Starting phenix.real_space_refine on Tue May 13 18:12:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xfp_38307/05_2025/8xfp_38307.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xfp_38307/05_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_38307/05_2025/8xfp_38307.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xfp_38307/05_2025/8xfp_38307.map" model { file = "/net/cci-nas-00/data/ceres_data/8xfp_38307/05_2025/8xfp_38307.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xfp_38307/05_2025/8xfp_38307.cif" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG: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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 6.52, per 1000 atoms: 0.61 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: 2.43 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.36 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: 3.96 Time building geometry restraints manager: 2.90 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: 18.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 25.160 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.830 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (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 TRP 0.016 0.001 TRP A 546 HIS 0.003 0.000 HIS A 209 PHE 0.009 0.001 PHE A 696 TYR 0.011 0.001 TYR A 590 ARG 0.002 0.000 ARG C 202 Details of bonding type rmsd hydrogen bonds : bond 0.07775 ( 382) hydrogen bonds : angle 4.54563 ( 1098) SS BOND : bond 0.00153 ( 19) SS BOND : angle 0.58498 ( 38) covalent geometry : bond 0.00214 (10975) covalent geometry : angle 0.49153 (14866) *********************** 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 : 1.340 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: 0.7470 (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: 0.7013 (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: 0.2928 time to fit residues: 108.9713 Evaluate side-chains 174 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 163 time to evaluate : 1.289 ------------------------------------------------------------------------------- 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 115 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 65 optimal weight: 20.0000 chunk 79 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 HIS A 219 HIS A 242 GLN A 258 ASN A 271 ASN ** A 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 ASN A 458 ASN A 658 HIS A 714 ASN A 742 GLN ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 496 GLN E 508 ASN G 50 ASN G 120 HIS ** 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.107927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.075626 restraints weight = 28558.840| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 4.57 r_work: 0.3114 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.071 10994 Z= 0.395 Angle : 0.825 11.146 14904 Z= 0.420 Chirality : 0.051 0.189 1684 Planarity : 0.005 0.051 1907 Dihedral : 6.714 59.575 1487 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.41 % Favored : 91.51 % Rotamer: Outliers : 5.72 % Allowed : 11.77 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.23), residues: 1355 helix: 1.26 (0.29), residues: 335 sheet: -1.37 (0.32), residues: 284 loop : -1.29 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 546 HIS 0.010 0.002 HIS A 209 PHE 0.028 0.002 PHE A 662 TYR 0.017 0.003 TYR C 118 ARG 0.007 0.001 ARG C 202 Details of bonding type rmsd hydrogen bonds : bond 0.04665 ( 382) hydrogen bonds : angle 5.10527 ( 1098) SS BOND : bond 0.00760 ( 19) SS BOND : angle 1.58828 ( 38) covalent geometry : bond 0.00905 (10975) covalent geometry : angle 0.82168 (14866) *********************** 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 244 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 176 time to evaluate : 1.268 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: 0.8420 (tt0) cc_final: 0.7699 (tp30) REVERT: A 274 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8780 (tt) REVERT: A 354 ASN cc_start: 0.8147 (OUTLIER) cc_final: 0.7889 (p0) REVERT: A 596 PHE cc_start: 0.8841 (m-80) cc_final: 0.8356 (m-10) REVERT: A 643 ARG cc_start: 0.5083 (mmp-170) cc_final: 0.4870 (tpp-160) REVERT: A 670 PHE cc_start: 0.3433 (OUTLIER) cc_final: 0.3035 (m-80) REVERT: A 687 TYR cc_start: 0.7352 (m-10) cc_final: 0.7065 (m-80) REVERT: A 725 TYR cc_start: 0.6711 (t80) cc_final: 0.5596 (t80) REVERT: A 729 TYR cc_start: 0.2143 (OUTLIER) cc_final: 0.1282 (m-10) REVERT: E 454 TYR cc_start: 0.8582 (p90) cc_final: 0.8245 (p90) REVERT: E 517 MET cc_start: 0.8431 (tpp) cc_final: 0.8228 (mmm) REVERT: E 539 TYR cc_start: 0.8319 (m-80) cc_final: 0.8027 (m-80) REVERT: C 74 TYR cc_start: 0.8265 (OUTLIER) cc_final: 0.7570 (m-80) REVERT: C 107 CYS cc_start: 0.4441 (OUTLIER) cc_final: 0.4229 (t) REVERT: C 144 LYS cc_start: 0.8936 (pttt) cc_final: 0.8624 (ptpp) REVERT: C 193 ASN cc_start: 0.8238 (t0) cc_final: 0.7946 (t0) REVERT: C 198 GLN cc_start: 0.8563 (tp40) cc_final: 0.7784 (mp10) REVERT: C 240 ILE cc_start: 0.5759 (mm) cc_final: 0.5540 (mp) REVERT: G 68 MET cc_start: 0.8243 (mtp) cc_final: 0.7868 (mtm) REVERT: G 83 TYR cc_start: 0.8162 (p90) cc_final: 0.7435 (p90) REVERT: H 97 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7446 (tp30) REVERT: H 197 LYS cc_start: 0.9275 (mmtp) cc_final: 0.9004 (mmtp) REVERT: H 207 HIS cc_start: 0.7618 (OUTLIER) cc_final: 0.7346 (t-90) REVERT: J 64 ARG cc_start: 0.8031 (ttm-80) cc_final: 0.7826 (ttm-80) REVERT: J 92 ARG cc_start: 0.8359 (mtm-85) cc_final: 0.8038 (mtm-85) REVERT: J 102 ASP cc_start: 0.8624 (m-30) cc_final: 0.8063 (m-30) REVERT: J 108 ASP cc_start: 0.8919 (p0) cc_final: 0.8715 (p0) REVERT: J 112 LYS cc_start: 0.8275 (tmtt) cc_final: 0.7999 (tmmt) outliers start: 68 outliers final: 32 residues processed: 227 average time/residue: 0.2558 time to fit residues: 79.1643 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 : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 354 ASN 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 523 THR Chi-restraints excluded: chain A residue 543 LEU 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 A residue 799 VAL Chi-restraints excluded: chain E residue 493 THR Chi-restraints excluded: chain E residue 530 CYS 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 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 G residue 77 SER Chi-restraints excluded: chain H residue 65 LEU 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 207 HIS Chi-restraints excluded: chain J residue 136 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 57 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 49 optimal weight: 8.9990 chunk 22 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 chunk 133 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 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 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 GLN A 742 GLN E 496 GLN ** E 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN H 207 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.111907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.080030 restraints weight = 28572.165| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 4.67 r_work: 0.3188 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10994 Z= 0.127 Angle : 0.627 9.085 14904 Z= 0.314 Chirality : 0.044 0.170 1684 Planarity : 0.004 0.033 1907 Dihedral : 5.771 59.013 1481 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.31 % Favored : 94.61 % Rotamer: Outliers : 3.53 % Allowed : 14.55 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.24), residues: 1355 helix: 1.56 (0.29), residues: 342 sheet: -1.22 (0.32), residues: 280 loop : -1.17 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 612 HIS 0.010 0.001 HIS H 207 PHE 0.027 0.001 PHE A 696 TYR 0.012 0.001 TYR H 182 ARG 0.003 0.000 ARG J 64 Details of bonding type rmsd hydrogen bonds : bond 0.03394 ( 382) hydrogen bonds : angle 4.62603 ( 1098) SS BOND : bond 0.00398 ( 19) SS BOND : angle 1.21733 ( 38) covalent geometry : bond 0.00279 (10975) covalent geometry : angle 0.62428 (14866) *********************** 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 226 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 184 time to evaluate : 1.368 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: 0.8017 (tpt) cc_final: 0.7796 (tpt) REVERT: A 353 ASN cc_start: 0.8361 (OUTLIER) cc_final: 0.7927 (m-40) REVERT: A 449 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7684 (pt0) REVERT: A 596 PHE cc_start: 0.8855 (m-80) cc_final: 0.8336 (m-10) REVERT: A 643 ARG cc_start: 0.4718 (mmp-170) cc_final: 0.4340 (tpp-160) REVERT: A 670 PHE cc_start: 0.3241 (OUTLIER) cc_final: 0.2744 (m-80) REVERT: A 725 TYR cc_start: 0.6692 (t80) cc_final: 0.5619 (t80) REVERT: A 729 TYR cc_start: 0.1989 (OUTLIER) cc_final: 0.1302 (m-10) REVERT: E 539 TYR cc_start: 0.8175 (m-80) cc_final: 0.7810 (m-80) REVERT: C 74 TYR cc_start: 0.7780 (OUTLIER) cc_final: 0.7401 (m-80) REVERT: C 144 LYS cc_start: 0.8872 (pttt) cc_final: 0.8518 (ptpp) REVERT: C 193 ASN cc_start: 0.8156 (t0) cc_final: 0.7937 (t0) REVERT: C 198 GLN cc_start: 0.8478 (tp40) cc_final: 0.7685 (mp10) REVERT: G 68 MET cc_start: 0.7866 (mtp) cc_final: 0.7550 (mtm) REVERT: G 83 TYR cc_start: 0.8104 (p90) cc_final: 0.7088 (p90) REVERT: G 107 LYS cc_start: 0.8849 (ptpp) cc_final: 0.8526 (mttp) REVERT: G 118 TYR cc_start: 0.9057 (m-80) cc_final: 0.8648 (m-80) REVERT: H 87 ARG cc_start: 0.8509 (tpp-160) cc_final: 0.8142 (tpp-160) REVERT: H 97 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7427 (tp30) REVERT: H 148 GLN cc_start: 0.8909 (mt0) cc_final: 0.8516 (mt0) REVERT: H 197 LYS cc_start: 0.9296 (mmtp) cc_final: 0.9031 (mmtp) REVERT: J 48 LYS cc_start: 0.9140 (tppt) cc_final: 0.8817 (tmmt) REVERT: J 64 ARG cc_start: 0.7918 (ttm-80) cc_final: 0.7655 (ttm-80) REVERT: J 68 MET cc_start: 0.8436 (ptp) cc_final: 0.8197 (ptm) REVERT: J 92 ARG cc_start: 0.8151 (mtm-85) cc_final: 0.7867 (mtm-85) REVERT: J 102 ASP cc_start: 0.8768 (m-30) cc_final: 0.8473 (m-30) outliers start: 42 outliers final: 25 residues processed: 211 average time/residue: 0.2763 time to fit residues: 80.0019 Evaluate side-chains 196 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 353 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 575 LEU Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 616 SER 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 814 LEU Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 493 THR 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 139 VAL Chi-restraints excluded: chain C residue 205 ILE 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 91 THR Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 136 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 72 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 96 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 70 optimal weight: 0.0170 chunk 118 optimal weight: 4.9990 overall best weight: 0.9220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 50 ASN G 100 ASN H 207 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.111550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.079723 restraints weight = 28365.555| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 4.66 r_work: 0.3198 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10994 Z= 0.137 Angle : 0.628 9.713 14904 Z= 0.314 Chirality : 0.044 0.243 1684 Planarity : 0.004 0.034 1907 Dihedral : 5.628 57.563 1479 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.54 % Favored : 94.39 % Rotamer: Outliers : 3.78 % Allowed : 15.14 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.24), residues: 1355 helix: 1.53 (0.29), residues: 342 sheet: -1.19 (0.32), residues: 279 loop : -1.14 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 612 HIS 0.005 0.001 HIS A 209 PHE 0.041 0.001 PHE A 662 TYR 0.017 0.002 TYR A 687 ARG 0.003 0.000 ARG E 491 Details of bonding type rmsd hydrogen bonds : bond 0.03386 ( 382) hydrogen bonds : angle 4.59858 ( 1098) SS BOND : bond 0.00260 ( 19) SS BOND : angle 0.99852 ( 38) covalent geometry : bond 0.00311 (10975) covalent geometry : angle 0.62627 (14866) *********************** 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 216 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 171 time to evaluate : 1.256 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: 0.8085 (tpt) cc_final: 0.7800 (tpt) REVERT: A 353 ASN cc_start: 0.8397 (OUTLIER) cc_final: 0.7857 (m-40) REVERT: A 354 ASN cc_start: 0.8306 (OUTLIER) cc_final: 0.7940 (p0) REVERT: A 540 MET cc_start: 0.7126 (ptp) cc_final: 0.6893 (ptp) REVERT: A 596 PHE cc_start: 0.8825 (m-80) cc_final: 0.8270 (m-10) REVERT: A 633 ILE cc_start: 0.6422 (mm) cc_final: 0.6181 (mt) REVERT: A 643 ARG cc_start: 0.4781 (mmp-170) cc_final: 0.4380 (tpp-160) REVERT: A 670 PHE cc_start: 0.3424 (OUTLIER) cc_final: 0.2949 (m-80) REVERT: A 687 TYR cc_start: 0.7324 (m-80) cc_final: 0.6759 (m-10) REVERT: E 492 PHE cc_start: 0.8979 (m-10) cc_final: 0.8172 (m-10) REVERT: E 507 MET cc_start: 0.8983 (mmm) cc_final: 0.8781 (mmm) REVERT: E 517 MET cc_start: 0.8598 (tpp) cc_final: 0.8141 (tpp) REVERT: E 539 TYR cc_start: 0.7895 (m-80) cc_final: 0.7549 (m-80) REVERT: C 74 TYR cc_start: 0.7919 (OUTLIER) cc_final: 0.7501 (m-80) REVERT: C 144 LYS cc_start: 0.8861 (pttt) cc_final: 0.8506 (ptpp) REVERT: C 193 ASN cc_start: 0.8195 (t0) cc_final: 0.7969 (t0) REVERT: C 198 GLN cc_start: 0.8461 (tp40) cc_final: 0.7664 (mp10) REVERT: C 217 PHE cc_start: 0.7901 (m-80) cc_final: 0.7678 (m-80) REVERT: G 50 ASN cc_start: 0.8258 (OUTLIER) cc_final: 0.7985 (m110) REVERT: G 68 MET cc_start: 0.8000 (mtp) cc_final: 0.7656 (mtm) REVERT: G 83 TYR cc_start: 0.8126 (p90) cc_final: 0.7117 (p90) REVERT: G 107 LYS cc_start: 0.8832 (ptpp) cc_final: 0.8519 (mttp) REVERT: G 118 TYR cc_start: 0.9165 (m-80) cc_final: 0.8481 (m-80) REVERT: H 56 LYS cc_start: 0.8926 (mptt) cc_final: 0.7827 (tptt) REVERT: H 87 ARG cc_start: 0.8527 (tpp-160) cc_final: 0.8150 (mmm160) REVERT: H 97 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7416 (tp30) REVERT: H 148 GLN cc_start: 0.8944 (mt0) cc_final: 0.8570 (mt0) REVERT: H 197 LYS cc_start: 0.9302 (mmtp) cc_final: 0.9089 (mmtp) REVERT: J 48 LYS cc_start: 0.9134 (tppt) cc_final: 0.8844 (tmmt) REVERT: J 64 ARG cc_start: 0.7960 (ttm-80) cc_final: 0.7659 (ttm-80) REVERT: J 92 ARG cc_start: 0.8181 (mtm-85) cc_final: 0.7897 (mtm-85) REVERT: J 102 ASP cc_start: 0.8751 (m-30) cc_final: 0.8499 (m-30) REVERT: J 139 MET cc_start: 0.8153 (tpt) cc_final: 0.7751 (tpt) outliers start: 45 outliers final: 28 residues processed: 201 average time/residue: 0.2515 time to fit residues: 69.2864 Evaluate side-chains 200 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 166 time to evaluate : 1.311 ------------------------------------------------------------------------------- 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 281 ASP 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 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 24 VAL Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 493 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 98 ILE 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 50 ASN Chi-restraints excluded: chain G residue 76 HIS 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 97 GLU Chi-restraints excluded: chain H residue 136 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 70 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 136 optimal weight: 0.5980 chunk 29 optimal weight: 4.9990 chunk 111 optimal weight: 20.0000 chunk 117 optimal weight: 0.3980 chunk 51 optimal weight: 0.7980 chunk 112 optimal weight: 5.9990 chunk 125 optimal weight: 0.7980 chunk 91 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 50 ASN H 207 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.112178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.080543 restraints weight = 28411.048| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 4.63 r_work: 0.3213 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10994 Z= 0.120 Angle : 0.605 9.079 14904 Z= 0.302 Chirality : 0.044 0.193 1684 Planarity : 0.003 0.033 1907 Dihedral : 5.453 59.031 1479 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.68 % Favored : 94.24 % Rotamer: Outliers : 3.62 % Allowed : 15.64 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.24), residues: 1355 helix: 1.58 (0.29), residues: 342 sheet: -1.13 (0.32), residues: 279 loop : -1.14 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 612 HIS 0.005 0.001 HIS A 209 PHE 0.030 0.001 PHE A 696 TYR 0.015 0.001 TYR A 687 ARG 0.003 0.000 ARG E 491 Details of bonding type rmsd hydrogen bonds : bond 0.03195 ( 382) hydrogen bonds : angle 4.49678 ( 1098) SS BOND : bond 0.00220 ( 19) SS BOND : angle 0.94337 ( 38) covalent geometry : bond 0.00270 (10975) covalent geometry : angle 0.60383 (14866) *********************** 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 219 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 176 time to evaluate : 1.472 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: 0.8138 (tpt) cc_final: 0.7814 (tpt) REVERT: A 353 ASN cc_start: 0.8386 (OUTLIER) cc_final: 0.7911 (m-40) REVERT: A 633 ILE cc_start: 0.6573 (mm) cc_final: 0.6147 (mt) REVERT: A 670 PHE cc_start: 0.3392 (OUTLIER) cc_final: 0.2911 (m-80) REVERT: A 687 TYR cc_start: 0.7456 (m-80) cc_final: 0.6757 (m-10) REVERT: A 728 LEU cc_start: 0.6163 (mt) cc_final: 0.5792 (pp) REVERT: E 492 PHE cc_start: 0.9011 (m-10) cc_final: 0.8117 (m-10) REVERT: E 507 MET cc_start: 0.8895 (mmm) cc_final: 0.8631 (mmm) REVERT: E 517 MET cc_start: 0.8641 (tpp) cc_final: 0.8212 (tpp) REVERT: C 74 TYR cc_start: 0.7876 (OUTLIER) cc_final: 0.7447 (m-80) REVERT: C 144 LYS cc_start: 0.8819 (pttt) cc_final: 0.8457 (ptpp) REVERT: C 193 ASN cc_start: 0.8195 (t0) cc_final: 0.7805 (t0) REVERT: C 197 LYS cc_start: 0.8918 (mmtt) cc_final: 0.8687 (mmtt) REVERT: C 198 GLN cc_start: 0.8409 (tp40) cc_final: 0.7890 (mp10) REVERT: G 68 MET cc_start: 0.7999 (mtp) cc_final: 0.7536 (mtm) REVERT: G 83 TYR cc_start: 0.8157 (p90) cc_final: 0.7123 (p90) REVERT: G 107 LYS cc_start: 0.8848 (ptpp) cc_final: 0.8547 (mttp) REVERT: H 67 GLU cc_start: 0.9029 (tt0) cc_final: 0.8516 (mp0) REVERT: H 87 ARG cc_start: 0.8555 (tpp-160) cc_final: 0.7974 (tpp-160) REVERT: H 116 TYR cc_start: 0.8906 (m-80) cc_final: 0.8068 (m-80) REVERT: J 48 LYS cc_start: 0.9022 (tppt) cc_final: 0.8804 (tmmt) REVERT: J 64 ARG cc_start: 0.7972 (ttm-80) cc_final: 0.7690 (ttm-80) REVERT: J 92 ARG cc_start: 0.8174 (mtm-85) cc_final: 0.7896 (mtm-85) REVERT: J 114 LYS cc_start: 0.8489 (ttmm) cc_final: 0.8289 (mtpp) REVERT: J 139 MET cc_start: 0.8096 (tpt) cc_final: 0.7676 (tpt) outliers start: 43 outliers final: 26 residues processed: 202 average time/residue: 0.2774 time to fit residues: 77.7127 Evaluate side-chains 193 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 353 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 590 TYR Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 493 THR Chi-restraints excluded: chain C residue 63 VAL 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 G residue 76 HIS 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 67 optimal weight: 5.9990 chunk 105 optimal weight: 9.9990 chunk 91 optimal weight: 0.6980 chunk 108 optimal weight: 9.9990 chunk 96 optimal weight: 0.4980 chunk 87 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 59 optimal weight: 10.0000 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 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** ** E 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 HIS G 120 HIS H 207 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.109780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.077780 restraints weight = 28541.834| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 4.63 r_work: 0.3156 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10994 Z= 0.213 Angle : 0.676 9.834 14904 Z= 0.342 Chirality : 0.046 0.179 1684 Planarity : 0.004 0.034 1907 Dihedral : 5.475 59.816 1474 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.94 % Favored : 92.99 % Rotamer: Outliers : 4.29 % Allowed : 16.99 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.23), residues: 1355 helix: 1.23 (0.29), residues: 344 sheet: -1.26 (0.31), residues: 282 loop : -1.15 (0.23), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 612 HIS 0.008 0.001 HIS A 209 PHE 0.040 0.002 PHE A 662 TYR 0.018 0.002 TYR E 452 ARG 0.004 0.000 ARG C 202 Details of bonding type rmsd hydrogen bonds : bond 0.03763 ( 382) hydrogen bonds : angle 4.72195 ( 1098) SS BOND : bond 0.00318 ( 19) SS BOND : angle 0.99440 ( 38) covalent geometry : bond 0.00489 (10975) covalent geometry : angle 0.67516 (14866) *********************** 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 213 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 162 time to evaluate : 1.142 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 187 ASN cc_start: 0.8534 (OUTLIER) cc_final: 0.8016 (m-40) REVERT: A 344 MET cc_start: 0.8115 (tpt) cc_final: 0.7826 (tpt) REVERT: A 353 ASN cc_start: 0.8419 (OUTLIER) cc_final: 0.7977 (m110) REVERT: A 354 ASN cc_start: 0.8268 (OUTLIER) cc_final: 0.7935 (p0) REVERT: A 612 TRP cc_start: 0.8055 (t-100) cc_final: 0.7750 (t-100) REVERT: A 633 ILE cc_start: 0.6506 (mm) cc_final: 0.6096 (mt) REVERT: A 670 PHE cc_start: 0.3402 (OUTLIER) cc_final: 0.2958 (m-80) REVERT: A 687 TYR cc_start: 0.7426 (m-80) cc_final: 0.6713 (m-10) REVERT: E 23 LEU cc_start: 0.6773 (mm) cc_final: 0.5085 (mm) REVERT: E 492 PHE cc_start: 0.9038 (m-10) cc_final: 0.8285 (m-10) REVERT: E 496 GLN cc_start: 0.8217 (tt0) cc_final: 0.7422 (tm-30) REVERT: E 507 MET cc_start: 0.9007 (mmm) cc_final: 0.8745 (mmt) REVERT: E 517 MET cc_start: 0.8713 (tpp) cc_final: 0.8352 (tpp) REVERT: C 108 ASN cc_start: 0.7896 (t0) cc_final: 0.7357 (p0) REVERT: C 144 LYS cc_start: 0.8863 (pttt) cc_final: 0.8513 (ptpp) REVERT: C 193 ASN cc_start: 0.8228 (t0) cc_final: 0.7828 (t0) REVERT: C 197 LYS cc_start: 0.8944 (mmtt) cc_final: 0.8700 (mmtt) REVERT: C 198 GLN cc_start: 0.8470 (tp40) cc_final: 0.7945 (mp10) REVERT: G 68 MET cc_start: 0.8112 (mtp) cc_final: 0.7748 (mtm) REVERT: G 118 TYR cc_start: 0.9119 (m-80) cc_final: 0.8453 (m-80) REVERT: H 56 LYS cc_start: 0.8964 (mptt) cc_final: 0.7847 (tptt) REVERT: H 87 ARG cc_start: 0.8606 (tpp-160) cc_final: 0.8189 (mmm160) REVERT: H 97 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7453 (tp30) REVERT: J 64 ARG cc_start: 0.7953 (ttm-80) cc_final: 0.7676 (ttm-80) REVERT: J 92 ARG cc_start: 0.8208 (mtm-85) cc_final: 0.7923 (mtm-85) REVERT: J 112 LYS cc_start: 0.8309 (tptm) cc_final: 0.8057 (tmtt) REVERT: J 114 LYS cc_start: 0.8711 (ttmm) cc_final: 0.8420 (mtpp) REVERT: J 139 MET cc_start: 0.8074 (tpt) cc_final: 0.7667 (tpt) outliers start: 51 outliers final: 33 residues processed: 196 average time/residue: 0.2627 time to fit residues: 71.2546 Evaluate side-chains 195 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 157 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 281 ASP 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 455 ASP 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 590 TYR Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 692 LEU 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 471 GLU Chi-restraints excluded: chain E residue 493 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 73 ASP 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 76 HIS 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 192 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 55 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 133 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 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 H 207 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.111767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.079967 restraints weight = 28625.033| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 4.67 r_work: 0.3201 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10994 Z= 0.133 Angle : 0.641 9.840 14904 Z= 0.320 Chirality : 0.044 0.171 1684 Planarity : 0.003 0.034 1907 Dihedral : 5.178 58.244 1474 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.90 % Favored : 94.02 % Rotamer: Outliers : 4.12 % Allowed : 17.58 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.23), residues: 1355 helix: 1.48 (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 TRP 0.020 0.001 TRP A 612 HIS 0.006 0.001 HIS A 209 PHE 0.031 0.001 PHE A 696 TYR 0.016 0.002 TYR E 452 ARG 0.002 0.000 ARG A 374 Details of bonding type rmsd hydrogen bonds : bond 0.03432 ( 382) hydrogen bonds : angle 4.58897 ( 1098) SS BOND : bond 0.00240 ( 19) SS BOND : angle 0.98815 ( 38) covalent geometry : bond 0.00303 (10975) covalent geometry : angle 0.64005 (14866) *********************** 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 213 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 164 time to evaluate : 1.448 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 66 MET cc_start: 0.8620 (mmt) cc_final: 0.8393 (mmm) REVERT: A 344 MET cc_start: 0.8159 (tpt) cc_final: 0.7816 (tpt) REVERT: A 353 ASN cc_start: 0.8408 (OUTLIER) cc_final: 0.7885 (m-40) REVERT: A 354 ASN cc_start: 0.8233 (OUTLIER) cc_final: 0.7851 (p0) REVERT: A 670 PHE cc_start: 0.3407 (OUTLIER) cc_final: 0.2938 (m-80) REVERT: A 687 TYR cc_start: 0.7448 (m-80) cc_final: 0.6733 (m-80) REVERT: E 23 LEU cc_start: 0.6191 (mm) cc_final: 0.5442 (mm) REVERT: E 463 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.8898 (ptt180) REVERT: E 478 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8254 (pt) REVERT: E 492 PHE cc_start: 0.8908 (m-10) cc_final: 0.7995 (m-10) REVERT: E 496 GLN cc_start: 0.8056 (tt0) cc_final: 0.7521 (tm-30) REVERT: E 507 MET cc_start: 0.8923 (mmm) cc_final: 0.8581 (mmt) REVERT: E 517 MET cc_start: 0.8732 (tpp) cc_final: 0.8370 (tpp) REVERT: C 74 TYR cc_start: 0.7839 (OUTLIER) cc_final: 0.7400 (m-80) REVERT: C 108 ASN cc_start: 0.7816 (t0) cc_final: 0.7425 (p0) REVERT: C 144 LYS cc_start: 0.8830 (pttt) cc_final: 0.8465 (ptpp) REVERT: C 193 ASN cc_start: 0.8237 (t0) cc_final: 0.7842 (t0) REVERT: C 197 LYS cc_start: 0.8949 (mmtt) cc_final: 0.8711 (mmtt) REVERT: C 198 GLN cc_start: 0.8412 (tp40) cc_final: 0.7890 (mp10) REVERT: G 68 MET cc_start: 0.7979 (mtp) cc_final: 0.7629 (mtm) REVERT: G 107 LYS cc_start: 0.9014 (ptpp) cc_final: 0.8673 (tppt) REVERT: G 118 TYR cc_start: 0.9227 (m-80) cc_final: 0.8595 (m-80) REVERT: H 73 ASP cc_start: 0.7820 (t0) cc_final: 0.7185 (m-30) REVERT: H 87 ARG cc_start: 0.8609 (tpp-160) cc_final: 0.8002 (tpp-160) REVERT: H 97 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7367 (tp30) REVERT: J 48 LYS cc_start: 0.9014 (tppt) cc_final: 0.8797 (tmmt) REVERT: J 64 ARG cc_start: 0.7948 (ttm-80) cc_final: 0.7682 (ttm-80) REVERT: J 92 ARG cc_start: 0.8209 (mtm-85) cc_final: 0.7945 (mtm-85) REVERT: J 112 LYS cc_start: 0.8239 (tptm) cc_final: 0.7984 (tmtt) REVERT: J 114 LYS cc_start: 0.8714 (ttmm) cc_final: 0.8381 (mtpp) REVERT: J 139 MET cc_start: 0.8034 (tpt) cc_final: 0.7624 (tpt) outliers start: 49 outliers final: 28 residues processed: 197 average time/residue: 0.2665 time to fit residues: 72.3335 Evaluate side-chains 192 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 157 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 281 ASP 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 590 TYR Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 616 SER 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 463 ARG Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 478 LEU Chi-restraints excluded: chain E residue 493 THR Chi-restraints excluded: chain C residue 63 VAL 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 76 HIS 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 106 optimal weight: 10.0000 chunk 104 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 119 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 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 H 207 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.110342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.078297 restraints weight = 28493.752| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 4.64 r_work: 0.3172 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10994 Z= 0.193 Angle : 0.681 10.058 14904 Z= 0.343 Chirality : 0.045 0.178 1684 Planarity : 0.004 0.034 1907 Dihedral : 5.425 58.711 1474 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.86 % Favored : 93.06 % Rotamer: Outliers : 4.12 % Allowed : 18.84 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.23), residues: 1355 helix: 1.29 (0.29), residues: 345 sheet: -1.25 (0.31), residues: 282 loop : -1.14 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 612 HIS 0.006 0.001 HIS A 209 PHE 0.032 0.002 PHE A 696 TYR 0.020 0.002 TYR E 452 ARG 0.003 0.000 ARG C 202 Details of bonding type rmsd hydrogen bonds : bond 0.03692 ( 382) hydrogen bonds : angle 4.74783 ( 1098) SS BOND : bond 0.00311 ( 19) SS BOND : angle 1.00190 ( 38) covalent geometry : bond 0.00448 (10975) covalent geometry : angle 0.68021 (14866) *********************** 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: 49 poor density : 156 time to evaluate : 1.228 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 187 ASN cc_start: 0.8430 (OUTLIER) cc_final: 0.7843 (m-40) REVERT: A 344 MET cc_start: 0.8187 (tpt) cc_final: 0.7877 (tpt) REVERT: A 353 ASN cc_start: 0.8433 (OUTLIER) cc_final: 0.8023 (m110) REVERT: A 354 ASN cc_start: 0.8292 (OUTLIER) cc_final: 0.7953 (p0) REVERT: A 670 PHE cc_start: 0.3448 (OUTLIER) cc_final: 0.2966 (m-80) REVERT: A 687 TYR cc_start: 0.7451 (m-80) cc_final: 0.6746 (m-80) REVERT: A 745 MET cc_start: 0.4794 (ttp) cc_final: 0.4464 (tmm) REVERT: E 21 VAL cc_start: 0.8709 (t) cc_final: 0.8431 (m) REVERT: E 23 LEU cc_start: 0.6056 (mm) cc_final: 0.5496 (mm) REVERT: E 463 ARG cc_start: 0.9104 (OUTLIER) cc_final: 0.8874 (ptt180) REVERT: E 478 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8289 (pt) REVERT: E 492 PHE cc_start: 0.8832 (m-10) cc_final: 0.7957 (m-10) REVERT: E 496 GLN cc_start: 0.8257 (tt0) cc_final: 0.7524 (tm-30) REVERT: E 507 MET cc_start: 0.8985 (mmm) cc_final: 0.8718 (mmt) REVERT: E 517 MET cc_start: 0.8719 (tpp) cc_final: 0.8346 (tpp) REVERT: C 108 ASN cc_start: 0.7935 (t0) cc_final: 0.7558 (p0) REVERT: C 144 LYS cc_start: 0.8867 (pttt) cc_final: 0.8512 (ptpp) REVERT: C 193 ASN cc_start: 0.8242 (t0) cc_final: 0.7866 (t0) REVERT: C 197 LYS cc_start: 0.8959 (mmtt) cc_final: 0.8602 (mmtt) REVERT: G 68 MET cc_start: 0.8073 (mtp) cc_final: 0.7700 (mtm) REVERT: G 107 LYS cc_start: 0.9082 (ptpp) cc_final: 0.8736 (tttm) REVERT: G 118 TYR cc_start: 0.9263 (m-80) cc_final: 0.8652 (m-80) REVERT: H 57 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7047 (tt0) REVERT: H 87 ARG cc_start: 0.8585 (tpp-160) cc_final: 0.7978 (tpp-160) REVERT: H 97 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7438 (tp30) REVERT: H 117 GLU cc_start: 0.7872 (pm20) cc_final: 0.7650 (pm20) REVERT: H 207 HIS cc_start: 0.7546 (OUTLIER) cc_final: 0.6722 (t-90) REVERT: J 48 LYS cc_start: 0.9076 (tppt) cc_final: 0.8813 (tmmt) REVERT: J 64 ARG cc_start: 0.7962 (ttm-80) cc_final: 0.7700 (ttm-80) REVERT: J 92 ARG cc_start: 0.8214 (mtm-85) cc_final: 0.7957 (mtm-85) REVERT: J 112 LYS cc_start: 0.8304 (tptm) cc_final: 0.8031 (tmtt) REVERT: J 114 LYS cc_start: 0.8733 (ttmm) cc_final: 0.8406 (mtpp) REVERT: J 139 MET cc_start: 0.8116 (tpt) cc_final: 0.7726 (tpt) outliers start: 49 outliers final: 34 residues processed: 189 average time/residue: 0.2665 time to fit residues: 69.1736 Evaluate side-chains 199 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 156 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 281 ASP 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 590 TYR Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 616 SER 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 463 ARG Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 478 LEU Chi-restraints excluded: chain E residue 493 THR Chi-restraints excluded: chain C residue 63 VAL 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 76 HIS Chi-restraints excluded: chain H residue 57 GLU 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 Chi-restraints excluded: chain H residue 200 VAL Chi-restraints excluded: chain H residue 207 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 109 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 chunk 45 optimal weight: 0.0570 chunk 93 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 28 optimal weight: 0.0270 chunk 19 optimal weight: 2.9990 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 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 = 0.3953 r_free = 0.3953 target = 0.111878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.080204 restraints weight = 28336.353| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 4.64 r_work: 0.3202 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10994 Z= 0.131 Angle : 0.652 10.004 14904 Z= 0.325 Chirality : 0.044 0.173 1684 Planarity : 0.003 0.037 1907 Dihedral : 5.152 57.646 1474 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.13 % Favored : 93.80 % Rotamer: Outliers : 3.45 % Allowed : 19.60 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.24), residues: 1355 helix: 1.45 (0.29), residues: 344 sheet: -1.04 (0.33), residues: 265 loop : -1.11 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 612 HIS 0.007 0.001 HIS H 207 PHE 0.033 0.001 PHE A 696 TYR 0.023 0.001 TYR E 452 ARG 0.002 0.000 ARG C 202 Details of bonding type rmsd hydrogen bonds : bond 0.03434 ( 382) hydrogen bonds : angle 4.62085 ( 1098) SS BOND : bond 0.00222 ( 19) SS BOND : angle 0.87706 ( 38) covalent geometry : bond 0.00300 (10975) covalent geometry : angle 0.65129 (14866) *********************** 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 202 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 161 time to evaluate : 1.221 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 66 MET cc_start: 0.8572 (mmt) cc_final: 0.8344 (mmm) REVERT: A 187 ASN cc_start: 0.8404 (OUTLIER) cc_final: 0.7718 (m-40) REVERT: A 344 MET cc_start: 0.8178 (tpt) cc_final: 0.7828 (tpt) REVERT: A 353 ASN cc_start: 0.8411 (OUTLIER) cc_final: 0.7898 (m-40) REVERT: A 354 ASN cc_start: 0.8242 (OUTLIER) cc_final: 0.7876 (p0) REVERT: A 670 PHE cc_start: 0.3424 (OUTLIER) cc_final: 0.2950 (m-80) REVERT: A 687 TYR cc_start: 0.7472 (m-80) cc_final: 0.6820 (m-80) REVERT: A 745 MET cc_start: 0.4695 (ttp) cc_final: 0.4379 (tmm) REVERT: E 21 VAL cc_start: 0.8680 (t) cc_final: 0.8457 (m) REVERT: E 23 LEU cc_start: 0.6254 (mm) cc_final: 0.5302 (mm) REVERT: E 492 PHE cc_start: 0.8639 (m-10) cc_final: 0.7747 (m-10) REVERT: E 496 GLN cc_start: 0.8186 (tt0) cc_final: 0.7554 (tm-30) REVERT: E 507 MET cc_start: 0.8932 (mmm) cc_final: 0.8583 (mmt) REVERT: E 517 MET cc_start: 0.8725 (tpp) cc_final: 0.8431 (tpp) REVERT: C 74 TYR cc_start: 0.7797 (OUTLIER) cc_final: 0.7350 (m-80) REVERT: C 108 ASN cc_start: 0.7978 (t0) cc_final: 0.7511 (p0) REVERT: C 144 LYS cc_start: 0.8800 (pttt) cc_final: 0.8437 (ptpp) REVERT: C 193 ASN cc_start: 0.8224 (t0) cc_final: 0.7815 (t0) REVERT: C 197 LYS cc_start: 0.8953 (mmtt) cc_final: 0.8730 (mmtt) REVERT: C 198 GLN cc_start: 0.8383 (tp40) cc_final: 0.7846 (mp10) REVERT: G 68 MET cc_start: 0.7951 (mtp) cc_final: 0.7608 (mtm) REVERT: G 107 LYS cc_start: 0.9122 (ptpp) cc_final: 0.8747 (tppt) REVERT: G 108 ASP cc_start: 0.9464 (p0) cc_final: 0.9117 (p0) REVERT: G 118 TYR cc_start: 0.9400 (m-80) cc_final: 0.8892 (m-80) REVERT: H 73 ASP cc_start: 0.7816 (t0) cc_final: 0.7186 (m-30) REVERT: H 84 ARG cc_start: 0.7100 (tpp-160) cc_final: 0.6877 (tpp-160) REVERT: H 87 ARG cc_start: 0.8574 (tpp-160) cc_final: 0.7956 (tpp-160) REVERT: H 97 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7366 (tp30) REVERT: H 116 TYR cc_start: 0.8959 (m-80) cc_final: 0.8086 (m-80) REVERT: H 117 GLU cc_start: 0.7845 (pm20) cc_final: 0.7627 (pm20) REVERT: H 144 LYS cc_start: 0.9294 (tmmt) cc_final: 0.8923 (tmmt) REVERT: H 207 HIS cc_start: 0.6893 (t70) cc_final: 0.5980 (p-80) REVERT: J 48 LYS cc_start: 0.9020 (tppt) cc_final: 0.8778 (tmmt) REVERT: J 64 ARG cc_start: 0.7926 (ttm-80) cc_final: 0.7668 (ttm-80) REVERT: J 92 ARG cc_start: 0.8145 (mtm-85) cc_final: 0.7902 (mtm-85) REVERT: J 112 LYS cc_start: 0.8199 (tptm) cc_final: 0.7946 (tmtt) REVERT: J 114 LYS cc_start: 0.8733 (ttmm) cc_final: 0.8372 (mtpp) REVERT: J 139 MET cc_start: 0.8098 (tpt) cc_final: 0.7701 (tpt) outliers start: 41 outliers final: 29 residues processed: 188 average time/residue: 0.2556 time to fit residues: 65.8848 Evaluate side-chains 190 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 155 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 281 ASP 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 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 471 GLU Chi-restraints excluded: chain E residue 493 THR Chi-restraints excluded: chain C residue 63 VAL 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 205 ILE Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 222 PHE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 116 optimal weight: 0.9980 chunk 95 optimal weight: 7.9990 chunk 20 optimal weight: 0.0170 chunk 11 optimal weight: 0.6980 chunk 115 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 85 optimal weight: 0.1980 chunk 107 optimal weight: 0.0570 chunk 88 optimal weight: 2.9990 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN ** 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** C 196 ASN G 120 HIS H 206 GLN H 207 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.114715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.083227 restraints weight = 28681.524| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 4.73 r_work: 0.3266 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10994 Z= 0.111 Angle : 0.649 9.620 14904 Z= 0.320 Chirality : 0.043 0.180 1684 Planarity : 0.003 0.035 1907 Dihedral : 4.839 55.009 1474 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.54 % Favored : 94.39 % Rotamer: Outliers : 2.86 % Allowed : 20.19 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.24), residues: 1355 helix: 1.58 (0.29), residues: 343 sheet: -0.97 (0.33), residues: 265 loop : -1.09 (0.23), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 612 HIS 0.005 0.000 HIS A 209 PHE 0.034 0.001 PHE A 696 TYR 0.025 0.001 TYR E 452 ARG 0.002 0.000 ARG G 65 Details of bonding type rmsd hydrogen bonds : bond 0.03201 ( 382) hydrogen bonds : angle 4.53597 ( 1098) SS BOND : bond 0.00184 ( 19) SS BOND : angle 0.83906 ( 38) covalent geometry : bond 0.00249 (10975) covalent geometry : angle 0.64836 (14866) ********************** 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 203 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 169 time to evaluate : 1.269 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 66 MET cc_start: 0.8458 (mmt) cc_final: 0.8248 (mmm) REVERT: A 344 MET cc_start: 0.8116 (tpt) cc_final: 0.7759 (tpt) REVERT: A 352 TYR cc_start: 0.7710 (m-80) cc_final: 0.7491 (m-80) REVERT: A 354 ASN cc_start: 0.8176 (OUTLIER) cc_final: 0.7860 (p0) REVERT: A 612 TRP cc_start: 0.7595 (t-100) cc_final: 0.7041 (t-100) REVERT: A 670 PHE cc_start: 0.3419 (OUTLIER) cc_final: 0.2906 (m-80) REVERT: A 687 TYR cc_start: 0.7415 (m-80) cc_final: 0.6774 (m-80) REVERT: A 696 PHE cc_start: 0.8285 (p90) cc_final: 0.7837 (p90) REVERT: A 728 LEU cc_start: 0.6131 (mt) cc_final: 0.5369 (pp) REVERT: A 745 MET cc_start: 0.4712 (ttp) cc_final: 0.4420 (tmm) REVERT: E 23 LEU cc_start: 0.6120 (mm) cc_final: 0.5772 (mm) REVERT: E 492 PHE cc_start: 0.8453 (m-10) cc_final: 0.7585 (m-10) REVERT: E 496 GLN cc_start: 0.8190 (tt0) cc_final: 0.7581 (tm-30) REVERT: E 500 LYS cc_start: 0.9219 (pttm) cc_final: 0.8741 (tptp) REVERT: E 507 MET cc_start: 0.8768 (mmm) cc_final: 0.8340 (mmt) REVERT: C 74 TYR cc_start: 0.7592 (OUTLIER) cc_final: 0.7185 (m-80) REVERT: C 108 ASN cc_start: 0.7895 (t0) cc_final: 0.7341 (p0) REVERT: C 127 GLU cc_start: 0.7181 (mp0) cc_final: 0.6889 (pm20) REVERT: C 144 LYS cc_start: 0.8727 (pttt) cc_final: 0.8378 (ptpp) REVERT: C 193 ASN cc_start: 0.8167 (t0) cc_final: 0.7799 (t0) REVERT: C 197 LYS cc_start: 0.8949 (mmtt) cc_final: 0.8624 (mmtt) REVERT: C 219 MET cc_start: 0.7655 (OUTLIER) cc_final: 0.7340 (mmm) REVERT: G 68 MET cc_start: 0.7865 (mtp) cc_final: 0.7558 (mtm) REVERT: G 107 LYS cc_start: 0.9201 (ptpp) cc_final: 0.8839 (tppt) REVERT: G 108 ASP cc_start: 0.9467 (p0) cc_final: 0.9143 (p0) REVERT: G 118 TYR cc_start: 0.9418 (m-80) cc_final: 0.8691 (m-80) REVERT: H 73 ASP cc_start: 0.7599 (t0) cc_final: 0.7009 (m-30) REVERT: H 75 THR cc_start: 0.7754 (p) cc_final: 0.7527 (p) REVERT: H 87 ARG cc_start: 0.8565 (tpp-160) cc_final: 0.8240 (mmm160) REVERT: H 116 TYR cc_start: 0.8838 (m-80) cc_final: 0.7927 (m-80) REVERT: H 117 GLU cc_start: 0.7733 (pm20) cc_final: 0.7524 (pm20) REVERT: H 144 LYS cc_start: 0.9222 (tmmt) cc_final: 0.8852 (tmmt) REVERT: H 183 VAL cc_start: 0.8159 (t) cc_final: 0.7914 (t) REVERT: J 48 LYS cc_start: 0.8907 (tppt) cc_final: 0.8690 (tmmt) REVERT: J 64 ARG cc_start: 0.7875 (ttm-80) cc_final: 0.7633 (ttm-80) REVERT: J 92 ARG cc_start: 0.8106 (mtm-85) cc_final: 0.7855 (mtm-85) REVERT: J 112 LYS cc_start: 0.7959 (tptm) cc_final: 0.7724 (tmtt) REVERT: J 114 LYS cc_start: 0.8636 (ttmm) cc_final: 0.8265 (mtpp) REVERT: J 139 MET cc_start: 0.8076 (tpt) cc_final: 0.7661 (tpt) outliers start: 34 outliers final: 24 residues processed: 190 average time/residue: 0.2517 time to fit residues: 66.2986 Evaluate side-chains 185 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 281 ASP 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 457 VAL Chi-restraints excluded: chain A residue 471 CYS 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 E residue 493 THR Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 222 PHE 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 91 THR Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 136 CYS Chi-restraints excluded: chain H residue 200 VAL Chi-restraints excluded: chain H residue 206 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 58 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 136 optimal weight: 0.2980 chunk 108 optimal weight: 0.7980 chunk 64 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 3 optimal weight: 0.1980 chunk 99 optimal weight: 0.0050 chunk 66 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 ASN A 797 ASN G 120 HIS H 206 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.113722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.082003 restraints weight = 28535.390| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 4.73 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10994 Z= 0.135 Angle : 0.663 9.994 14904 Z= 0.327 Chirality : 0.044 0.183 1684 Planarity : 0.003 0.044 1907 Dihedral : 4.929 55.142 1474 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.68 % Favored : 94.24 % Rotamer: Outliers : 2.94 % Allowed : 20.19 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.23), residues: 1355 helix: 1.47 (0.29), residues: 344 sheet: -0.95 (0.33), residues: 265 loop : -1.08 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 612 HIS 0.008 0.001 HIS H 207 PHE 0.033 0.001 PHE A 696 TYR 0.016 0.001 TYR E 452 ARG 0.003 0.000 ARG H 84 Details of bonding type rmsd hydrogen bonds : bond 0.03368 ( 382) hydrogen bonds : angle 4.55976 ( 1098) SS BOND : bond 0.00216 ( 19) SS BOND : angle 0.80647 ( 38) covalent geometry : bond 0.00312 (10975) covalent geometry : angle 0.66282 (14866) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6912.16 seconds wall clock time: 120 minutes 53.96 seconds (7253.96 seconds total)