc_final: 0.8054 (tmm) REVERT: E 539 TYR cc_start: 0.8115 (m-80) cc_final: 0.7716 (m-80) REVERT: C 74 TYR cc_start: 0.7869 (OUTLIER) cc_final: 0.7111 (m-80) REVERT: C 144 LYS cc_start: 0.8807 (pttt) cc_final: 0.8440 (ptpp) REVERT: C 193 ASN cc_start: 0.8181 (t0) cc_final: 0.7790 (t0) REVERT: C 198 GLN cc_start: 0.8467 (tp40) cc_final: 0.7666 (mp10) REVERT: G 68 MET cc_start: 0.8045 (mtp) cc_final: 0.7674 (mtm) REVERT: H 56 LYS cc_start: 0.8926 (mptt) cc_final: 0.7860 (tptt) REVERT: H 87 ARG cc_start: 0.8504 (tpp-160) cc_final: 0.8080 (mmm160) REVERT: H 97 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7434 (tp30) REVERT: H 148 GLN cc_start: 0.8921 (mt0) cc_final: 0.8552 (mt0) REVERT: H 207 HIS cc_start: 0.7633 (t-90) cc_final: 0.7293 (t-90) REVERT: J 48 LYS cc_start: 0.9204 (tppt) cc_final: 0.8901 (tmmt) REVERT: J 56 GLN cc_start: 0.8549 (tp40) cc_final: 0.8227 (tt0) REVERT: J 64 ARG cc_start: 0.7880 (ttm-80) cc_final: 0.7596 (ttm-80) REVERT: J 92 ARG cc_start: 0.8150 (mtm-85) cc_final: 0.7816 (mtm-85) REVERT: J 108 ASP cc_start: 0.8870 (p0) cc_final: 0.8654 (p0) outliers start: 46 outliers final: 26 residues processed: 223 average time/residue: 0.1123 time to fit residues: 34.4869 Evaluate side-chains 190 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 161 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain E residue 493 THR Chi-restraints excluded: chain E residue 532 LEU Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 107 CYS Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 85 PHE Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 136 CYS Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 200 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 60 optimal weight: 0.4980 chunk 88 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 115 optimal weight: 0.3980 chunk 81 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN A 742 GLN E 496 GLN ** E 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.112854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.081074 restraints weight = 28623.905| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 4.69 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10994 Z= 0.121 Angle : 0.603 8.964 14904 Z= 0.300 Chirality : 0.043 0.157 1684 Planarity : 0.003 0.032 1907 Dihedral : 5.616 59.851 1482 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.46 % Favored : 94.46 % Rotamer: Outliers : 3.78 % Allowed : 12.87 % Favored : 83.35 % 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: -0.52 (0.24), residues: 1355 helix: 1.78 (0.29), residues: 343 sheet: -1.06 (0.34), residues: 256 loop : -1.10 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 491 TYR 0.012 0.001 TYR E 454 PHE 0.027 0.001 PHE A 696 TRP 0.016 0.001 TRP A 546 HIS 0.005 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00270 (10975) covalent geometry : angle 0.60129 (14866) SS BOND : bond 0.00230 ( 19) SS BOND : angle 1.11900 ( 38) hydrogen bonds : bond 0.03157 ( 382) hydrogen bonds : angle 4.34580 ( 1098) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 187 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 MET cc_start: 0.7710 (tpt) cc_final: 0.7358 (tpt) REVERT: A 354 ASN cc_start: 0.8229 (OUTLIER) cc_final: 0.7930 (p0) REVERT: A 596 PHE cc_start: 0.8781 (m-80) cc_final: 0.8153 (m-10) REVERT: A 643 ARG cc_start: 0.4441 (mmp-170) cc_final: 0.4163 (tpp-160) REVERT: A 670 PHE cc_start: 0.3362 (OUTLIER) cc_final: 0.2848 (m-80) REVERT: A 687 TYR cc_start: 0.7408 (m-10) cc_final: 0.7005 (m-10) REVERT: A 729 TYR cc_start: 0.1738 (OUTLIER) cc_final: 0.1113 (m-10) REVERT: E 459 MET cc_start: 0.6897 (mtm) cc_final: 0.6424 (ttp) REVERT: E 539 TYR cc_start: 0.7874 (m-80) cc_final: 0.7454 (m-80) REVERT: C 74 TYR cc_start: 0.7547 (OUTLIER) cc_final: 0.7238 (m-80) REVERT: C 92 LEU cc_start: 0.6877 (OUTLIER) cc_final: 0.6593 (pp) REVERT: C 144 LYS cc_start: 0.8751 (pttt) cc_final: 0.8361 (ptpp) REVERT: C 193 ASN cc_start: 0.7968 (t0) cc_final: 0.7734 (t0) REVERT: C 198 GLN cc_start: 0.8193 (tp40) cc_final: 0.7371 (mp10) REVERT: G 68 MET cc_start: 0.7716 (mtp) cc_final: 0.7422 (mtm) REVERT: G 107 LYS cc_start: 0.8907 (ptpp) cc_final: 0.8564 (tttp) REVERT: G 117 PHE cc_start: 0.8730 (m-80) cc_final: 0.8525 (m-10) REVERT: G 118 TYR cc_start: 0.8997 (m-80) cc_final: 0.8289 (m-80) REVERT: H 87 ARG cc_start: 0.8479 (tpp-160) cc_final: 0.8210 (tpp-160) REVERT: H 97 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7119 (tp30) REVERT: H 116 TYR cc_start: 0.8770 (m-80) cc_final: 0.7887 (m-80) REVERT: H 148 GLN cc_start: 0.8799 (mt0) cc_final: 0.8400 (mt0) REVERT: H 167 GLN cc_start: 0.9087 (mt0) cc_final: 0.8857 (mt0) REVERT: H 197 LYS cc_start: 0.9281 (mmtp) cc_final: 0.9043 (mmtp) REVERT: J 48 LYS cc_start: 0.9102 (tppt) cc_final: 0.8793 (tmmt) REVERT: J 56 GLN cc_start: 0.8421 (tp40) cc_final: 0.8132 (tt0) REVERT: J 64 ARG cc_start: 0.7710 (ttm-80) cc_final: 0.7427 (ttm-80) REVERT: J 92 ARG cc_start: 0.7871 (mtm-85) cc_final: 0.7453 (mtm-85) REVERT: J 108 ASP cc_start: 0.8731 (p0) cc_final: 0.8521 (p0) REVERT: J 114 LYS cc_start: 0.8464 (ttmm) cc_final: 0.8182 (ttmm) outliers start: 45 outliers final: 26 residues processed: 219 average time/residue: 0.1176 time to fit residues: 35.4338 Evaluate side-chains 202 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 170 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 729 TYR Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain E residue 493 THR Chi-restraints excluded: chain E residue 532 LEU Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain G residue 76 HIS Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 85 PHE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 136 CYS Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 200 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 25 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 71 optimal weight: 0.1980 chunk 88 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 130 optimal weight: 0.2980 chunk 119 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 136 optimal weight: 8.9990 chunk 135 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN A 458 ASN ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 50 ASN G 85 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.110412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.078116 restraints weight = 28848.590| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 4.67 r_work: 0.3161 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10994 Z= 0.220 Angle : 0.656 9.685 14904 Z= 0.330 Chirality : 0.046 0.263 1684 Planarity : 0.004 0.033 1907 Dihedral : 5.959 57.211 1482 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.72 % Favored : 93.21 % Rotamer: Outliers : 4.21 % Allowed : 14.05 % Favored : 81.75 % 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: -0.71 (0.24), residues: 1355 helix: 1.50 (0.29), residues: 343 sheet: -1.21 (0.32), residues: 282 loop : -1.12 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 121 TYR 0.016 0.002 TYR E 452 PHE 0.040 0.002 PHE A 662 TRP 0.016 0.001 TRP A 546 HIS 0.006 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00508 (10975) covalent geometry : angle 0.65410 (14866) SS BOND : bond 0.00330 ( 19) SS BOND : angle 1.08282 ( 38) hydrogen bonds : bond 0.03676 ( 382) hydrogen bonds : angle 4.61416 ( 1098) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 176 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 MET cc_start: 0.8090 (tpt) cc_final: 0.7805 (tpt) REVERT: A 353 ASN cc_start: 0.8486 (OUTLIER) cc_final: 0.7870 (m-40) REVERT: A 354 ASN cc_start: 0.8173 (OUTLIER) cc_final: 0.7823 (p0) REVERT: A 596 PHE cc_start: 0.8829 (m-80) cc_final: 0.8281 (m-10) REVERT: A 643 ARG cc_start: 0.4619 (mmp-170) cc_final: 0.4306 (tpp-160) REVERT: A 670 PHE cc_start: 0.3371 (OUTLIER) cc_final: 0.2820 (m-80) REVERT: A 687 TYR cc_start: 0.7318 (m-10) cc_final: 0.6787 (m-80) REVERT: A 729 TYR cc_start: 0.1792 (OUTLIER) cc_final: 0.1173 (m-10) REVERT: E 24 VAL cc_start: 0.8802 (OUTLIER) cc_final: 0.8547 (m) REVERT: E 459 MET cc_start: 0.7254 (mtm) cc_final: 0.6780 (ttp) REVERT: E 492 PHE cc_start: 0.9122 (m-10) cc_final: 0.8776 (m-10) REVERT: E 505 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.9076 (tt) REVERT: E 517 MET cc_start: 0.8684 (tpp) cc_final: 0.8233 (tpp) REVERT: C 144 LYS cc_start: 0.8880 (pttt) cc_final: 0.8535 (ptpp) REVERT: C 193 ASN cc_start: 0.8204 (t0) cc_final: 0.7862 (t0) REVERT: C 198 GLN cc_start: 0.8487 (tp40) cc_final: 0.7986 (mp10) REVERT: G 68 MET cc_start: 0.8085 (mtp) cc_final: 0.7711 (mtm) REVERT: G 107 LYS cc_start: 0.8930 (ptpp) cc_final: 0.8530 (tttp) REVERT: H 56 LYS cc_start: 0.8956 (mptt) cc_final: 0.7872 (tptt) REVERT: H 87 ARG cc_start: 0.8577 (tpp-160) cc_final: 0.8101 (mmm160) REVERT: H 97 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7445 (tp30) REVERT: J 56 GLN cc_start: 0.8602 (tp40) cc_final: 0.8294 (tt0) REVERT: J 64 ARG cc_start: 0.7955 (ttm-80) cc_final: 0.7659 (ttm-80) REVERT: J 92 ARG cc_start: 0.8235 (mtm-85) cc_final: 0.7912 (mtm-85) REVERT: J 108 ASP cc_start: 0.8887 (p0) cc_final: 0.8668 (p0) REVERT: J 114 LYS cc_start: 0.8512 (ttmm) cc_final: 0.8287 (ttmm) REVERT: J 139 MET cc_start: 0.8130 (tpt) cc_final: 0.7922 (tpt) outliers start: 50 outliers final: 28 residues processed: 209 average time/residue: 0.1157 time to fit residues: 33.1804 Evaluate side-chains 195 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 160 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 729 TYR Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 493 THR Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 532 LEU Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 136 CYS Chi-restraints excluded: chain H residue 192 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 81 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 135 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 37 optimal weight: 0.0050 overall best weight: 1.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 50 ASN G 100 ASN G 120 HIS H 207 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.111155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.078999 restraints weight = 28624.756| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 4.67 r_work: 0.3179 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10994 Z= 0.168 Angle : 0.628 8.729 14904 Z= 0.315 Chirality : 0.044 0.229 1684 Planarity : 0.004 0.033 1907 Dihedral : 5.712 58.420 1479 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.13 % Favored : 93.80 % Rotamer: Outliers : 4.37 % Allowed : 15.73 % Favored : 79.90 % 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: -0.75 (0.23), residues: 1355 helix: 1.42 (0.29), residues: 343 sheet: -1.17 (0.32), residues: 279 loop : -1.15 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 84 TYR 0.018 0.002 TYR E 452 PHE 0.029 0.001 PHE A 696 TRP 0.016 0.001 TRP A 546 HIS 0.006 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00387 (10975) covalent geometry : angle 0.62634 (14866) SS BOND : bond 0.00295 ( 19) SS BOND : angle 0.99588 ( 38) hydrogen bonds : bond 0.03587 ( 382) hydrogen bonds : angle 4.58334 ( 1098) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 171 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 MET cc_start: 0.8155 (tpt) cc_final: 0.7878 (tpt) REVERT: A 353 ASN cc_start: 0.8432 (OUTLIER) cc_final: 0.7890 (m110) REVERT: A 354 ASN cc_start: 0.8188 (OUTLIER) cc_final: 0.7832 (p0) REVERT: A 542 ARG cc_start: 0.6514 (ttt180) cc_final: 0.5446 (ptm160) REVERT: A 596 PHE cc_start: 0.8826 (m-80) cc_final: 0.8272 (m-10) REVERT: A 643 ARG cc_start: 0.4851 (mmp-170) cc_final: 0.4636 (tpp-160) REVERT: A 670 PHE cc_start: 0.3340 (OUTLIER) cc_final: 0.2820 (m-80) REVERT: A 728 LEU cc_start: 0.6433 (mt) cc_final: 0.6138 (pp) REVERT: A 753 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7959 (mt) REVERT: E 24 VAL cc_start: 0.8949 (OUTLIER) cc_final: 0.8731 (m) REVERT: E 459 MET cc_start: 0.7418 (mtm) cc_final: 0.6843 (ttp) REVERT: E 492 PHE cc_start: 0.9006 (m-10) cc_final: 0.8756 (m-10) REVERT: E 505 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8717 (tt) REVERT: E 517 MET cc_start: 0.8751 (tpp) cc_final: 0.8317 (tpp) REVERT: C 74 TYR cc_start: 0.7976 (OUTLIER) cc_final: 0.7534 (m-80) REVERT: C 92 LEU cc_start: 0.6954 (OUTLIER) cc_final: 0.6697 (pp) REVERT: C 144 LYS cc_start: 0.8829 (pttt) cc_final: 0.8471 (ptpp) REVERT: G 68 MET cc_start: 0.8043 (mtp) cc_final: 0.7612 (mtm) REVERT: G 107 LYS cc_start: 0.8933 (ptpp) cc_final: 0.8618 (tttm) REVERT: G 118 TYR cc_start: 0.9149 (m-80) cc_final: 0.8441 (m-80) REVERT: G 121 ARG cc_start: 0.8297 (pmt-80) cc_final: 0.8049 (pmt-80) REVERT: H 57 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7529 (mt-10) REVERT: H 87 ARG cc_start: 0.8623 (tpp-160) cc_final: 0.8159 (tpp-160) REVERT: H 97 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7440 (tp30) REVERT: J 48 LYS cc_start: 0.9075 (tppt) cc_final: 0.8783 (tmmt) REVERT: J 56 GLN cc_start: 0.8512 (tp40) cc_final: 0.8235 (tt0) REVERT: J 64 ARG cc_start: 0.7943 (ttm-80) cc_final: 0.7671 (ttm-80) REVERT: J 92 ARG cc_start: 0.8255 (mtm-85) cc_final: 0.7957 (mtm-85) REVERT: J 108 ASP cc_start: 0.8846 (p0) cc_final: 0.8636 (p0) outliers start: 52 outliers final: 30 residues processed: 206 average time/residue: 0.1163 time to fit residues: 32.9078 Evaluate side-chains 198 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 158 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 493 THR Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 532 LEU Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain G residue 76 HIS Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 136 CYS Chi-restraints excluded: chain H residue 207 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 135 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 131 optimal weight: 0.0980 chunk 93 optimal weight: 2.9990 chunk 110 optimal weight: 20.0000 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 0.0770 chunk 84 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 overall best weight: 1.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 GLN G 50 ASN H 207 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.111543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.079529 restraints weight = 28478.821| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 4.65 r_work: 0.3195 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10994 Z= 0.147 Angle : 0.630 9.882 14904 Z= 0.317 Chirality : 0.044 0.192 1684 Planarity : 0.004 0.035 1907 Dihedral : 5.602 58.774 1479 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.27 % Favored : 93.65 % Rotamer: Outliers : 4.54 % Allowed : 16.06 % Favored : 79.39 % 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: -0.73 (0.23), residues: 1355 helix: 1.41 (0.29), residues: 342 sheet: -1.15 (0.32), residues: 279 loop : -1.13 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 121 TYR 0.018 0.002 TYR G 83 PHE 0.040 0.001 PHE A 662 TRP 0.016 0.001 TRP A 546 HIS 0.010 0.001 HIS H 207 Details of bonding type rmsd covalent geometry : bond 0.00335 (10975) covalent geometry : angle 0.62917 (14866) SS BOND : bond 0.00246 ( 19) SS BOND : angle 0.92183 ( 38) hydrogen bonds : bond 0.03499 ( 382) hydrogen bonds : angle 4.61918 ( 1098) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 166 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 MET cc_start: 0.8186 (tpt) cc_final: 0.7912 (tpt) REVERT: A 354 ASN cc_start: 0.8218 (OUTLIER) cc_final: 0.7907 (p0) REVERT: A 412 LEU cc_start: 0.9129 (tt) cc_final: 0.8919 (tp) REVERT: A 542 ARG cc_start: 0.6512 (ttt180) cc_final: 0.5449 (ptm160) REVERT: A 596 PHE cc_start: 0.8828 (m-80) cc_final: 0.8257 (m-10) REVERT: A 643 ARG cc_start: 0.4783 (mmp-170) cc_final: 0.4456 (tpp-160) REVERT: A 670 PHE cc_start: 0.3441 (OUTLIER) cc_final: 0.2940 (m-80) REVERT: A 687 TYR cc_start: 0.7231 (m-80) cc_final: 0.6810 (m-80) REVERT: E 24 VAL cc_start: 0.8969 (OUTLIER) cc_final: 0.8754 (m) REVERT: E 459 MET cc_start: 0.7431 (mtm) cc_final: 0.7114 (ttm) REVERT: E 505 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8505 (tt) REVERT: E 517 MET cc_start: 0.8746 (tpp) cc_final: 0.8319 (tpp) REVERT: C 74 TYR cc_start: 0.7935 (OUTLIER) cc_final: 0.7483 (m-80) REVERT: C 92 LEU cc_start: 0.6889 (OUTLIER) cc_final: 0.6671 (pp) REVERT: C 144 LYS cc_start: 0.8803 (pttt) cc_final: 0.8442 (ptpp) REVERT: C 193 ASN cc_start: 0.8250 (t0) cc_final: 0.8018 (t0) REVERT: C 198 GLN cc_start: 0.8210 (tp40) cc_final: 0.7686 (mp10) REVERT: G 68 MET cc_start: 0.8040 (mtp) cc_final: 0.7680 (mtm) REVERT: G 107 LYS cc_start: 0.9036 (ptpp) cc_final: 0.8673 (tttm) REVERT: G 118 TYR cc_start: 0.9300 (m-80) cc_final: 0.8649 (m-80) REVERT: H 56 LYS cc_start: 0.8959 (mptt) cc_final: 0.7899 (tptt) REVERT: H 57 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7637 (mt-10) REVERT: H 87 ARG cc_start: 0.8592 (tpp-160) cc_final: 0.8198 (mmm160) REVERT: H 97 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7360 (tp30) REVERT: J 48 LYS cc_start: 0.9097 (tppt) cc_final: 0.8808 (tmmt) REVERT: J 56 GLN cc_start: 0.8492 (tp40) cc_final: 0.8250 (tt0) REVERT: J 64 ARG cc_start: 0.7959 (ttm-80) cc_final: 0.7698 (ttm-80) REVERT: J 92 ARG cc_start: 0.8209 (mtm-85) cc_final: 0.7920 (mtm-85) REVERT: J 112 LYS cc_start: 0.8424 (tptm) cc_final: 0.8169 (tmtt) outliers start: 54 outliers final: 28 residues processed: 203 average time/residue: 0.1150 time to fit residues: 31.8606 Evaluate side-chains 195 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 159 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 493 THR Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 532 LEU Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain G residue 74 CYS Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 136 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 30 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 71 optimal weight: 0.6980 chunk 99 optimal weight: 0.0040 chunk 98 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.111416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.079489 restraints weight = 28421.988| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 4.64 r_work: 0.3189 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10994 Z= 0.153 Angle : 0.649 10.061 14904 Z= 0.325 Chirality : 0.044 0.187 1684 Planarity : 0.004 0.038 1907 Dihedral : 5.607 59.303 1479 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.42 % Favored : 93.51 % Rotamer: Outliers : 4.21 % Allowed : 16.32 % Favored : 79.48 % 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 aren not related in a simple way. whole: -0.76 (0.23), residues: 1355 helix: 1.35 (0.29), residues: 344 sheet: -1.18 (0.32), residues: 279 loop : -1.13 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 202 TYR 0.018 0.002 TYR E 452 PHE 0.031 0.001 PHE A 696 TRP 0.015 0.001 TRP A 546 HIS 0.005 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00351 (10975) covalent geometry : angle 0.64784 (14866) SS BOND : bond 0.00285 ( 19) SS BOND : angle 1.02495 ( 38) hydrogen bonds : bond 0.03564 ( 382) hydrogen bonds : angle 4.64745 ( 1098) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 161 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 MET cc_start: 0.8193 (tpt) cc_final: 0.7908 (tpt) REVERT: A 353 ASN cc_start: 0.8428 (OUTLIER) cc_final: 0.7914 (m-40) REVERT: A 354 ASN cc_start: 0.8221 (OUTLIER) cc_final: 0.7858 (p0) REVERT: A 542 ARG cc_start: 0.6452 (ttt180) cc_final: 0.5631 (ptm160) REVERT: A 596 PHE cc_start: 0.8823 (m-80) cc_final: 0.8258 (m-10) REVERT: A 670 PHE cc_start: 0.3427 (OUTLIER) cc_final: 0.2942 (m-80) REVERT: A 687 TYR cc_start: 0.7376 (m-80) cc_final: 0.6799 (m-80) REVERT: E 24 VAL cc_start: 0.8969 (OUTLIER) cc_final: 0.8761 (m) REVERT: E 459 MET cc_start: 0.7453 (mtm) cc_final: 0.7165 (ttm) REVERT: E 505 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8700 (tt) REVERT: E 506 GLN cc_start: 0.8418 (tp40) cc_final: 0.8178 (tp40) REVERT: E 517 MET cc_start: 0.8766 (tpp) cc_final: 0.8352 (tpp) REVERT: C 74 TYR cc_start: 0.7957 (OUTLIER) cc_final: 0.7457 (m-80) REVERT: C 92 LEU cc_start: 0.6935 (OUTLIER) cc_final: 0.6717 (pp) REVERT: C 144 LYS cc_start: 0.8790 (pttt) cc_final: 0.8431 (ptpp) REVERT: G 68 MET cc_start: 0.8051 (mtp) cc_final: 0.7720 (mtm) REVERT: G 107 LYS cc_start: 0.9047 (ptpp) cc_final: 0.8671 (tttp) REVERT: H 57 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7640 (mt-10) REVERT: H 87 ARG cc_start: 0.8593 (tpp-160) cc_final: 0.7993 (tpp-160) REVERT: H 97 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7463 (tp30) REVERT: H 207 HIS cc_start: 0.7586 (OUTLIER) cc_final: 0.7221 (t70) REVERT: J 48 LYS cc_start: 0.9053 (tppt) cc_final: 0.8789 (tmmt) REVERT: J 56 GLN cc_start: 0.8501 (tp40) cc_final: 0.8266 (tt0) REVERT: J 64 ARG cc_start: 0.7982 (ttm-80) cc_final: 0.7739 (ttm-80) REVERT: J 92 ARG cc_start: 0.8233 (mtm-85) cc_final: 0.7955 (mtm-85) REVERT: J 112 LYS cc_start: 0.8383 (tptm) cc_final: 0.8063 (tmtt) outliers start: 50 outliers final: 32 residues processed: 193 average time/residue: 0.1237 time to fit residues: 32.8226 Evaluate side-chains 199 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 157 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 493 THR Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 532 LEU Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 222 PHE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain G residue 74 CYS Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 136 CYS Chi-restraints excluded: chain H residue 167 GLN Chi-restraints excluded: chain H residue 207 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 1 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 4 optimal weight: 0.0370 chunk 76 optimal weight: 1.9990 chunk 136 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 overall best weight: 0.9262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.111973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.080068 restraints weight = 28195.442| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 4.65 r_work: 0.3206 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10994 Z= 0.139 Angle : 0.643 9.390 14904 Z= 0.320 Chirality : 0.044 0.169 1684 Planarity : 0.003 0.036 1907 Dihedral : 5.506 59.961 1479 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.13 % Favored : 93.80 % Rotamer: Outliers : 4.21 % Allowed : 16.23 % Favored : 79.56 % 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: -0.73 (0.23), residues: 1355 helix: 1.43 (0.29), residues: 344 sheet: -1.18 (0.32), residues: 279 loop : -1.14 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 643 TYR 0.017 0.001 TYR E 452 PHE 0.032 0.001 PHE A 696 TRP 0.015 0.001 TRP A 546 HIS 0.005 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00320 (10975) covalent geometry : angle 0.64228 (14866) SS BOND : bond 0.00220 ( 19) SS BOND : angle 0.92037 ( 38) hydrogen bonds : bond 0.03434 ( 382) hydrogen bonds : angle 4.57467 ( 1098) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 155 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 MET cc_start: 0.8221 (tpt) cc_final: 0.7942 (tpt) REVERT: A 353 ASN cc_start: 0.8441 (OUTLIER) cc_final: 0.7958 (m-40) REVERT: A 354 ASN cc_start: 0.8173 (OUTLIER) cc_final: 0.7799 (p0) REVERT: A 542 ARG cc_start: 0.6430 (ttt180) cc_final: 0.5626 (ptm160) REVERT: A 670 PHE cc_start: 0.3516 (OUTLIER) cc_final: 0.2995 (m-80) REVERT: A 687 TYR cc_start: 0.7391 (m-80) cc_final: 0.6830 (m-80) REVERT: E 21 VAL cc_start: 0.8458 (t) cc_final: 0.8250 (m) REVERT: E 459 MET cc_start: 0.7481 (mtm) cc_final: 0.7147 (ttm) REVERT: E 505 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8432 (tt) REVERT: E 517 MET cc_start: 0.8747 (tpp) cc_final: 0.8543 (mmm) REVERT: C 74 TYR cc_start: 0.7888 (OUTLIER) cc_final: 0.7380 (m-80) REVERT: C 92 LEU cc_start: 0.6879 (OUTLIER) cc_final: 0.6665 (pp) REVERT: C 144 LYS cc_start: 0.8801 (pttt) cc_final: 0.8432 (ptpp) REVERT: G 68 MET cc_start: 0.8013 (mtp) cc_final: 0.7683 (mtm) REVERT: G 107 LYS cc_start: 0.9062 (ptpp) cc_final: 0.8681 (tttm) REVERT: G 118 TYR cc_start: 0.9168 (m-80) cc_final: 0.8644 (m-80) REVERT: H 57 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7616 (mt-10) REVERT: H 67 GLU cc_start: 0.9047 (tt0) cc_final: 0.8543 (mp0) REVERT: H 87 ARG cc_start: 0.8538 (tpp-160) cc_final: 0.7929 (tpp-160) REVERT: H 97 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7425 (tp30) REVERT: J 48 LYS cc_start: 0.9009 (tppt) cc_final: 0.8787 (tmmt) REVERT: J 56 GLN cc_start: 0.8462 (tp40) cc_final: 0.8233 (tt0) REVERT: J 64 ARG cc_start: 0.7977 (ttm-80) cc_final: 0.7736 (ttm-80) REVERT: J 92 ARG cc_start: 0.8200 (mtm-85) cc_final: 0.7932 (mtm-85) REVERT: J 112 LYS cc_start: 0.8373 (tptm) cc_final: 0.8104 (tmtt) REVERT: J 139 MET cc_start: 0.8227 (tpt) cc_final: 0.7688 (tpp) outliers start: 50 outliers final: 32 residues processed: 190 average time/residue: 0.1225 time to fit residues: 32.1029 Evaluate side-chains 191 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 151 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain E residue 493 THR Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 532 LEU Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 222 PHE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain G residue 74 CYS Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 136 CYS Chi-restraints excluded: chain H residue 167 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 120 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 61 optimal weight: 0.0980 chunk 41 optimal weight: 0.3980 chunk 99 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 GLN ** 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 = 0.3967 r_free = 0.3967 target = 0.113075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.081305 restraints weight = 28352.460| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 4.68 r_work: 0.3228 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10994 Z= 0.120 Angle : 0.646 9.497 14904 Z= 0.319 Chirality : 0.043 0.169 1684 Planarity : 0.003 0.035 1907 Dihedral : 5.338 58.385 1479 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.61 % Favored : 94.32 % Rotamer: Outliers : 3.28 % Allowed : 17.33 % Favored : 79.39 % 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: -0.63 (0.24), residues: 1355 helix: 1.54 (0.29), residues: 345 sheet: -1.10 (0.32), residues: 279 loop : -1.09 (0.23), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 643 TYR 0.015 0.001 TYR E 452 PHE 0.033 0.001 PHE A 696 TRP 0.014 0.001 TRP A 546 HIS 0.005 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00274 (10975) covalent geometry : angle 0.64505 (14866) SS BOND : bond 0.00179 ( 19) SS BOND : angle 0.90919 ( 38) hydrogen bonds : bond 0.03205 ( 382) hydrogen bonds : angle 4.46665 ( 1098) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 160 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 MET cc_start: 0.8197 (tpt) cc_final: 0.7913 (tpt) REVERT: A 353 ASN cc_start: 0.8419 (OUTLIER) cc_final: 0.7707 (m-40) REVERT: A 354 ASN cc_start: 0.8203 (OUTLIER) cc_final: 0.7801 (p0) REVERT: A 542 ARG cc_start: 0.6450 (ttt180) cc_final: 0.5688 (ptm160) REVERT: A 670 PHE cc_start: 0.3561 (OUTLIER) cc_final: 0.2992 (m-80) REVERT: A 687 TYR cc_start: 0.7459 (m-80) cc_final: 0.6879 (m-80) REVERT: E 459 MET cc_start: 0.7478 (mtm) cc_final: 0.7149 (ttm) REVERT: E 517 MET cc_start: 0.8761 (tpp) cc_final: 0.8351 (tpp) REVERT: C 74 TYR cc_start: 0.7782 (OUTLIER) cc_final: 0.7335 (m-80) REVERT: C 127 GLU cc_start: 0.7164 (mp0) cc_final: 0.6835 (pm20) REVERT: C 144 LYS cc_start: 0.8794 (pttt) cc_final: 0.8428 (ptpp) REVERT: G 68 MET cc_start: 0.7906 (mtp) cc_final: 0.7628 (mtm) REVERT: G 107 LYS cc_start: 0.9076 (ptpp) cc_final: 0.8797 (tttm) REVERT: G 118 TYR cc_start: 0.9253 (m-80) cc_final: 0.8737 (m-80) REVERT: H 57 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7762 (mt-10) REVERT: H 87 ARG cc_start: 0.8563 (tpp-160) cc_final: 0.7925 (tpp-160) REVERT: H 97 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7342 (tp30) REVERT: H 116 TYR cc_start: 0.8926 (m-80) cc_final: 0.8114 (m-80) REVERT: H 144 LYS cc_start: 0.9333 (tmmt) cc_final: 0.8989 (tmmt) REVERT: H 183 VAL cc_start: 0.8170 (t) cc_final: 0.7936 (t) REVERT: H 207 HIS cc_start: 0.7592 (t-90) cc_final: 0.7138 (t70) REVERT: J 48 LYS cc_start: 0.8920 (tppt) cc_final: 0.8717 (tmmt) REVERT: J 64 ARG cc_start: 0.7964 (ttm-80) cc_final: 0.7731 (ttm-80) REVERT: J 92 ARG cc_start: 0.8182 (mtm-85) cc_final: 0.7920 (mtm-85) REVERT: J 112 LYS cc_start: 0.8366 (tptm) cc_final: 0.8100 (tmtt) REVERT: J 139 MET cc_start: 0.8275 (tpt) cc_final: 0.7726 (tpp) outliers start: 39 outliers final: 29 residues processed: 185 average time/residue: 0.1219 time to fit residues: 31.1777 Evaluate side-chains 186 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 151 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain E residue 532 LEU Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 222 PHE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain G residue 74 CYS Chi-restraints excluded: chain G residue 76 HIS Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 136 CYS Chi-restraints excluded: chain H residue 167 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 36 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 123 optimal weight: 0.0170 chunk 82 optimal weight: 0.2980 chunk 66 optimal weight: 0.0670 chunk 55 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 ASN A 797 ASN ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.112403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.080588 restraints weight = 28288.315| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 4.67 r_work: 0.3214 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10994 Z= 0.137 Angle : 0.668 10.401 14904 Z= 0.330 Chirality : 0.044 0.186 1684 Planarity : 0.004 0.041 1907 Dihedral : 5.380 58.803 1479 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.83 % Favored : 94.10 % Rotamer: Outliers : 2.69 % Allowed : 18.25 % Favored : 79.06 % 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 (0.24), residues: 1355 helix: 1.45 (0.29), residues: 346 sheet: -1.12 (0.32), residues: 279 loop : -1.09 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 202 TYR 0.012 0.001 TYR G 83 PHE 0.033 0.001 PHE A 696 TRP 0.013 0.001 TRP A 546 HIS 0.005 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00315 (10975) covalent geometry : angle 0.66693 (14866) SS BOND : bond 0.00215 ( 19) SS BOND : angle 0.87562 ( 38) hydrogen bonds : bond 0.03331 ( 382) hydrogen bonds : angle 4.52962 ( 1098) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 158 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 MET cc_start: 0.8237 (tpt) cc_final: 0.7959 (tpt) REVERT: A 353 ASN cc_start: 0.8448 (OUTLIER) cc_final: 0.7968 (m-40) REVERT: A 354 ASN cc_start: 0.8212 (OUTLIER) cc_final: 0.7853 (p0) REVERT: A 412 LEU cc_start: 0.9149 (tt) cc_final: 0.8889 (tp) REVERT: A 542 ARG cc_start: 0.6472 (ttt180) cc_final: 0.5715 (ptm160) REVERT: A 670 PHE cc_start: 0.3602 (OUTLIER) cc_final: 0.3020 (m-80) REVERT: A 687 TYR cc_start: 0.7459 (m-80) cc_final: 0.6892 (m-80) REVERT: A 696 PHE cc_start: 0.8345 (p90) cc_final: 0.7912 (p90) REVERT: A 745 MET cc_start: 0.5546 (ttp) cc_final: 0.5269 (tmm) REVERT: E 459 MET cc_start: 0.7530 (mtm) cc_final: 0.7198 (ttm) REVERT: E 517 MET cc_start: 0.8771 (tpp) cc_final: 0.8517 (mmm) REVERT: C 74 TYR cc_start: 0.7895 (OUTLIER) cc_final: 0.7350 (m-80) REVERT: C 127 GLU cc_start: 0.7186 (mp0) cc_final: 0.6856 (pm20) REVERT: G 68 MET cc_start: 0.7968 (mtp) cc_final: 0.7689 (mtm) REVERT: G 107 LYS cc_start: 0.9170 (ptpp) cc_final: 0.8827 (tttp) REVERT: G 118 TYR cc_start: 0.9303 (m-80) cc_final: 0.8816 (m-80) REVERT: H 57 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7600 (mt-10) REVERT: H 67 GLU cc_start: 0.9056 (tt0) cc_final: 0.8538 (mp0) REVERT: H 84 ARG cc_start: 0.7138 (tpp-160) cc_final: 0.6918 (tpp-160) REVERT: H 87 ARG cc_start: 0.8593 (tpp-160) cc_final: 0.8020 (tpp-160) REVERT: H 116 TYR cc_start: 0.8903 (m-80) cc_final: 0.8186 (m-80) REVERT: H 207 HIS cc_start: 0.7502 (t-90) cc_final: 0.7021 (t70) REVERT: J 64 ARG cc_start: 0.7970 (ttm-80) cc_final: 0.7736 (ttm-80) REVERT: J 92 ARG cc_start: 0.8203 (mtm-85) cc_final: 0.7938 (mtm-85) REVERT: J 112 LYS cc_start: 0.8259 (tptm) cc_final: 0.7994 (tmtt) REVERT: J 139 MET cc_start: 0.8224 (tpt) cc_final: 0.7645 (tpp) outliers start: 32 outliers final: 26 residues processed: 179 average time/residue: 0.1260 time to fit residues: 31.1699 Evaluate side-chains 184 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 153 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain E residue 532 LEU Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 222 PHE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain G residue 74 CYS Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 136 CYS Chi-restraints excluded: chain H residue 167 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 102 optimal weight: 0.4980 chunk 25 optimal weight: 0.0870 chunk 121 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 61 optimal weight: 0.0040 chunk 94 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.6572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 206 GLN ** 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 = 0.3965 r_free = 0.3965 target = 0.112909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.081177 restraints weight = 28426.751| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 4.68 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10994 Z= 0.126 Angle : 0.678 10.818 14904 Z= 0.334 Chirality : 0.043 0.179 1684 Planarity : 0.004 0.045 1907 Dihedral : 5.144 58.690 1476 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.68 % Favored : 94.24 % Rotamer: Outliers : 3.03 % Allowed : 18.42 % Favored : 78.55 % 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: -0.58 (0.24), residues: 1355 helix: 1.51 (0.29), residues: 345 sheet: -1.04 (0.32), residues: 279 loop : -1.04 (0.23), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 84 TYR 0.018 0.001 TYR E 452 PHE 0.033 0.001 PHE A 696 TRP 0.013 0.001 TRP A 546 HIS 0.005 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00290 (10975) covalent geometry : angle 0.67736 (14866) SS BOND : bond 0.00188 ( 19) SS BOND : angle 0.85772 ( 38) hydrogen bonds : bond 0.03218 ( 382) hydrogen bonds : angle 4.50388 ( 1098) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3435.48 seconds wall clock time: 59 minutes 27.12 seconds (3567.12 seconds total)