Starting phenix.real_space_refine on Fri Jan 17 13:06:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xfp_38307/01_2025/8xfp_38307.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xfp_38307/01_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_38307/01_2025/8xfp_38307.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xfp_38307/01_2025/8xfp_38307.map" model { file = "/net/cci-nas-00/data/ceres_data/8xfp_38307/01_2025/8xfp_38307.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xfp_38307/01_2025/8xfp_38307.cif" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 81 5.16 5 C 6865 2.51 5 N 1814 2.21 5 O 1982 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 10742 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 5733 Classifications: {'peptide': 734} Link IDs: {'PTRANS': 36, 'TRANS': 697} Chain breaks: 3 Chain: "E" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 876 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain breaks: 1 Chain: "C" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1400 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 171} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 781 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1171 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 8, 'TRANS': 143} Chain: "J" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 781 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 6.79, per 1000 atoms: 0.63 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: 2.49 Conformation dependent library (CDL) restraints added in 1.4 seconds 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2576 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 16 sheets defined 28.5% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 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: 3.61 Time building geometry restraints manager: 2.92 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: 3.750 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: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.130 Find NCS groups from input model: 0.150 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.650 ------------------------------------------------------------------------------- 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 10975 Z= 0.141 Angle : 0.492 7.036 14866 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 *********************** 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 : 1.291 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: 0.2896 time to fit residues: 107.7701 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 : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 85 PHE Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 200 VAL Chi-restraints excluded: chain J residue 136 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 65 optimal weight: 20.0000 chunk 79 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 HIS A 219 HIS A 242 GLN A 258 ASN A 271 ASN ** A 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 ASN A 458 ASN A 658 HIS A 714 ASN A 742 GLN ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 496 GLN E 508 ASN G 50 ASN G 120 HIS ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 207 HIS J 91 ASN J 120 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.107927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.075626 restraints weight = 28558.840| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 4.57 r_work: 0.3114 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.071 10975 Z= 0.593 Angle : 0.822 11.146 14866 Z= 0.419 Chirality : 0.051 0.189 1684 Planarity : 0.005 0.051 1907 Dihedral : 6.714 59.575 1487 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.41 % Favored : 91.51 % Rotamer: Outliers : 5.72 % Allowed : 11.77 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.23), residues: 1355 helix: 1.26 (0.29), residues: 335 sheet: -1.37 (0.32), residues: 284 loop : -1.29 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 546 HIS 0.010 0.002 HIS A 209 PHE 0.028 0.002 PHE A 662 TYR 0.017 0.003 TYR C 118 ARG 0.007 0.001 ARG C 202 *********************** 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 : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 GLU cc_start: 0.8420 (tt0) cc_final: 0.7699 (tp30) REVERT: A 274 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8780 (tt) REVERT: A 354 ASN cc_start: 0.8147 (OUTLIER) cc_final: 0.7889 (p0) REVERT: A 596 PHE cc_start: 0.8841 (m-80) cc_final: 0.8356 (m-10) REVERT: A 643 ARG cc_start: 0.5083 (mmp-170) cc_final: 0.4870 (tpp-160) REVERT: A 670 PHE cc_start: 0.3433 (OUTLIER) cc_final: 0.3035 (m-80) REVERT: A 687 TYR cc_start: 0.7352 (m-10) cc_final: 0.7065 (m-80) REVERT: A 725 TYR cc_start: 0.6711 (t80) cc_final: 0.5596 (t80) REVERT: A 729 TYR cc_start: 0.2143 (OUTLIER) cc_final: 0.1282 (m-10) REVERT: E 454 TYR cc_start: 0.8582 (p90) cc_final: 0.8245 (p90) REVERT: E 517 MET cc_start: 0.8431 (tpp) cc_final: 0.8228 (mmm) REVERT: E 539 TYR cc_start: 0.8319 (m-80) cc_final: 0.8027 (m-80) REVERT: C 74 TYR cc_start: 0.8265 (OUTLIER) cc_final: 0.7570 (m-80) REVERT: C 107 CYS cc_start: 0.4441 (OUTLIER) cc_final: 0.4229 (t) REVERT: C 144 LYS cc_start: 0.8936 (pttt) cc_final: 0.8624 (ptpp) REVERT: C 193 ASN cc_start: 0.8238 (t0) cc_final: 0.7946 (t0) REVERT: C 198 GLN cc_start: 0.8563 (tp40) cc_final: 0.7784 (mp10) REVERT: C 240 ILE cc_start: 0.5759 (mm) cc_final: 0.5540 (mp) REVERT: G 68 MET cc_start: 0.8243 (mtp) cc_final: 0.7868 (mtm) REVERT: G 83 TYR cc_start: 0.8162 (p90) cc_final: 0.7435 (p90) REVERT: H 97 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7446 (tp30) REVERT: H 197 LYS cc_start: 0.9275 (mmtp) cc_final: 0.9004 (mmtp) REVERT: H 207 HIS cc_start: 0.7618 (OUTLIER) cc_final: 0.7346 (t-90) REVERT: J 64 ARG cc_start: 0.8031 (ttm-80) cc_final: 0.7826 (ttm-80) REVERT: J 92 ARG cc_start: 0.8359 (mtm-85) cc_final: 0.8038 (mtm-85) REVERT: J 102 ASP cc_start: 0.8624 (m-30) cc_final: 0.8063 (m-30) REVERT: J 108 ASP cc_start: 0.8919 (p0) cc_final: 0.8715 (p0) REVERT: J 112 LYS cc_start: 0.8275 (tmtt) cc_final: 0.7999 (tmmt) outliers start: 68 outliers final: 32 residues processed: 227 average time/residue: 0.2693 time to fit residues: 83.3375 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 : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 113 GLN Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 729 TYR Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain E residue 493 THR Chi-restraints excluded: chain E residue 530 CYS Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 107 CYS Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 136 CYS Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 207 HIS Chi-restraints excluded: chain J residue 136 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 57 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 49 optimal weight: 8.9990 chunk 22 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 chunk 133 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 GLN A 742 GLN E 496 GLN ** E 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN H 207 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.111907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.080030 restraints weight = 28572.165| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 4.67 r_work: 0.3188 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10975 Z= 0.185 Angle : 0.624 9.085 14866 Z= 0.313 Chirality : 0.044 0.170 1684 Planarity : 0.004 0.033 1907 Dihedral : 5.771 59.013 1481 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.31 % Favored : 94.61 % Rotamer: Outliers : 3.53 % Allowed : 14.55 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.24), residues: 1355 helix: 1.56 (0.29), residues: 342 sheet: -1.22 (0.32), residues: 280 loop : -1.17 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 612 HIS 0.010 0.001 HIS H 207 PHE 0.027 0.001 PHE A 696 TYR 0.012 0.001 TYR H 182 ARG 0.003 0.000 ARG J 64 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 184 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 MET cc_start: 0.8017 (tpt) cc_final: 0.7796 (tpt) REVERT: A 353 ASN cc_start: 0.8361 (OUTLIER) cc_final: 0.7927 (m-40) REVERT: A 449 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7684 (pt0) REVERT: A 596 PHE cc_start: 0.8855 (m-80) cc_final: 0.8336 (m-10) REVERT: A 643 ARG cc_start: 0.4718 (mmp-170) cc_final: 0.4340 (tpp-160) REVERT: A 670 PHE cc_start: 0.3241 (OUTLIER) cc_final: 0.2744 (m-80) REVERT: A 725 TYR cc_start: 0.6692 (t80) cc_final: 0.5619 (t80) REVERT: A 729 TYR cc_start: 0.1989 (OUTLIER) cc_final: 0.1302 (m-10) REVERT: E 539 TYR cc_start: 0.8175 (m-80) cc_final: 0.7810 (m-80) REVERT: C 74 TYR cc_start: 0.7780 (OUTLIER) cc_final: 0.7401 (m-80) REVERT: C 144 LYS cc_start: 0.8872 (pttt) cc_final: 0.8518 (ptpp) REVERT: C 193 ASN cc_start: 0.8156 (t0) cc_final: 0.7937 (t0) REVERT: C 198 GLN cc_start: 0.8478 (tp40) cc_final: 0.7685 (mp10) REVERT: G 68 MET cc_start: 0.7866 (mtp) cc_final: 0.7550 (mtm) REVERT: G 83 TYR cc_start: 0.8104 (p90) cc_final: 0.7088 (p90) REVERT: G 107 LYS cc_start: 0.8849 (ptpp) cc_final: 0.8526 (mttp) REVERT: G 118 TYR cc_start: 0.9057 (m-80) cc_final: 0.8648 (m-80) REVERT: H 87 ARG cc_start: 0.8509 (tpp-160) cc_final: 0.8142 (tpp-160) REVERT: H 97 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7427 (tp30) REVERT: H 148 GLN cc_start: 0.8909 (mt0) cc_final: 0.8516 (mt0) REVERT: H 197 LYS cc_start: 0.9296 (mmtp) cc_final: 0.9031 (mmtp) REVERT: J 48 LYS cc_start: 0.9140 (tppt) cc_final: 0.8817 (tmmt) REVERT: J 64 ARG cc_start: 0.7918 (ttm-80) cc_final: 0.7655 (ttm-80) REVERT: J 68 MET cc_start: 0.8436 (ptp) cc_final: 0.8197 (ptm) REVERT: J 92 ARG cc_start: 0.8151 (mtm-85) cc_final: 0.7867 (mtm-85) REVERT: J 102 ASP cc_start: 0.8768 (m-30) cc_final: 0.8473 (m-30) outliers start: 42 outliers final: 25 residues processed: 211 average time/residue: 0.2739 time to fit residues: 79.1140 Evaluate side-chains 196 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 729 TYR Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 493 THR Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 107 CYS Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain G residue 76 HIS Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 136 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 72 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 96 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 70 optimal weight: 0.0170 chunk 118 optimal weight: 4.9990 overall best weight: 0.9220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 50 ASN G 100 ASN H 207 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.111550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.079723 restraints weight = 28365.555| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 4.66 r_work: 0.3198 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10975 Z= 0.205 Angle : 0.626 9.713 14866 Z= 0.313 Chirality : 0.044 0.243 1684 Planarity : 0.004 0.034 1907 Dihedral : 5.628 57.563 1479 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.54 % Favored : 94.39 % Rotamer: Outliers : 3.78 % Allowed : 15.14 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.24), residues: 1355 helix: 1.53 (0.29), residues: 342 sheet: -1.19 (0.32), residues: 279 loop : -1.14 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 612 HIS 0.005 0.001 HIS A 209 PHE 0.041 0.001 PHE A 662 TYR 0.017 0.002 TYR A 687 ARG 0.003 0.000 ARG E 491 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 171 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 MET cc_start: 0.8085 (tpt) cc_final: 0.7800 (tpt) REVERT: A 353 ASN cc_start: 0.8397 (OUTLIER) cc_final: 0.7857 (m-40) REVERT: A 354 ASN cc_start: 0.8306 (OUTLIER) cc_final: 0.7940 (p0) REVERT: A 540 MET cc_start: 0.7126 (ptp) cc_final: 0.6893 (ptp) REVERT: A 596 PHE cc_start: 0.8825 (m-80) cc_final: 0.8270 (m-10) REVERT: A 633 ILE cc_start: 0.6422 (mm) cc_final: 0.6181 (mt) REVERT: A 643 ARG cc_start: 0.4781 (mmp-170) cc_final: 0.4380 (tpp-160) REVERT: A 670 PHE cc_start: 0.3424 (OUTLIER) cc_final: 0.2949 (m-80) REVERT: A 687 TYR cc_start: 0.7324 (m-80) cc_final: 0.6759 (m-10) REVERT: E 492 PHE cc_start: 0.8979 (m-10) cc_final: 0.8172 (m-10) REVERT: E 507 MET cc_start: 0.8983 (mmm) cc_final: 0.8781 (mmm) REVERT: E 517 MET cc_start: 0.8598 (tpp) cc_final: 0.8141 (tpp) REVERT: E 539 TYR cc_start: 0.7895 (m-80) cc_final: 0.7549 (m-80) REVERT: C 74 TYR cc_start: 0.7919 (OUTLIER) cc_final: 0.7501 (m-80) REVERT: C 144 LYS cc_start: 0.8861 (pttt) cc_final: 0.8506 (ptpp) REVERT: C 193 ASN cc_start: 0.8195 (t0) cc_final: 0.7969 (t0) REVERT: C 198 GLN cc_start: 0.8461 (tp40) cc_final: 0.7664 (mp10) REVERT: C 217 PHE cc_start: 0.7901 (m-80) cc_final: 0.7678 (m-80) REVERT: G 50 ASN cc_start: 0.8258 (OUTLIER) cc_final: 0.7985 (m110) REVERT: G 68 MET cc_start: 0.8000 (mtp) cc_final: 0.7656 (mtm) REVERT: G 83 TYR cc_start: 0.8126 (p90) cc_final: 0.7117 (p90) REVERT: G 107 LYS cc_start: 0.8832 (ptpp) cc_final: 0.8519 (mttp) REVERT: G 118 TYR cc_start: 0.9165 (m-80) cc_final: 0.8481 (m-80) REVERT: H 56 LYS cc_start: 0.8926 (mptt) cc_final: 0.7827 (tptt) REVERT: H 87 ARG cc_start: 0.8527 (tpp-160) cc_final: 0.8150 (mmm160) REVERT: H 97 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7416 (tp30) REVERT: H 148 GLN cc_start: 0.8944 (mt0) cc_final: 0.8570 (mt0) REVERT: H 197 LYS cc_start: 0.9302 (mmtp) cc_final: 0.9089 (mmtp) REVERT: J 48 LYS cc_start: 0.9134 (tppt) cc_final: 0.8844 (tmmt) REVERT: J 64 ARG cc_start: 0.7960 (ttm-80) cc_final: 0.7659 (ttm-80) REVERT: J 92 ARG cc_start: 0.8181 (mtm-85) cc_final: 0.7897 (mtm-85) REVERT: J 102 ASP cc_start: 0.8751 (m-30) cc_final: 0.8499 (m-30) REVERT: J 139 MET cc_start: 0.8153 (tpt) cc_final: 0.7751 (tpt) outliers start: 45 outliers final: 28 residues processed: 201 average time/residue: 0.2625 time to fit residues: 72.6153 Evaluate side-chains 200 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 166 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 493 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 222 PHE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain G residue 76 HIS Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 136 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 70 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 136 optimal weight: 0.5980 chunk 29 optimal weight: 4.9990 chunk 111 optimal weight: 20.0000 chunk 117 optimal weight: 0.0170 chunk 51 optimal weight: 0.7980 chunk 112 optimal weight: 5.9990 chunk 125 optimal weight: 0.7980 chunk 91 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 50 ASN H 207 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.112449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.080772 restraints weight = 28410.994| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 4.67 r_work: 0.3219 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10975 Z= 0.170 Angle : 0.600 9.209 14866 Z= 0.299 Chirality : 0.043 0.192 1684 Planarity : 0.003 0.033 1907 Dihedral : 5.404 58.722 1479 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.61 % Favored : 94.32 % Rotamer: Outliers : 3.45 % Allowed : 15.98 % Favored : 80.57 % 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: 1.60 (0.29), residues: 342 sheet: -1.12 (0.32), residues: 279 loop : -1.14 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 612 HIS 0.005 0.001 HIS A 209 PHE 0.029 0.001 PHE A 696 TYR 0.015 0.001 TYR A 687 ARG 0.003 0.000 ARG E 491 *********************** 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 218 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 177 time to evaluate : 1.180 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: 0.8141 (tpt) cc_final: 0.7815 (tpt) REVERT: A 353 ASN cc_start: 0.8383 (OUTLIER) cc_final: 0.7925 (m-40) REVERT: A 633 ILE cc_start: 0.6626 (mm) cc_final: 0.6187 (mt) REVERT: A 670 PHE cc_start: 0.3462 (OUTLIER) cc_final: 0.2919 (m-80) REVERT: A 687 TYR cc_start: 0.7453 (m-80) cc_final: 0.6753 (m-10) REVERT: A 728 LEU cc_start: 0.6140 (mt) cc_final: 0.5765 (pp) REVERT: E 492 PHE cc_start: 0.8967 (m-10) cc_final: 0.7972 (m-10) REVERT: E 507 MET cc_start: 0.8885 (mmm) cc_final: 0.8617 (mmm) REVERT: E 517 MET cc_start: 0.8639 (tpp) cc_final: 0.8208 (tpp) REVERT: C 74 TYR cc_start: 0.7830 (OUTLIER) cc_final: 0.7435 (m-80) REVERT: C 144 LYS cc_start: 0.8793 (pttt) cc_final: 0.8432 (ptpp) REVERT: C 193 ASN cc_start: 0.8190 (t0) cc_final: 0.7799 (t0) REVERT: C 197 LYS cc_start: 0.8918 (mmtt) cc_final: 0.8686 (mmtt) REVERT: C 198 GLN cc_start: 0.8410 (tp40) cc_final: 0.7902 (mp10) REVERT: G 68 MET cc_start: 0.7963 (mtp) cc_final: 0.7496 (mtm) REVERT: G 83 TYR cc_start: 0.8148 (p90) cc_final: 0.7374 (p90) REVERT: H 67 GLU cc_start: 0.9032 (tt0) cc_final: 0.8517 (mp0) REVERT: H 87 ARG cc_start: 0.8558 (tpp-160) cc_final: 0.7970 (tpp-160) REVERT: H 116 TYR cc_start: 0.8899 (m-80) cc_final: 0.8082 (m-80) REVERT: J 48 LYS cc_start: 0.8985 (tppt) cc_final: 0.8760 (tmmt) REVERT: J 64 ARG cc_start: 0.7977 (ttm-80) cc_final: 0.7696 (ttm-80) REVERT: J 92 ARG cc_start: 0.8174 (mtm-85) cc_final: 0.7899 (mtm-85) REVERT: J 114 LYS cc_start: 0.8493 (ttmm) cc_final: 0.8250 (mtpp) REVERT: J 139 MET cc_start: 0.8086 (tpt) cc_final: 0.7668 (tpt) outliers start: 41 outliers final: 25 residues processed: 202 average time/residue: 0.2587 time to fit residues: 71.9510 Evaluate side-chains 190 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 493 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 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: 6.9990 chunk 105 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 49 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 59 optimal weight: 10.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 207 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.110822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.078958 restraints weight = 28486.571| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 4.64 r_work: 0.3180 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10975 Z= 0.256 Angle : 0.644 9.689 14866 Z= 0.323 Chirality : 0.045 0.174 1684 Planarity : 0.004 0.034 1907 Dihedral : 5.244 58.783 1474 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.27 % Favored : 93.65 % Rotamer: Outliers : 4.29 % Allowed : 16.90 % Favored : 78.81 % 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: -0.76 (0.23), residues: 1355 helix: 1.37 (0.29), residues: 344 sheet: -1.16 (0.32), residues: 279 loop : -1.15 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 612 HIS 0.006 0.001 HIS A 209 PHE 0.039 0.002 PHE A 662 TYR 0.016 0.002 TYR E 452 ARG 0.003 0.000 ARG C 202 *********************** 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 218 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 167 time to evaluate : 1.244 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: 0.8719 (OUTLIER) cc_final: 0.8031 (m-40) REVERT: A 344 MET cc_start: 0.8146 (tpt) cc_final: 0.7845 (tpt) REVERT: A 353 ASN cc_start: 0.8387 (OUTLIER) cc_final: 0.8018 (m110) REVERT: A 354 ASN cc_start: 0.8313 (OUTLIER) cc_final: 0.7971 (p0) REVERT: A 633 ILE cc_start: 0.6487 (mm) cc_final: 0.6023 (mt) REVERT: A 670 PHE cc_start: 0.3482 (OUTLIER) cc_final: 0.2978 (m-80) REVERT: A 687 TYR cc_start: 0.7457 (m-80) cc_final: 0.6749 (m-10) REVERT: E 23 LEU cc_start: 0.6661 (mm) cc_final: 0.4362 (mm) REVERT: E 492 PHE cc_start: 0.9007 (m-10) cc_final: 0.8222 (m-10) REVERT: E 496 GLN cc_start: 0.8216 (tt0) cc_final: 0.7451 (tm-30) REVERT: E 507 MET cc_start: 0.8940 (mmm) cc_final: 0.8640 (mmt) REVERT: E 517 MET cc_start: 0.8712 (tpp) cc_final: 0.8337 (tpp) REVERT: C 74 TYR cc_start: 0.8006 (OUTLIER) cc_final: 0.7520 (m-80) REVERT: C 108 ASN cc_start: 0.7806 (t0) cc_final: 0.7276 (p0) REVERT: C 144 LYS cc_start: 0.8816 (pttt) cc_final: 0.8458 (ptpp) REVERT: C 193 ASN cc_start: 0.8241 (t0) cc_final: 0.7843 (t0) REVERT: C 197 LYS cc_start: 0.8963 (mmtt) cc_final: 0.8719 (mmtt) REVERT: C 198 GLN cc_start: 0.8433 (tp40) cc_final: 0.7902 (mp10) REVERT: G 68 MET cc_start: 0.8042 (mtp) cc_final: 0.7689 (mtm) REVERT: G 83 TYR cc_start: 0.8171 (p90) cc_final: 0.7739 (p90) REVERT: G 118 TYR cc_start: 0.9121 (m-80) cc_final: 0.8467 (m-80) REVERT: H 67 GLU cc_start: 0.9020 (tt0) cc_final: 0.8542 (mp0) REVERT: H 87 ARG cc_start: 0.8590 (tpp-160) cc_final: 0.8020 (tpp-160) REVERT: H 97 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7410 (tp30) REVERT: J 48 LYS cc_start: 0.8981 (tppt) cc_final: 0.8761 (tmmt) REVERT: J 64 ARG cc_start: 0.7982 (ttm-80) cc_final: 0.7715 (ttm-80) REVERT: J 92 ARG cc_start: 0.8216 (mtm-85) cc_final: 0.7940 (mtm-85) REVERT: J 112 LYS cc_start: 0.8280 (tptm) cc_final: 0.8037 (tmtt) REVERT: J 114 LYS cc_start: 0.8704 (ttmm) cc_final: 0.8381 (mtpp) REVERT: J 139 MET cc_start: 0.8079 (tpt) cc_final: 0.7672 (tpt) outliers start: 51 outliers final: 34 residues processed: 202 average time/residue: 0.2514 time to fit residues: 70.2500 Evaluate side-chains 199 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 159 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 MET 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 455 ASP Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 493 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 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 69 SER Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 136 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 55 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 133 optimal weight: 0.3980 chunk 122 optimal weight: 3.9990 chunk 94 optimal weight: 0.0020 chunk 48 optimal weight: 6.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN G 120 HIS H 207 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.112532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.080818 restraints weight = 28737.467| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 4.68 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10975 Z= 0.179 Angle : 0.635 9.737 14866 Z= 0.317 Chirality : 0.044 0.168 1684 Planarity : 0.003 0.033 1907 Dihedral : 5.036 57.392 1474 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.76 % Favored : 94.17 % Rotamer: Outliers : 4.21 % Allowed : 17.24 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.54 (0.29), residues: 344 sheet: -1.10 (0.32), residues: 279 loop : -1.10 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 612 HIS 0.005 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 *********************** 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 221 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 171 time to evaluate : 1.337 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: 0.8449 (OUTLIER) cc_final: 0.8222 (mmm) REVERT: A 344 MET cc_start: 0.7850 (tpt) cc_final: 0.7493 (tpt) REVERT: A 353 ASN cc_start: 0.8241 (OUTLIER) cc_final: 0.7393 (m-40) REVERT: A 354 ASN cc_start: 0.8308 (OUTLIER) cc_final: 0.7908 (p0) REVERT: A 670 PHE cc_start: 0.3343 (OUTLIER) cc_final: 0.2915 (m-80) REVERT: A 687 TYR cc_start: 0.7504 (m-80) cc_final: 0.6869 (m-80) REVERT: E 23 LEU cc_start: 0.5813 (mm) cc_final: 0.5014 (mm) REVERT: E 478 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8266 (pt) REVERT: E 492 PHE cc_start: 0.8812 (m-10) cc_final: 0.7798 (m-10) REVERT: E 496 GLN cc_start: 0.8004 (tt0) cc_final: 0.7528 (tm-30) REVERT: E 507 MET cc_start: 0.8896 (mmm) cc_final: 0.8512 (mmt) REVERT: E 517 MET cc_start: 0.8417 (tpp) cc_final: 0.8036 (tpp) REVERT: C 74 TYR cc_start: 0.7627 (OUTLIER) cc_final: 0.7316 (m-80) REVERT: C 108 ASN cc_start: 0.7772 (t0) cc_final: 0.7265 (p0) REVERT: C 144 LYS cc_start: 0.8744 (pttt) cc_final: 0.8362 (ptpp) REVERT: C 193 ASN cc_start: 0.8097 (t0) cc_final: 0.7663 (t0) REVERT: C 197 LYS cc_start: 0.8920 (mmtt) cc_final: 0.8659 (mmtt) REVERT: C 198 GLN cc_start: 0.8149 (tp40) cc_final: 0.7619 (mp10) REVERT: G 68 MET cc_start: 0.7720 (mtp) cc_final: 0.7412 (mtm) REVERT: G 83 TYR cc_start: 0.8243 (p90) cc_final: 0.7780 (p90) REVERT: G 108 ASP cc_start: 0.9384 (OUTLIER) cc_final: 0.9150 (p0) REVERT: G 118 TYR cc_start: 0.9246 (m-80) cc_final: 0.8554 (m-80) REVERT: H 87 ARG cc_start: 0.8603 (tpp-160) cc_final: 0.7962 (tpp-160) REVERT: H 116 TYR cc_start: 0.8844 (m-80) cc_final: 0.7962 (m-80) REVERT: J 64 ARG cc_start: 0.7746 (ttm-80) cc_final: 0.7522 (ttm-80) REVERT: J 92 ARG cc_start: 0.7891 (mtm-85) cc_final: 0.7575 (mtm-85) REVERT: J 112 LYS cc_start: 0.8083 (tptm) cc_final: 0.7826 (tmtt) REVERT: J 114 LYS cc_start: 0.8624 (ttmm) cc_final: 0.8290 (mtpp) REVERT: J 139 MET cc_start: 0.8013 (tpt) cc_final: 0.7621 (tpt) outliers start: 50 outliers final: 32 residues processed: 202 average time/residue: 0.2554 time to fit residues: 71.3303 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 : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 MET 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 455 ASP 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 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 69 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 136 CYS Chi-restraints excluded: chain H residue 167 GLN Chi-restraints excluded: chain H residue 192 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 106 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 102 optimal weight: 0.0670 chunk 71 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 119 optimal weight: 0.1980 chunk 81 optimal weight: 2.9990 overall best weight: 1.4524 ------------------------------------------------------------------------------- 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 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 HIS H 148 GLN H 207 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.110614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.078721 restraints weight = 28313.577| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 4.62 r_work: 0.3180 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10975 Z= 0.282 Angle : 0.669 9.157 14866 Z= 0.336 Chirality : 0.045 0.174 1684 Planarity : 0.004 0.035 1907 Dihedral : 5.318 57.903 1474 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.64 % Favored : 93.28 % Rotamer: Outliers : 4.21 % Allowed : 18.00 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.75 (0.23), residues: 1355 helix: 1.35 (0.29), residues: 345 sheet: -1.18 (0.32), residues: 282 loop : -1.12 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 612 HIS 0.005 0.001 HIS A 209 PHE 0.031 0.001 PHE A 696 TYR 0.027 0.002 TYR E 452 ARG 0.003 0.000 ARG C 202 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 155 time to evaluate : 1.414 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: 0.8179 (tpt) cc_final: 0.7857 (tpt) REVERT: A 353 ASN cc_start: 0.8419 (OUTLIER) cc_final: 0.7970 (m110) REVERT: A 354 ASN cc_start: 0.8268 (OUTLIER) cc_final: 0.7925 (p0) REVERT: A 670 PHE cc_start: 0.3414 (OUTLIER) cc_final: 0.2926 (m-80) REVERT: A 687 TYR cc_start: 0.7452 (m-80) cc_final: 0.6826 (m-80) REVERT: A 745 MET cc_start: 0.4727 (ttp) cc_final: 0.4412 (tmm) REVERT: E 23 LEU cc_start: 0.5659 (mm) cc_final: 0.5211 (mm) REVERT: E 478 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8305 (pt) REVERT: E 492 PHE cc_start: 0.8830 (m-10) cc_final: 0.7955 (m-10) REVERT: E 496 GLN cc_start: 0.8235 (tt0) cc_final: 0.7517 (tm-30) REVERT: E 507 MET cc_start: 0.9002 (mmm) cc_final: 0.8711 (mmt) REVERT: E 517 MET cc_start: 0.8721 (tpp) cc_final: 0.8368 (tpp) REVERT: C 108 ASN cc_start: 0.7953 (t0) cc_final: 0.7418 (p0) REVERT: C 144 LYS cc_start: 0.8830 (pttt) cc_final: 0.8466 (ptpp) REVERT: C 193 ASN cc_start: 0.8244 (t0) cc_final: 0.7825 (t0) REVERT: C 197 LYS cc_start: 0.8963 (mmtt) cc_final: 0.8711 (mmtt) REVERT: C 198 GLN cc_start: 0.8431 (tp40) cc_final: 0.7886 (mp10) REVERT: G 68 MET cc_start: 0.8044 (mtp) cc_final: 0.7693 (mtm) REVERT: G 83 TYR cc_start: 0.8180 (p90) cc_final: 0.7697 (p90) REVERT: G 118 TYR cc_start: 0.9273 (m-80) cc_final: 0.8657 (m-80) REVERT: H 57 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7080 (tt0) REVERT: H 87 ARG cc_start: 0.8586 (tpp-160) cc_final: 0.7969 (tpp-160) REVERT: H 97 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7425 (tp30) REVERT: H 144 LYS cc_start: 0.9338 (tmmt) cc_final: 0.8968 (tmmt) REVERT: H 207 HIS cc_start: 0.7533 (OUTLIER) cc_final: 0.6704 (t-90) REVERT: J 64 ARG cc_start: 0.7963 (ttm-80) cc_final: 0.7706 (ttm-80) REVERT: J 92 ARG cc_start: 0.8204 (mtm-85) cc_final: 0.7947 (mtm-85) REVERT: J 112 LYS cc_start: 0.8289 (tptm) cc_final: 0.8029 (tmtt) REVERT: J 114 LYS cc_start: 0.8755 (ttmm) cc_final: 0.8337 (mtpp) REVERT: J 127 GLU cc_start: 0.8283 (tp30) cc_final: 0.8078 (pp20) REVERT: J 139 MET cc_start: 0.8123 (tpt) cc_final: 0.7912 (tpt) outliers start: 50 outliers final: 32 residues processed: 187 average time/residue: 0.2656 time to fit residues: 68.3977 Evaluate side-chains 193 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 154 time to evaluate : 1.295 ------------------------------------------------------------------------------- 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 548 ILE Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 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 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 57 GLU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 136 CYS Chi-restraints excluded: chain H residue 167 GLN Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 207 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 109 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 8 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 28 optimal weight: 0.0570 chunk 19 optimal weight: 3.9990 overall best weight: 1.3304 ------------------------------------------------------------------------------- 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 85 HIS G 120 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.110929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.078968 restraints weight = 28589.399| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 4.65 r_work: 0.3176 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10975 Z= 0.263 Angle : 0.668 9.845 14866 Z= 0.334 Chirality : 0.045 0.175 1684 Planarity : 0.004 0.041 1907 Dihedral : 5.315 58.272 1474 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.57 % Favored : 93.36 % Rotamer: Outliers : 3.53 % Allowed : 19.01 % 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: -0.73 (0.23), residues: 1355 helix: 1.33 (0.29), residues: 345 sheet: -1.08 (0.32), residues: 267 loop : -1.14 (0.23), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 612 HIS 0.008 0.001 HIS A 209 PHE 0.032 0.001 PHE A 696 TYR 0.021 0.002 TYR E 452 ARG 0.003 0.000 ARG C 202 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2710 Ramachandran restraints generated. 1355 Oldfield, 0 Emsley, 1355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 160 time to evaluate : 1.195 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: 0.8188 (tpt) cc_final: 0.7862 (tpt) REVERT: A 353 ASN cc_start: 0.8363 (OUTLIER) cc_final: 0.7707 (m-40) REVERT: A 354 ASN cc_start: 0.8191 (OUTLIER) cc_final: 0.7819 (p0) REVERT: A 670 PHE cc_start: 0.3465 (OUTLIER) cc_final: 0.2979 (m-80) REVERT: A 687 TYR cc_start: 0.7418 (m-80) cc_final: 0.6790 (m-80) REVERT: A 745 MET cc_start: 0.4823 (ttp) cc_final: 0.4495 (tmm) REVERT: E 21 VAL cc_start: 0.8438 (t) cc_final: 0.8070 (m) REVERT: E 23 LEU cc_start: 0.5741 (mm) cc_final: 0.5328 (mm) REVERT: E 478 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8230 (pt) REVERT: E 492 PHE cc_start: 0.8690 (m-10) cc_final: 0.7808 (m-10) REVERT: E 496 GLN cc_start: 0.8217 (tt0) cc_final: 0.7557 (tm-30) REVERT: E 500 LYS cc_start: 0.9231 (pttm) cc_final: 0.8828 (tptp) REVERT: E 507 MET cc_start: 0.8974 (mmm) cc_final: 0.8679 (mmt) REVERT: E 517 MET cc_start: 0.8696 (tpp) cc_final: 0.8406 (tpp) REVERT: C 74 TYR cc_start: 0.7984 (OUTLIER) cc_final: 0.7405 (m-80) REVERT: C 108 ASN cc_start: 0.7937 (t0) cc_final: 0.7435 (p0) REVERT: C 144 LYS cc_start: 0.8831 (pttt) cc_final: 0.8472 (ptpp) REVERT: C 193 ASN cc_start: 0.8251 (t0) cc_final: 0.7834 (t0) REVERT: C 197 LYS cc_start: 0.8968 (mmtt) cc_final: 0.8723 (mmtt) REVERT: C 198 GLN cc_start: 0.8430 (tp40) cc_final: 0.7896 (mp10) REVERT: G 68 MET cc_start: 0.8024 (mtp) cc_final: 0.7666 (mtm) REVERT: G 83 TYR cc_start: 0.8278 (p90) cc_final: 0.7801 (p90) REVERT: G 118 TYR cc_start: 0.9374 (m-80) cc_final: 0.8835 (m-80) REVERT: H 67 GLU cc_start: 0.9053 (tt0) cc_final: 0.8560 (mp0) REVERT: H 87 ARG cc_start: 0.8591 (tpp-160) cc_final: 0.7987 (tpp-160) REVERT: H 97 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7350 (tp30) REVERT: H 207 HIS cc_start: 0.7091 (t70) cc_final: 0.6199 (p90) REVERT: J 64 ARG cc_start: 0.7942 (ttm-80) cc_final: 0.7686 (ttm-80) REVERT: J 92 ARG cc_start: 0.8201 (mtm-85) cc_final: 0.7949 (mtm-85) REVERT: J 112 LYS cc_start: 0.8262 (tptm) cc_final: 0.8002 (tmtt) REVERT: J 114 LYS cc_start: 0.8741 (ttmm) cc_final: 0.8392 (mtpp) REVERT: J 139 MET cc_start: 0.8095 (tpt) cc_final: 0.7691 (tpt) outliers start: 42 outliers final: 32 residues processed: 187 average time/residue: 0.2640 time to fit residues: 68.4045 Evaluate side-chains 194 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 156 time to evaluate : 1.197 ------------------------------------------------------------------------------- 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 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 167 GLN Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 200 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 116 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 85 optimal weight: 0.0770 chunk 107 optimal weight: 20.0000 chunk 88 optimal weight: 1.9990 overall best weight: 0.9940 ------------------------------------------------------------------------------- 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 206 GLN H 207 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.111619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.079714 restraints weight = 28492.927| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 4.66 r_work: 0.3186 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10975 Z= 0.223 Angle : 0.660 9.743 14866 Z= 0.329 Chirality : 0.044 0.193 1684 Planarity : 0.004 0.047 1907 Dihedral : 5.194 57.587 1474 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.42 % Favored : 93.51 % Rotamer: Outliers : 3.62 % Allowed : 19.09 % 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: -0.69 (0.23), residues: 1355 helix: 1.38 (0.29), residues: 345 sheet: -1.03 (0.33), residues: 265 loop : -1.13 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 612 HIS 0.005 0.001 HIS A 209 PHE 0.033 0.001 PHE A 696 TYR 0.017 0.002 TYR E 452 ARG 0.002 0.000 ARG C 202 ********************** 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 201 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 158 time to evaluate : 1.262 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: 0.8622 (mmt) cc_final: 0.8394 (mmm) REVERT: A 344 MET cc_start: 0.8192 (tpt) cc_final: 0.7905 (tpt) REVERT: A 353 ASN cc_start: 0.8400 (OUTLIER) cc_final: 0.7786 (m-40) REVERT: A 354 ASN cc_start: 0.8184 (OUTLIER) cc_final: 0.7808 (p0) REVERT: A 612 TRP cc_start: 0.8032 (t-100) cc_final: 0.7357 (t-100) REVERT: A 670 PHE cc_start: 0.3489 (OUTLIER) cc_final: 0.3001 (m-80) REVERT: A 687 TYR cc_start: 0.7452 (m-80) cc_final: 0.6820 (m-80) REVERT: A 745 MET cc_start: 0.4809 (ttp) cc_final: 0.4485 (tmm) REVERT: E 21 VAL cc_start: 0.8511 (t) cc_final: 0.8204 (m) REVERT: E 23 LEU cc_start: 0.5936 (mm) cc_final: 0.5626 (mm) REVERT: E 492 PHE cc_start: 0.8619 (m-10) cc_final: 0.7752 (m-10) REVERT: E 496 GLN cc_start: 0.8215 (tt0) cc_final: 0.7544 (tm-30) REVERT: E 500 LYS cc_start: 0.9254 (pttm) cc_final: 0.8792 (tptp) REVERT: E 507 MET cc_start: 0.8943 (mmm) cc_final: 0.8620 (mmt) REVERT: E 517 MET cc_start: 0.8748 (tpp) cc_final: 0.8482 (mmm) REVERT: C 74 TYR cc_start: 0.7908 (OUTLIER) cc_final: 0.7419 (m-80) REVERT: C 108 ASN cc_start: 0.7989 (t0) cc_final: 0.7485 (p0) REVERT: C 144 LYS cc_start: 0.8797 (pttt) cc_final: 0.8437 (ptpp) REVERT: C 193 ASN cc_start: 0.8236 (t0) cc_final: 0.7820 (t0) REVERT: C 197 LYS cc_start: 0.8955 (mmtt) cc_final: 0.8719 (mmtt) REVERT: C 198 GLN cc_start: 0.8400 (tp40) cc_final: 0.7866 (mp10) REVERT: G 68 MET cc_start: 0.7986 (mtp) cc_final: 0.7632 (mtm) REVERT: G 83 TYR cc_start: 0.8271 (p90) cc_final: 0.7770 (p90) REVERT: G 107 LYS cc_start: 0.9179 (mmtt) cc_final: 0.8936 (mmtt) REVERT: G 118 TYR cc_start: 0.9404 (m-80) cc_final: 0.8682 (m-80) REVERT: H 57 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7254 (tt0) REVERT: H 84 ARG cc_start: 0.7103 (tpp-160) cc_final: 0.6873 (tpp-160) REVERT: H 87 ARG cc_start: 0.8589 (tpp-160) cc_final: 0.8037 (tpp-160) REVERT: H 97 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7334 (tp30) REVERT: H 144 LYS cc_start: 0.9271 (tmmt) cc_final: 0.8899 (tmmt) REVERT: J 64 ARG cc_start: 0.7914 (ttm-80) cc_final: 0.7659 (ttm-80) REVERT: J 92 ARG cc_start: 0.8169 (mtm-85) cc_final: 0.7920 (mtm-85) REVERT: J 112 LYS cc_start: 0.8239 (tptm) cc_final: 0.7979 (tmtt) REVERT: J 114 LYS cc_start: 0.8725 (ttmm) cc_final: 0.8380 (mtpp) REVERT: J 139 MET cc_start: 0.8089 (tpt) cc_final: 0.7690 (tpt) outliers start: 43 outliers final: 31 residues processed: 186 average time/residue: 0.2676 time to fit residues: 68.3774 Evaluate side-chains 191 residues out of total 1196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 154 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 590 TYR Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 493 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 222 PHE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain G residue 76 HIS Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 97 GLU Chi-restraints excluded: chain H residue 136 CYS Chi-restraints excluded: chain H residue 167 GLN Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 200 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 58 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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** C 196 ASN G 120 HIS H 206 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.109357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.077279 restraints weight = 28263.875| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 4.60 r_work: 0.3155 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 10975 Z= 0.377 Angle : 0.728 9.984 14866 Z= 0.366 Chirality : 0.047 0.193 1684 Planarity : 0.004 0.050 1907 Dihedral : 5.622 59.585 1474 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.45 % Favored : 92.47 % Rotamer: Outliers : 3.28 % Allowed : 19.09 % Favored : 77.63 % 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: -0.90 (0.23), residues: 1355 helix: 1.10 (0.29), residues: 349 sheet: -1.17 (0.32), residues: 268 loop : -1.21 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 612 HIS 0.010 0.001 HIS A 209 PHE 0.032 0.002 PHE A 696 TYR 0.016 0.002 TYR E 452 ARG 0.004 0.000 ARG C 202 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6738.90 seconds wall clock time: 120 minutes 8.81 seconds (7208.81 seconds total)