Starting phenix.real_space_refine on Tue Jul 29 00:25:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xfp_38307/07_2025/8xfp_38307.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xfp_38307/07_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_38307/07_2025/8xfp_38307.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xfp_38307/07_2025/8xfp_38307.map" model { file = "/net/cci-nas-00/data/ceres_data/8xfp_38307/07_2025/8xfp_38307.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xfp_38307/07_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 7.45, per 1000 atoms: 0.69 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: 2.70 Conformation dependent library (CDL) restraints added in 1.3 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: 1.14 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: 3.15 Time building geometry restraints manager: 3.18 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: 2.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.720 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.010 ------------------------------------------------------------------------------- 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 : 1.116 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: 0.2892 time to fit residues: 108.1071 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 : 1.388 ------------------------------------------------------------------------------- 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 = 0.107926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.075626 restraints weight = 28558.662| |-----------------------------------------------------------------------------| 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: 0.7540 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 11.147 14904 Z= 0.420 Chirality : 0.051 0.189 1684 Planarity : 0.005 0.051 1907 Dihedral : 6.715 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 5.10531 ( 1098) SS BOND : bond 0.00760 ( 19) SS BOND : angle 1.58770 ( 38) covalent geometry : bond 0.00905 (10975) covalent geometry : angle 0.82169 (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 : 1.295 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: 0.8422 (tt0) cc_final: 0.7701 (tp30) REVERT: A 274 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8780 (tt) REVERT: A 354 ASN cc_start: 0.8150 (OUTLIER) cc_final: 0.7891 (p0) REVERT: A 596 PHE cc_start: 0.8838 (m-80) cc_final: 0.8354 (m-10) REVERT: A 643 ARG cc_start: 0.5110 (mmp-170) cc_final: 0.4901 (tpp-160) REVERT: A 670 PHE cc_start: 0.3477 (OUTLIER) cc_final: 0.3076 (m-80) REVERT: A 687 TYR cc_start: 0.7341 (m-10) cc_final: 0.7053 (m-80) REVERT: A 725 TYR cc_start: 0.6695 (t80) cc_final: 0.5559 (t80) REVERT: A 729 TYR cc_start: 0.2185 (OUTLIER) cc_final: 0.1295 (m-10) REVERT: E 454 TYR cc_start: 0.8594 (p90) cc_final: 0.8259 (p90) REVERT: E 517 MET cc_start: 0.8427 (tpp) cc_final: 0.8225 (mmm) REVERT: E 539 TYR cc_start: 0.8319 (m-80) cc_final: 0.8027 (m-80) REVERT: C 74 TYR cc_start: 0.8269 (OUTLIER) cc_final: 0.7574 (m-80) REVERT: C 107 CYS cc_start: 0.4453 (OUTLIER) cc_final: 0.4239 (t) REVERT: C 144 LYS cc_start: 0.8934 (pttt) cc_final: 0.8625 (ptpp) REVERT: C 193 ASN cc_start: 0.8234 (t0) cc_final: 0.7941 (t0) REVERT: C 198 GLN cc_start: 0.8562 (tp40) cc_final: 0.7783 (mp10) REVERT: C 240 ILE cc_start: 0.5751 (mm) cc_final: 0.5533 (mp) REVERT: G 68 MET cc_start: 0.8245 (mtp) cc_final: 0.7869 (mtm) REVERT: G 83 TYR cc_start: 0.8160 (p90) cc_final: 0.7430 (p90) REVERT: H 97 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7449 (tp30) REVERT: H 197 LYS cc_start: 0.9277 (mmtp) cc_final: 0.9007 (mmtp) REVERT: H 207 HIS cc_start: 0.7622 (OUTLIER) cc_final: 0.7348 (t-90) REVERT: J 64 ARG cc_start: 0.8034 (ttm-80) cc_final: 0.7828 (ttm-80) REVERT: J 92 ARG cc_start: 0.8361 (mtm-85) cc_final: 0.8040 (mtm-85) REVERT: J 102 ASP cc_start: 0.8623 (m-30) cc_final: 0.8063 (m-30) REVERT: J 108 ASP cc_start: 0.8920 (p0) cc_final: 0.8716 (p0) REVERT: J 112 LYS cc_start: 0.8276 (tmtt) cc_final: 0.8000 (tmmt) outliers start: 68 outliers final: 32 residues processed: 227 average time/residue: 0.3012 time to fit residues: 92.6821 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 : 1.146 ------------------------------------------------------------------------------- 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: 0.9980 chunk 28 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 49 optimal weight: 10.0000 chunk 22 optimal weight: 0.4980 chunk 70 optimal weight: 0.5980 chunk 133 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.111954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.080100 restraints weight = 28581.161| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 4.66 r_work: 0.3190 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.2695 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 : 0.628 9.015 14904 Z= 0.314 Chirality : 0.044 0.170 1684 Planarity : 0.004 0.033 1907 Dihedral : 5.763 58.914 1481 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.46 % Favored : 94.46 % Rotamer: Outliers : 3.53 % Allowed : 14.47 % Favored : 82.00 % 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 : -1.18 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 612 HIS 0.012 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 0.03384 ( 382) hydrogen bonds : angle 4.62597 ( 1098) SS BOND : bond 0.00310 ( 19) SS BOND : angle 1.20433 ( 38) covalent geometry : bond 0.00280 (10975) covalent geometry : angle 0.62597 (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 227 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 185 time to evaluate : 2.254 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: 0.8002 (tpt) cc_final: 0.7790 (tpt) REVERT: A 353 ASN cc_start: 0.8365 (OUTLIER) cc_final: 0.8011 (m-40) REVERT: A 449 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7691 (pt0) REVERT: A 596 PHE cc_start: 0.8890 (m-80) cc_final: 0.8366 (m-10) REVERT: A 643 ARG cc_start: 0.4706 (mmp-170) cc_final: 0.4324 (tpp-160) REVERT: A 670 PHE cc_start: 0.3244 (OUTLIER) cc_final: 0.2748 (m-80) REVERT: A 725 TYR cc_start: 0.6688 (t80) cc_final: 0.5612 (t80) REVERT: A 729 TYR cc_start: 0.1981 (OUTLIER) cc_final: 0.1298 (m-10) REVERT: E 539 TYR cc_start: 0.8176 (m-80) cc_final: 0.7814 (m-80) REVERT: C 74 TYR cc_start: 0.7805 (OUTLIER) cc_final: 0.7452 (m-80) REVERT: C 144 LYS cc_start: 0.8872 (pttt) cc_final: 0.8517 (ptpp) REVERT: C 193 ASN cc_start: 0.8157 (t0) cc_final: 0.7937 (t0) REVERT: C 198 GLN cc_start: 0.8477 (tp40) cc_final: 0.7684 (mp10) REVERT: G 68 MET cc_start: 0.7896 (mtp) cc_final: 0.7577 (mtm) REVERT: G 83 TYR cc_start: 0.8104 (p90) cc_final: 0.7084 (p90) REVERT: G 107 LYS cc_start: 0.8846 (ptpp) cc_final: 0.8524 (mttp) REVERT: G 118 TYR cc_start: 0.9067 (m-80) cc_final: 0.8647 (m-80) REVERT: H 87 ARG cc_start: 0.8505 (tpp-160) cc_final: 0.8129 (tpp-160) REVERT: H 97 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7427 (tp30) REVERT: H 148 GLN cc_start: 0.8907 (mt0) cc_final: 0.8513 (mt0) REVERT: H 197 LYS cc_start: 0.9301 (mmtp) cc_final: 0.9034 (mmtp) REVERT: H 207 HIS cc_start: 0.6735 (OUTLIER) cc_final: 0.5988 (p90) REVERT: J 48 LYS cc_start: 0.9138 (tppt) cc_final: 0.8816 (tmmt) REVERT: J 64 ARG cc_start: 0.7917 (ttm-80) cc_final: 0.7653 (ttm-80) REVERT: J 68 MET cc_start: 0.8438 (ptp) cc_final: 0.8203 (ptm) REVERT: J 92 ARG cc_start: 0.8134 (mtm-85) cc_final: 0.7847 (mtm-85) REVERT: J 102 ASP cc_start: 0.8771 (m-30) cc_final: 0.8475 (m-30) outliers start: 42 outliers final: 25 residues processed: 212 average time/residue: 0.3495 time to fit residues: 102.1768 Evaluate side-chains 196 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 165 time to evaluate : 1.428 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain H residue 207 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 72 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 45 optimal weight: 0.0050 chunk 21 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 96 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 70 optimal weight: 0.0170 chunk 118 optimal weight: 4.9990 overall best weight: 1.1636 ------------------------------------------------------------------------------- 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** C 196 ASN G 50 ASN G 100 ASN H 207 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.110961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.079155 restraints weight = 28407.365| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 4.64 r_work: 0.3187 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10994 Z= 0.156 Angle : 0.638 9.690 14904 Z= 0.321 Chirality : 0.045 0.256 1684 Planarity : 0.004 0.034 1907 Dihedral : 5.718 57.216 1479 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.13 % Favored : 93.80 % Rotamer: Outliers : 4.04 % Allowed : 14.80 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.50 (0.29), residues: 343 sheet: -1.24 (0.32), residues: 279 loop : -1.14 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 612 HIS 0.012 0.001 HIS H 207 PHE 0.042 0.001 PHE A 662 TYR 0.017 0.002 TYR A 687 ARG 0.003 0.000 ARG C 202 Details of bonding type rmsd hydrogen bonds : bond 0.03462 ( 382) hydrogen bonds : angle 4.65168 ( 1098) SS BOND : bond 0.00276 ( 19) SS BOND : angle 1.00967 ( 38) covalent geometry : bond 0.00354 (10975) covalent geometry : angle 0.63679 (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 218 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 170 time to evaluate : 1.087 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 344 MET cc_start: 0.8105 (tpt) cc_final: 0.7807 (tpt) REVERT: A 353 ASN cc_start: 0.8380 (OUTLIER) cc_final: 0.7776 (m-40) REVERT: A 354 ASN cc_start: 0.8306 (OUTLIER) cc_final: 0.7941 (p0) REVERT: A 596 PHE cc_start: 0.8828 (m-80) cc_final: 0.8281 (m-10) REVERT: A 643 ARG cc_start: 0.4834 (mmp-170) cc_final: 0.4613 (tpp-160) REVERT: A 670 PHE cc_start: 0.3415 (OUTLIER) cc_final: 0.2937 (m-80) REVERT: A 687 TYR cc_start: 0.7324 (m-80) cc_final: 0.6702 (m-10) REVERT: A 725 TYR cc_start: 0.6836 (t80) cc_final: 0.6610 (t80) REVERT: A 728 LEU cc_start: 0.6298 (mt) cc_final: 0.5913 (pp) REVERT: E 492 PHE cc_start: 0.9019 (m-10) cc_final: 0.8305 (m-10) REVERT: E 507 MET cc_start: 0.9006 (mmm) cc_final: 0.8796 (mmm) REVERT: E 517 MET cc_start: 0.8558 (tpp) cc_final: 0.8090 (tpp) REVERT: E 539 TYR cc_start: 0.7873 (m-80) cc_final: 0.7526 (m-80) REVERT: C 74 TYR cc_start: 0.7995 (OUTLIER) cc_final: 0.7439 (m-80) REVERT: C 144 LYS cc_start: 0.8870 (pttt) cc_final: 0.8517 (ptpp) REVERT: C 193 ASN cc_start: 0.8204 (t0) cc_final: 0.7731 (t0) REVERT: C 198 GLN cc_start: 0.8475 (tp40) cc_final: 0.7675 (mp10) REVERT: C 217 PHE cc_start: 0.7893 (m-80) cc_final: 0.7676 (m-80) REVERT: G 68 MET cc_start: 0.8053 (mtp) cc_final: 0.7695 (mtm) REVERT: G 83 TYR cc_start: 0.8132 (p90) cc_final: 0.7138 (p90) REVERT: G 107 LYS cc_start: 0.8803 (ptpp) cc_final: 0.8477 (mttp) REVERT: G 118 TYR cc_start: 0.9164 (m-80) cc_final: 0.8496 (m-80) REVERT: H 56 LYS cc_start: 0.8930 (mptt) cc_final: 0.7835 (tptt) REVERT: H 87 ARG cc_start: 0.8532 (tpp-160) cc_final: 0.8144 (mmm160) REVERT: H 97 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7429 (tp30) REVERT: H 197 LYS cc_start: 0.9306 (mmtp) cc_final: 0.9061 (mmtp) REVERT: H 207 HIS cc_start: 0.6136 (OUTLIER) cc_final: 0.5668 (p90) REVERT: J 48 LYS cc_start: 0.9147 (tppt) cc_final: 0.8856 (tmmt) REVERT: J 64 ARG cc_start: 0.7981 (ttm-80) cc_final: 0.7680 (ttm-80) REVERT: J 92 ARG cc_start: 0.8178 (mtm-85) cc_final: 0.7891 (mtm-85) REVERT: J 139 MET cc_start: 0.8152 (tpt) cc_final: 0.7746 (tpt) outliers start: 48 outliers final: 31 residues processed: 204 average time/residue: 0.3848 time to fit residues: 108.7490 Evaluate side-chains 203 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 166 time to evaluate : 2.588 ------------------------------------------------------------------------------- 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 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 575 LEU 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 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 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 207 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 70 optimal weight: 0.3980 chunk 23 optimal weight: 4.9990 chunk 136 optimal weight: 0.0170 chunk 29 optimal weight: 4.9990 chunk 111 optimal weight: 20.0000 chunk 117 optimal weight: 0.2980 chunk 51 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 125 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.5218 ------------------------------------------------------------------------------- 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** ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.112515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.081110 restraints weight = 28407.082| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 4.65 r_work: 0.3215 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10994 Z= 0.109 Angle : 0.617 9.261 14904 Z= 0.304 Chirality : 0.044 0.196 1684 Planarity : 0.003 0.034 1907 Dihedral : 5.177 58.970 1477 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.31 % Favored : 94.61 % Rotamer: Outliers : 3.03 % Allowed : 16.82 % Favored : 80.15 % 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: -0.63 (0.24), residues: 1355 helix: 1.64 (0.29), residues: 342 sheet: -1.15 (0.32), residues: 279 loop : -1.12 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 612 HIS 0.010 0.001 HIS H 207 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 0.03148 ( 382) hydrogen bonds : angle 4.50034 ( 1098) SS BOND : bond 0.00194 ( 19) SS BOND : angle 0.92276 ( 38) covalent geometry : bond 0.00240 (10975) covalent geometry : angle 0.61594 (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 214 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 178 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 MET cc_start: 0.8127 (tpt) cc_final: 0.7798 (tpt) REVERT: A 670 PHE cc_start: 0.3443 (OUTLIER) cc_final: 0.2859 (m-80) REVERT: A 687 TYR cc_start: 0.7419 (m-80) cc_final: 0.6720 (m-10) REVERT: A 728 LEU cc_start: 0.6201 (mt) cc_final: 0.5843 (pp) REVERT: E 492 PHE cc_start: 0.8929 (m-10) cc_final: 0.7873 (m-10) REVERT: E 507 MET cc_start: 0.8875 (mmm) cc_final: 0.8626 (mmm) REVERT: E 517 MET cc_start: 0.8612 (tpp) cc_final: 0.8181 (tpp) REVERT: C 74 TYR cc_start: 0.7766 (OUTLIER) cc_final: 0.7447 (m-80) REVERT: C 144 LYS cc_start: 0.8780 (pttt) cc_final: 0.8418 (ptpp) REVERT: C 198 GLN cc_start: 0.8209 (tp40) cc_final: 0.7700 (mp10) REVERT: G 68 MET cc_start: 0.7894 (mtp) cc_final: 0.7510 (mtm) REVERT: G 83 TYR cc_start: 0.8132 (p90) cc_final: 0.7365 (p90) REVERT: G 118 TYR cc_start: 0.9304 (m-80) cc_final: 0.8758 (m-80) REVERT: H 67 GLU cc_start: 0.9031 (tt0) cc_final: 0.8502 (mp0) REVERT: H 73 ASP cc_start: 0.7765 (t0) cc_final: 0.7105 (m-30) REVERT: H 87 ARG cc_start: 0.8571 (tpp-160) cc_final: 0.7993 (tpp-160) REVERT: H 116 TYR cc_start: 0.8895 (m-80) cc_final: 0.8112 (m-80) REVERT: H 207 HIS cc_start: 0.6695 (t70) cc_final: 0.5882 (p90) REVERT: J 48 LYS cc_start: 0.8982 (tppt) cc_final: 0.8756 (tmmt) REVERT: J 64 ARG cc_start: 0.7947 (ttm-80) cc_final: 0.7663 (ttm-80) REVERT: J 92 ARG cc_start: 0.8145 (mtm-85) cc_final: 0.7875 (mtm-85) REVERT: J 114 LYS cc_start: 0.8635 (ttmm) cc_final: 0.8290 (mtpp) REVERT: J 139 MET cc_start: 0.8105 (tpt) cc_final: 0.7686 (tpt) outliers start: 36 outliers final: 23 residues processed: 198 average time/residue: 0.2936 time to fit residues: 80.1523 Evaluate side-chains 185 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 1.291 ------------------------------------------------------------------------------- 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 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 74 TYR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 139 VAL 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: 3.9990 chunk 105 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 49 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 59 optimal weight: 10.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.109817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.077902 restraints weight = 28714.367| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 4.63 r_work: 0.3164 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.3266 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= 0.210 Angle : 0.682 9.713 14904 Z= 0.343 Chirality : 0.046 0.214 1684 Planarity : 0.004 0.034 1907 Dihedral : 5.423 59.486 1474 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.01 % Favored : 92.92 % Rotamer: Outliers : 4.12 % Allowed : 16.82 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.34 (0.29), residues: 344 sheet: -1.25 (0.32), residues: 281 loop : -1.17 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 612 HIS 0.007 0.001 HIS A 209 PHE 0.040 0.002 PHE A 662 TYR 0.016 0.002 TYR E 452 ARG 0.004 0.000 ARG C 202 Details of bonding type rmsd hydrogen bonds : bond 0.03702 ( 382) hydrogen bonds : angle 4.68727 ( 1098) SS BOND : bond 0.00317 ( 19) SS BOND : angle 0.96212 ( 38) covalent geometry : bond 0.00484 (10975) covalent geometry : angle 0.68120 (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 209 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 160 time to evaluate : 1.815 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: 0.8670 (OUTLIER) cc_final: 0.8045 (m-40) REVERT: A 252 GLU cc_start: 0.8119 (tt0) cc_final: 0.7540 (tp30) REVERT: A 344 MET cc_start: 0.8130 (tpt) cc_final: 0.7840 (tpt) REVERT: A 353 ASN cc_start: 0.8409 (OUTLIER) cc_final: 0.8013 (m110) REVERT: A 354 ASN cc_start: 0.8267 (OUTLIER) cc_final: 0.7921 (p0) REVERT: A 670 PHE cc_start: 0.3398 (OUTLIER) cc_final: 0.2923 (m-80) REVERT: A 687 TYR cc_start: 0.7446 (m-80) cc_final: 0.6730 (m-10) REVERT: E 23 LEU cc_start: 0.6648 (mm) cc_final: 0.4288 (mm) REVERT: E 478 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8277 (pt) REVERT: E 496 GLN cc_start: 0.8209 (tt0) cc_final: 0.7428 (tm-30) REVERT: E 517 MET cc_start: 0.8703 (tpp) cc_final: 0.8338 (tpp) REVERT: C 108 ASN cc_start: 0.7870 (t0) cc_final: 0.7270 (p0) REVERT: C 144 LYS cc_start: 0.8868 (pttt) cc_final: 0.8518 (ptpp) REVERT: C 198 GLN cc_start: 0.8444 (tp40) cc_final: 0.7911 (mp10) REVERT: G 68 MET cc_start: 0.8116 (mtp) cc_final: 0.7740 (mtm) REVERT: G 83 TYR cc_start: 0.8173 (p90) cc_final: 0.7722 (p90) REVERT: H 56 LYS cc_start: 0.8911 (mptt) cc_final: 0.7742 (tptt) REVERT: H 67 GLU cc_start: 0.9011 (tt0) cc_final: 0.8540 (mp0) REVERT: H 87 ARG cc_start: 0.8608 (tpp-160) cc_final: 0.8200 (mmm160) REVERT: H 97 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7458 (tp30) REVERT: H 207 HIS cc_start: 0.7028 (t-90) cc_final: 0.6601 (p90) REVERT: J 48 LYS cc_start: 0.9035 (tppt) cc_final: 0.8772 (tmmt) REVERT: J 64 ARG cc_start: 0.7976 (ttm-80) cc_final: 0.7697 (ttm-80) REVERT: J 92 ARG cc_start: 0.8222 (mtm-85) cc_final: 0.7938 (mtm-85) REVERT: J 114 LYS cc_start: 0.8713 (ttmm) cc_final: 0.8451 (mtpp) REVERT: J 139 MET cc_start: 0.8124 (tpt) cc_final: 0.7725 (tpt) outliers start: 49 outliers final: 29 residues processed: 194 average time/residue: 0.2920 time to fit residues: 77.8427 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 : 1.123 ------------------------------------------------------------------------------- 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 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 670 PHE Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 768 PHE 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 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: 5.9990 chunk 47 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 133 optimal weight: 0.1980 chunk 122 optimal weight: 1.9990 chunk 94 optimal weight: 0.3980 chunk 48 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN ** A 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 HIS ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.112442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.080896 restraints weight = 28731.995| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 4.67 r_work: 0.3208 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.3323 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= 0.119 Angle : 0.635 9.678 14904 Z= 0.317 Chirality : 0.044 0.172 1684 Planarity : 0.003 0.034 1907 Dihedral : 5.021 57.486 1474 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.31 % Favored : 94.61 % Rotamer: Outliers : 3.78 % Allowed : 17.83 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.56 (0.29), residues: 344 sheet: -1.15 (0.32), residues: 279 loop : -1.12 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 546 HIS 0.006 0.001 HIS A 209 PHE 0.031 0.001 PHE A 696 TYR 0.027 0.002 TYR E 452 ARG 0.002 0.000 ARG E 491 Details of bonding type rmsd hydrogen bonds : bond 0.03341 ( 382) hydrogen bonds : angle 4.55960 ( 1098) SS BOND : bond 0.00215 ( 19) SS BOND : angle 0.96828 ( 38) covalent geometry : bond 0.00265 (10975) covalent geometry : angle 0.63439 (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 206 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 161 time to evaluate : 1.317 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: 0.8547 (mmt) cc_final: 0.8317 (mmm) REVERT: A 344 MET cc_start: 0.8167 (tpt) cc_final: 0.7803 (tpt) REVERT: A 353 ASN cc_start: 0.8388 (OUTLIER) cc_final: 0.7912 (m-40) REVERT: A 354 ASN cc_start: 0.8224 (OUTLIER) cc_final: 0.7848 (p0) REVERT: A 670 PHE cc_start: 0.3370 (OUTLIER) cc_final: 0.2879 (m-80) REVERT: A 687 TYR cc_start: 0.7440 (m-80) cc_final: 0.6771 (m-80) REVERT: E 23 LEU cc_start: 0.6099 (mm) cc_final: 0.5260 (mm) REVERT: E 478 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8224 (pt) REVERT: E 496 GLN cc_start: 0.7990 (tt0) cc_final: 0.7536 (tm-30) REVERT: E 517 MET cc_start: 0.8708 (tpp) cc_final: 0.8340 (tpp) REVERT: C 74 TYR cc_start: 0.7717 (OUTLIER) cc_final: 0.7331 (m-80) REVERT: C 108 ASN cc_start: 0.7733 (t0) cc_final: 0.7370 (p0) REVERT: C 144 LYS cc_start: 0.8784 (pttt) cc_final: 0.8421 (ptpp) REVERT: C 219 MET cc_start: 0.7702 (tpt) cc_final: 0.7406 (mmm) REVERT: G 68 MET cc_start: 0.7938 (mtp) cc_final: 0.7594 (mtm) REVERT: G 83 TYR cc_start: 0.8202 (p90) cc_final: 0.7708 (p90) REVERT: G 108 ASP cc_start: 0.9377 (OUTLIER) cc_final: 0.9153 (p0) REVERT: G 118 TYR cc_start: 0.9134 (m-80) cc_final: 0.8523 (m-80) REVERT: H 67 GLU cc_start: 0.9023 (tt0) cc_final: 0.8521 (mp0) REVERT: H 73 ASP cc_start: 0.7740 (t0) cc_final: 0.7127 (m-30) REVERT: H 87 ARG cc_start: 0.8575 (tpp-160) cc_final: 0.8213 (mmm160) REVERT: H 97 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7329 (tp30) REVERT: H 116 TYR cc_start: 0.8922 (m-80) cc_final: 0.8097 (m-80) REVERT: J 64 ARG cc_start: 0.7958 (ttm-80) cc_final: 0.7697 (ttm-80) REVERT: J 92 ARG cc_start: 0.8167 (mtm-85) cc_final: 0.7907 (mtm-85) REVERT: J 112 LYS cc_start: 0.8158 (tptm) cc_final: 0.7933 (tmtt) REVERT: J 114 LYS cc_start: 0.8730 (ttmm) cc_final: 0.8379 (mtpp) REVERT: J 139 MET cc_start: 0.8210 (tpt) cc_final: 0.7809 (tpt) outliers start: 45 outliers final: 29 residues processed: 192 average time/residue: 0.6238 time to fit residues: 172.1334 Evaluate side-chains 188 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 3.484 ------------------------------------------------------------------------------- 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 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 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 G residue 108 ASP 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: 0.9990 chunk 104 optimal weight: 0.7980 chunk 95 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 102 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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** G 120 HIS H 148 GLN ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 207 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.111812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.080155 restraints weight = 28276.833| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 4.62 r_work: 0.3210 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10994 Z= 0.137 Angle : 0.657 9.204 14904 Z= 0.327 Chirality : 0.044 0.173 1684 Planarity : 0.003 0.034 1907 Dihedral : 5.068 56.791 1474 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.83 % Favored : 94.10 % Rotamer: Outliers : 3.87 % Allowed : 18.84 % Favored : 77.29 % 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: 1.47 (0.29), residues: 344 sheet: -1.18 (0.32), residues: 279 loop : -1.12 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 612 HIS 0.006 0.001 HIS A 209 PHE 0.032 0.001 PHE A 696 TYR 0.025 0.002 TYR E 452 ARG 0.003 0.000 ARG E 491 Details of bonding type rmsd hydrogen bonds : bond 0.03441 ( 382) hydrogen bonds : angle 4.58729 ( 1098) SS BOND : bond 0.00220 ( 19) SS BOND : angle 0.92551 ( 38) covalent geometry : bond 0.00313 (10975) covalent geometry : angle 0.65569 (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 202 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 156 time to evaluate : 2.117 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: 0.8609 (mmt) cc_final: 0.8405 (mmm) REVERT: A 252 GLU cc_start: 0.8072 (tt0) cc_final: 0.7496 (tp30) REVERT: A 344 MET cc_start: 0.8203 (tpt) cc_final: 0.7874 (tpt) REVERT: A 353 ASN cc_start: 0.8397 (OUTLIER) cc_final: 0.7837 (m-40) REVERT: A 354 ASN cc_start: 0.8331 (OUTLIER) cc_final: 0.7966 (p0) REVERT: A 670 PHE cc_start: 0.3553 (OUTLIER) cc_final: 0.2995 (m-80) REVERT: A 687 TYR cc_start: 0.7502 (m-80) cc_final: 0.6847 (m-80) REVERT: A 745 MET cc_start: 0.4562 (ttp) cc_final: 0.4244 (tmm) REVERT: E 23 LEU cc_start: 0.5653 (mm) cc_final: 0.5217 (mm) REVERT: E 496 GLN cc_start: 0.8243 (tt0) cc_final: 0.7604 (tm-30) REVERT: E 504 TYR cc_start: 0.8496 (m-80) cc_final: 0.8295 (m-80) REVERT: E 517 MET cc_start: 0.8713 (tpp) cc_final: 0.8350 (tpp) REVERT: C 74 TYR cc_start: 0.7926 (OUTLIER) cc_final: 0.7427 (m-80) REVERT: C 108 ASN cc_start: 0.7806 (t0) cc_final: 0.7405 (p0) REVERT: C 144 LYS cc_start: 0.8792 (pttt) cc_final: 0.8427 (ptpp) REVERT: G 68 MET cc_start: 0.7997 (mtp) cc_final: 0.7664 (mtm) REVERT: G 83 TYR cc_start: 0.8122 (p90) cc_final: 0.7632 (p90) REVERT: G 118 TYR cc_start: 0.9218 (m-80) cc_final: 0.8636 (m-80) REVERT: H 87 ARG cc_start: 0.8572 (tpp-160) cc_final: 0.7940 (tpp-160) REVERT: H 97 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7363 (tp30) REVERT: H 117 GLU cc_start: 0.7802 (pm20) cc_final: 0.7562 (pm20) REVERT: H 144 LYS cc_start: 0.9325 (tmmt) cc_final: 0.8958 (tmmt) REVERT: J 64 ARG cc_start: 0.7991 (ttm-80) cc_final: 0.7740 (ttm-80) REVERT: J 92 ARG cc_start: 0.8203 (mtm-85) cc_final: 0.7941 (mtm-85) REVERT: J 112 LYS cc_start: 0.8237 (tptm) cc_final: 0.7991 (tmtt) REVERT: J 114 LYS cc_start: 0.8769 (ttmm) cc_final: 0.8344 (mtpp) outliers start: 46 outliers final: 30 residues processed: 185 average time/residue: 0.4673 time to fit residues: 119.4789 Evaluate side-chains 187 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 152 time to evaluate : 1.366 ------------------------------------------------------------------------------- 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 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 115 LEU 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 Chi-restraints excluded: chain H residue 200 VAL 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: 5.9990 chunk 93 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 8 optimal weight: 0.1980 chunk 6 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 28 optimal weight: 0.0670 chunk 19 optimal weight: 3.9990 overall best weight: 0.7920 ------------------------------------------------------------------------------- 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** G 120 HIS ** H 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 207 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.112204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.080605 restraints weight = 28359.652| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 4.64 r_work: 0.3220 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.3558 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= 0.132 Angle : 0.664 11.482 14904 Z= 0.330 Chirality : 0.044 0.169 1684 Planarity : 0.003 0.040 1907 Dihedral : 4.995 56.047 1474 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.83 % Favored : 94.10 % Rotamer: Outliers : 3.28 % Allowed : 19.26 % Favored : 77.46 % 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: -0.69 (0.23), residues: 1355 helix: 1.36 (0.29), residues: 345 sheet: -1.03 (0.33), residues: 267 loop : -1.12 (0.23), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 612 HIS 0.005 0.001 HIS A 209 PHE 0.033 0.001 PHE A 696 TYR 0.021 0.001 TYR E 452 ARG 0.002 0.000 ARG G 123 Details of bonding type rmsd hydrogen bonds : bond 0.03381 ( 382) hydrogen bonds : angle 4.58314 ( 1098) SS BOND : bond 0.00216 ( 19) SS BOND : angle 0.88150 ( 38) covalent geometry : bond 0.00303 (10975) covalent geometry : angle 0.66362 (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 197 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 158 time to evaluate : 1.146 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: 0.8566 (mmt) cc_final: 0.8360 (mmm) REVERT: A 344 MET cc_start: 0.8221 (tpt) cc_final: 0.7936 (tpt) REVERT: A 353 ASN cc_start: 0.8437 (OUTLIER) cc_final: 0.7936 (m-40) REVERT: A 354 ASN cc_start: 0.8239 (OUTLIER) cc_final: 0.7854 (p0) REVERT: A 670 PHE cc_start: 0.3630 (OUTLIER) cc_final: 0.3073 (m-80) REVERT: A 687 TYR cc_start: 0.7487 (m-80) cc_final: 0.6861 (m-80) REVERT: A 696 PHE cc_start: 0.8360 (p90) cc_final: 0.7901 (p90) REVERT: A 745 MET cc_start: 0.4625 (ttp) cc_final: 0.4334 (tmm) REVERT: E 21 VAL cc_start: 0.8422 (t) cc_final: 0.8064 (m) REVERT: E 23 LEU cc_start: 0.5827 (mm) cc_final: 0.5429 (mm) REVERT: E 478 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8256 (pt) REVERT: E 496 GLN cc_start: 0.8258 (tt0) cc_final: 0.7621 (tm-30) REVERT: E 504 TYR cc_start: 0.8377 (m-80) cc_final: 0.8114 (m-80) REVERT: C 74 TYR cc_start: 0.7913 (OUTLIER) cc_final: 0.7395 (m-80) REVERT: C 108 ASN cc_start: 0.7790 (t0) cc_final: 0.7401 (p0) REVERT: C 127 GLU cc_start: 0.7189 (mp0) cc_final: 0.6851 (pm20) REVERT: C 144 LYS cc_start: 0.8791 (pttt) cc_final: 0.8426 (ptpp) REVERT: C 198 GLN cc_start: 0.8197 (tp40) cc_final: 0.7658 (mp10) REVERT: C 219 MET cc_start: 0.7631 (mmm) cc_final: 0.7138 (mmm) REVERT: G 68 MET cc_start: 0.7957 (mtp) cc_final: 0.7584 (mtm) REVERT: G 83 TYR cc_start: 0.8185 (p90) cc_final: 0.7663 (p90) REVERT: G 118 TYR cc_start: 0.9294 (m-80) cc_final: 0.8744 (m-80) REVERT: H 73 ASP cc_start: 0.7753 (t0) cc_final: 0.7133 (m-30) REVERT: H 84 ARG cc_start: 0.7133 (tpp-160) cc_final: 0.6927 (tpp-160) REVERT: H 87 ARG cc_start: 0.8601 (tpp-160) cc_final: 0.8024 (tpp-160) REVERT: H 97 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7350 (tp30) REVERT: H 116 TYR cc_start: 0.8956 (m-80) cc_final: 0.8112 (m-80) REVERT: H 117 GLU cc_start: 0.7789 (pm20) cc_final: 0.7566 (pm20) REVERT: H 144 LYS cc_start: 0.9319 (tmmt) cc_final: 0.8937 (tmmt) REVERT: J 64 ARG cc_start: 0.7986 (ttm-80) cc_final: 0.7745 (ttm-80) REVERT: J 92 ARG cc_start: 0.8202 (mtm-85) cc_final: 0.7942 (mtm-85) REVERT: J 112 LYS cc_start: 0.8242 (tptm) cc_final: 0.7995 (tmtt) REVERT: J 114 LYS cc_start: 0.8799 (ttmm) cc_final: 0.8510 (mtpp) REVERT: J 115 VAL cc_start: 0.9510 (m) cc_final: 0.9250 (p) REVERT: J 139 MET cc_start: 0.8017 (tpt) cc_final: 0.7504 (tpt) outliers start: 39 outliers final: 30 residues processed: 184 average time/residue: 0.2718 time to fit residues: 70.1542 Evaluate side-chains 190 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 154 time to evaluate : 1.225 ------------------------------------------------------------------------------- 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 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 115 LEU 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 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: 0.6980 chunk 95 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 115 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 85 optimal weight: 0.0070 chunk 107 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 overall best weight: 0.8800 ------------------------------------------------------------------------------- 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 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 207 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.111948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.080314 restraints weight = 28459.620| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 4.64 r_work: 0.3213 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10994 Z= 0.138 Angle : 0.694 12.970 14904 Z= 0.341 Chirality : 0.044 0.199 1684 Planarity : 0.004 0.044 1907 Dihedral : 5.010 55.984 1474 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.76 % Favored : 94.17 % Rotamer: Outliers : 3.20 % Allowed : 19.34 % Favored : 77.46 % 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: -0.65 (0.23), residues: 1355 helix: 1.39 (0.29), residues: 344 sheet: -1.02 (0.33), residues: 267 loop : -1.08 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 612 HIS 0.008 0.001 HIS A 209 PHE 0.032 0.001 PHE A 696 TYR 0.015 0.001 TYR E 452 ARG 0.002 0.000 ARG C 202 Details of bonding type rmsd hydrogen bonds : bond 0.03465 ( 382) hydrogen bonds : angle 4.59535 ( 1098) SS BOND : bond 0.00222 ( 19) SS BOND : angle 0.86348 ( 38) covalent geometry : bond 0.00317 (10975) covalent geometry : angle 0.69353 (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 195 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 157 time to evaluate : 1.316 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: 0.8570 (mmt) cc_final: 0.8369 (mmm) REVERT: A 252 GLU cc_start: 0.8078 (tt0) cc_final: 0.7495 (tp30) REVERT: A 344 MET cc_start: 0.8220 (tpt) cc_final: 0.7930 (tpt) REVERT: A 353 ASN cc_start: 0.8443 (OUTLIER) cc_final: 0.7919 (m-40) REVERT: A 354 ASN cc_start: 0.8233 (OUTLIER) cc_final: 0.7851 (p0) REVERT: A 670 PHE cc_start: 0.3606 (OUTLIER) cc_final: 0.3048 (m-80) REVERT: A 687 TYR cc_start: 0.7481 (m-80) cc_final: 0.6869 (m-80) REVERT: A 696 PHE cc_start: 0.8352 (p90) cc_final: 0.7895 (p90) REVERT: A 745 MET cc_start: 0.4804 (ttp) cc_final: 0.4522 (tmm) REVERT: E 21 VAL cc_start: 0.8437 (t) cc_final: 0.8098 (m) REVERT: E 23 LEU cc_start: 0.5966 (mm) cc_final: 0.5621 (mm) REVERT: E 496 GLN cc_start: 0.8238 (tt0) cc_final: 0.7602 (tm-30) REVERT: E 500 LYS cc_start: 0.9211 (pttm) cc_final: 0.8823 (tptp) REVERT: E 517 MET cc_start: 0.8743 (tpp) cc_final: 0.8072 (tpp) REVERT: C 74 TYR cc_start: 0.7933 (OUTLIER) cc_final: 0.7352 (m-80) REVERT: C 108 ASN cc_start: 0.7797 (t0) cc_final: 0.7409 (p0) REVERT: C 127 GLU cc_start: 0.7188 (mp0) cc_final: 0.6855 (pm20) REVERT: C 144 LYS cc_start: 0.8789 (pttt) cc_final: 0.8426 (ptpp) REVERT: C 219 MET cc_start: 0.7566 (mmm) cc_final: 0.7082 (mmm) REVERT: G 68 MET cc_start: 0.7978 (mtp) cc_final: 0.7643 (mtm) REVERT: G 83 TYR cc_start: 0.8207 (p90) cc_final: 0.7644 (p90) REVERT: G 107 LYS cc_start: 0.9213 (mmtt) cc_final: 0.8939 (mmtt) REVERT: G 118 TYR cc_start: 0.9313 (m-80) cc_final: 0.8504 (m-80) REVERT: H 73 ASP cc_start: 0.7780 (t0) cc_final: 0.7140 (m-30) REVERT: H 84 ARG cc_start: 0.7121 (tpp-160) cc_final: 0.6904 (tpp-160) REVERT: H 87 ARG cc_start: 0.8593 (tpp-160) cc_final: 0.8035 (tpp-160) REVERT: H 97 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7341 (tp30) REVERT: H 144 LYS cc_start: 0.9315 (tmmt) cc_final: 0.8938 (tmmt) REVERT: J 64 ARG cc_start: 0.7995 (ttm-80) cc_final: 0.7756 (ttm-80) REVERT: J 92 ARG cc_start: 0.8217 (mtm-85) cc_final: 0.7957 (mtm-85) REVERT: J 112 LYS cc_start: 0.8131 (tptm) cc_final: 0.7886 (tmtt) REVERT: J 114 LYS cc_start: 0.8780 (ttmm) cc_final: 0.8476 (mtpp) REVERT: J 115 VAL cc_start: 0.9514 (m) cc_final: 0.9242 (p) REVERT: J 139 MET cc_start: 0.8080 (tpt) cc_final: 0.7577 (tpt) outliers start: 38 outliers final: 29 residues processed: 183 average time/residue: 0.2623 time to fit residues: 66.3560 Evaluate side-chains 187 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 153 time to evaluate : 1.243 ------------------------------------------------------------------------------- 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 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 115 LEU 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 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 58 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 136 optimal weight: 0.0170 chunk 108 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 overall best weight: 2.2026 ------------------------------------------------------------------------------- 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** G 120 HIS ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 207 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.109197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.077219 restraints weight = 28365.182| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 4.57 r_work: 0.3153 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 10994 Z= 0.257 Angle : 0.759 12.090 14904 Z= 0.382 Chirality : 0.047 0.198 1684 Planarity : 0.004 0.047 1907 Dihedral : 5.651 59.461 1474 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.60 % Favored : 92.32 % Rotamer: Outliers : 3.45 % Allowed : 19.51 % 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: -0.89 (0.23), residues: 1355 helix: 1.12 (0.29), residues: 342 sheet: -1.20 (0.32), residues: 268 loop : -1.17 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 612 HIS 0.008 0.001 HIS A 209 PHE 0.030 0.002 PHE A 696 TYR 0.015 0.002 TYR E 452 ARG 0.004 0.000 ARG A 374 Details of bonding type rmsd hydrogen bonds : bond 0.04204 ( 382) hydrogen bonds : angle 4.91350 ( 1098) SS BOND : bond 0.00380 ( 19) SS BOND : angle 1.02434 ( 38) covalent geometry : bond 0.00589 (10975) covalent geometry : angle 0.75816 (14866) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8071.32 seconds wall clock time: 147 minutes 53.67 seconds (8873.67 seconds total)