Starting phenix.real_space_refine on Sat Jun 14 21:09:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jnx_61630/06_2025/9jnx_61630.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jnx_61630/06_2025/9jnx_61630.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jnx_61630/06_2025/9jnx_61630.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jnx_61630/06_2025/9jnx_61630.map" model { file = "/net/cci-nas-00/data/ceres_data/9jnx_61630/06_2025/9jnx_61630.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jnx_61630/06_2025/9jnx_61630.cif" } resolution = 3.0 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: 6 Type Number sf(0) Gaussians P 294 5.49 5 Mg 1 5.21 5 S 25 5.16 5 C 9692 2.51 5 N 3073 2.21 5 O 3724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16809 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 707 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 4766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4766 Classifications: {'peptide': 579} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 558} Chain breaks: 5 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.81, per 1000 atoms: 0.58 Number of scatterers: 16809 At special positions: 0 Unit cell: (106.085, 123.405, 158.045, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 25 16.00 P 294 15.00 Mg 1 11.99 O 3724 8.00 N 3073 7.00 C 9692 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 4.28 Conformation dependent library (CDL) restraints added in 1.5 seconds 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2550 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 13 sheets defined 63.2% alpha, 3.7% beta 145 base pairs and 266 stacking pairs defined. Time for finding SS restraints: 7.36 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 removed outlier: 3.736A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.503A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.773A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.698A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.453A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.610A pdb=" N GLN D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 removed outlier: 3.739A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 75 Processing helix chain 'E' and resid 76 through 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.520A pdb=" N ASP E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.581A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.119A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.509A pdb=" N ASN G 89 " --> pdb=" O LEU G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.552A pdb=" N VAL H 38 " --> pdb=" O TYR H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.877A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA H 107 " --> pdb=" O LEU H 103 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 91 removed outlier: 3.744A pdb=" N LYS K 88 " --> pdb=" O GLU K 84 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG K 89 " --> pdb=" O SER K 85 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU K 91 " --> pdb=" O LYS K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 113 removed outlier: 3.870A pdb=" N THR K 105 " --> pdb=" O ASP K 101 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LYS K 107 " --> pdb=" O GLU K 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 114 through 115 No H-bonds generated for 'chain 'K' and resid 114 through 115' Processing helix chain 'K' and resid 116 through 118 No H-bonds generated for 'chain 'K' and resid 116 through 118' Processing helix chain 'K' and resid 119 through 126 removed outlier: 4.398A pdb=" N ILE K 123 " --> pdb=" O PHE K 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 137 removed outlier: 4.399A pdb=" N GLN K 135 " --> pdb=" O LYS K 132 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL K 136 " --> pdb=" O PHE K 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 212 Processing helix chain 'K' and resid 227 through 241 Processing helix chain 'K' and resid 253 through 256 Processing helix chain 'K' and resid 257 through 268 removed outlier: 3.730A pdb=" N LEU K 261 " --> pdb=" O LEU K 257 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLU K 263 " --> pdb=" O ASN K 259 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR K 268 " --> pdb=" O ILE K 264 " (cutoff:3.500A) Processing helix chain 'K' and resid 279 through 290 Processing helix chain 'K' and resid 303 through 309 Processing helix chain 'K' and resid 334 through 342 Processing helix chain 'K' and resid 360 through 371 Processing helix chain 'K' and resid 377 through 386 Processing helix chain 'K' and resid 396 through 406 Processing helix chain 'K' and resid 434 through 446 Processing helix chain 'K' and resid 469 through 478 removed outlier: 3.715A pdb=" N ARG K 473 " --> pdb=" O MET K 469 " (cutoff:3.500A) Processing helix chain 'K' and resid 479 through 482 Processing helix chain 'K' and resid 494 through 498 removed outlier: 3.692A pdb=" N LEU K 497 " --> pdb=" O ASP K 494 " (cutoff:3.500A) Processing helix chain 'K' and resid 501 through 516 removed outlier: 3.811A pdb=" N VAL K 506 " --> pdb=" O ALA K 502 " (cutoff:3.500A) Processing helix chain 'K' and resid 527 through 541 Processing helix chain 'K' and resid 553 through 566 Processing helix chain 'K' and resid 601 through 614 removed outlier: 4.177A pdb=" N ASP K 605 " --> pdb=" O ASN K 601 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA K 612 " --> pdb=" O ALA K 608 " (cutoff:3.500A) Processing helix chain 'K' and resid 631 through 651 removed outlier: 3.913A pdb=" N LYS K 635 " --> pdb=" O SER K 631 " (cutoff:3.500A) Processing helix chain 'K' and resid 653 through 658 removed outlier: 4.392A pdb=" N SER K 657 " --> pdb=" O GLN K 653 " (cutoff:3.500A) Processing helix chain 'K' and resid 707 through 727 Processing helix chain 'K' and resid 730 through 735 removed outlier: 3.782A pdb=" N GLN K 735 " --> pdb=" O LEU K 731 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.931A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.109A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.917A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.156A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 301 through 302 removed outlier: 7.657A pdb=" N ALA K 301 " --> pdb=" O PHE K 248 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N VAL K 250 " --> pdb=" O ALA K 301 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ILE K 321 " --> pdb=" O LEU K 349 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ILE K 351 " --> pdb=" O ILE K 321 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ILE K 323 " --> pdb=" O ILE K 351 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE K 218 " --> pdb=" O LEU K 410 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 427 through 431 removed outlier: 6.335A pdb=" N LEU K 427 " --> pdb=" O ARG K 625 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N VAL K 627 " --> pdb=" O LEU K 427 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N LEU K 429 " --> pdb=" O VAL K 627 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 547 through 548 577 hydrogen bonds defined for protein. 1689 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 372 hydrogen bonds 744 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 266 stacking parallelities Total time for adding SS restraints: 8.76 Time building geometry restraints manager: 5.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3045 1.33 - 1.45: 5354 1.45 - 1.57: 8680 1.57 - 1.69: 585 1.69 - 1.81: 43 Bond restraints: 17707 Sorted by residual: bond pdb=" CA GLU K 418 " pdb=" C GLU K 418 " ideal model delta sigma weight residual 1.523 1.458 0.065 1.34e-02 5.57e+03 2.33e+01 bond pdb=" CA LEU K 422 " pdb=" C LEU K 422 " ideal model delta sigma weight residual 1.523 1.484 0.039 1.38e-02 5.25e+03 8.12e+00 bond pdb=" N GLU K 418 " pdb=" CA GLU K 418 " ideal model delta sigma weight residual 1.457 1.423 0.035 1.29e-02 6.01e+03 7.31e+00 bond pdb=" CA LEU K 421 " pdb=" C LEU K 421 " ideal model delta sigma weight residual 1.523 1.489 0.033 1.23e-02 6.61e+03 7.24e+00 bond pdb=" N SER K 420 " pdb=" CA SER K 420 " ideal model delta sigma weight residual 1.457 1.424 0.033 1.29e-02 6.01e+03 6.64e+00 ... (remaining 17702 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 24106 1.54 - 3.09: 909 3.09 - 4.63: 118 4.63 - 6.18: 34 6.18 - 7.72: 6 Bond angle restraints: 25173 Sorted by residual: angle pdb=" C GLU K 418 " pdb=" CA GLU K 418 " pdb=" CB GLU K 418 " ideal model delta sigma weight residual 110.42 103.31 7.11 1.99e+00 2.53e-01 1.28e+01 angle pdb=" N GLY D 101 " pdb=" CA GLY D 101 " pdb=" C GLY D 101 " ideal model delta sigma weight residual 110.77 116.70 -5.93 1.93e+00 2.68e-01 9.43e+00 angle pdb=" C ARG F 23 " pdb=" N ASP F 24 " pdb=" CA ASP F 24 " ideal model delta sigma weight residual 121.54 127.18 -5.64 1.91e+00 2.74e-01 8.72e+00 angle pdb=" C HIS B 18 " pdb=" N ARG B 19 " pdb=" CA ARG B 19 " ideal model delta sigma weight residual 121.54 126.75 -5.21 1.91e+00 2.74e-01 7.43e+00 angle pdb=" N PRO K 489 " pdb=" CA PRO K 489 " pdb=" C PRO K 489 " ideal model delta sigma weight residual 110.70 113.97 -3.27 1.22e+00 6.72e-01 7.18e+00 ... (remaining 25168 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.12: 8434 35.12 - 70.24: 1455 70.24 - 105.36: 30 105.36 - 140.49: 5 140.49 - 175.61: 9 Dihedral angle restraints: 9933 sinusoidal: 6000 harmonic: 3933 Sorted by residual: dihedral pdb=" CA LEU B 22 " pdb=" C LEU B 22 " pdb=" N ARG B 23 " pdb=" CA ARG B 23 " ideal model delta harmonic sigma weight residual 180.00 -144.53 -35.47 0 5.00e+00 4.00e-02 5.03e+01 dihedral pdb=" CA TYR K 545 " pdb=" C TYR K 545 " pdb=" N CYS K 546 " pdb=" CA CYS K 546 " ideal model delta harmonic sigma weight residual 180.00 146.23 33.77 0 5.00e+00 4.00e-02 4.56e+01 dihedral pdb=" CA HIS B 18 " pdb=" C HIS B 18 " pdb=" N ARG B 19 " pdb=" CA ARG B 19 " ideal model delta harmonic sigma weight residual -180.00 -150.83 -29.17 0 5.00e+00 4.00e-02 3.40e+01 ... (remaining 9930 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2502 0.058 - 0.117: 317 0.117 - 0.175: 31 0.175 - 0.233: 0 0.233 - 0.291: 2 Chirality restraints: 2852 Sorted by residual: chirality pdb=" CB ILE K 329 " pdb=" CA ILE K 329 " pdb=" CG1 ILE K 329 " pdb=" CG2 ILE K 329 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CB ILE K 548 " pdb=" CA ILE K 548 " pdb=" CG1 ILE K 548 " pdb=" CG2 ILE K 548 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" P DG I 99 " pdb=" OP1 DG I 99 " pdb=" OP2 DG I 99 " pdb=" O5' DG I 99 " both_signs ideal model delta sigma weight residual True 2.35 -2.50 -0.16 2.00e-01 2.50e+01 6.07e-01 ... (remaining 2849 not shown) Planarity restraints: 2181 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO K 489 " -0.034 5.00e-02 4.00e+02 5.16e-02 4.26e+00 pdb=" N PRO K 490 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO K 490 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO K 490 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP K 82 " 0.028 5.00e-02 4.00e+02 4.30e-02 2.95e+00 pdb=" N PRO K 83 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO K 83 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO K 83 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 39 " 0.023 2.00e-02 2.50e+03 1.02e-02 2.86e+00 pdb=" N9 DA I 39 " -0.021 2.00e-02 2.50e+03 pdb=" C8 DA I 39 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DA I 39 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DA I 39 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA I 39 " 0.002 2.00e-02 2.50e+03 pdb=" N6 DA I 39 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DA I 39 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DA I 39 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DA I 39 " -0.006 2.00e-02 2.50e+03 pdb=" C4 DA I 39 " -0.002 2.00e-02 2.50e+03 ... (remaining 2178 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 129 2.57 - 3.15: 13377 3.15 - 3.74: 29126 3.74 - 4.32: 40111 4.32 - 4.90: 59563 Nonbonded interactions: 142306 Sorted by model distance: nonbonded pdb="MG MG K1201 " pdb=" O2B ADP K1202 " model vdw 1.990 2.170 nonbonded pdb="MG MG K1201 " pdb=" O3A ADP K1202 " model vdw 2.074 2.170 nonbonded pdb=" O PHE K 122 " pdb=" OG SER K 125 " model vdw 2.135 3.040 nonbonded pdb=" O VAL K 398 " pdb=" ND1 HIS K 402 " model vdw 2.158 3.120 nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 65 " model vdw 2.178 3.040 ... (remaining 142301 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 'A' and resid 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and ((resid 17 and (name N or name CA or name C or name O or name CB \ )) or resid 18 or (resid 19 through 20 and (name N or name CA or name C or name \ O or name CB )) or resid 21 through 22 or (resid 23 and (name N or name CA or na \ me C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and resid 17 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } 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: 1.600 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: 0.020 Extract box with map and model: 0.670 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 46.560 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.090 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: 0.020 Load rotamer database and sin/cos tables:14.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 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 : 0.006 0.065 17707 Z= 0.258 Angle : 0.690 7.720 25173 Z= 0.397 Chirality : 0.040 0.291 2852 Planarity : 0.004 0.052 2181 Dihedral : 26.304 175.607 7383 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.28 % Favored : 92.56 % Rotamer: Outliers : 0.17 % Allowed : 0.43 % Favored : 99.39 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.07 (0.23), residues: 1318 helix: 1.19 (0.19), residues: 775 sheet: -1.81 (0.72), residues: 63 loop : -1.91 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP K 260 HIS 0.007 0.001 HIS A 39 PHE 0.025 0.002 PHE K 524 TYR 0.017 0.002 TYR K 320 ARG 0.006 0.001 ARG D 83 Details of bonding type rmsd hydrogen bonds : bond 0.11607 ( 949) hydrogen bonds : angle 4.47714 ( 2433) covalent geometry : bond 0.00570 (17707) covalent geometry : angle 0.68952 (25173) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 188 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8237 (tt0) cc_final: 0.7869 (tt0) REVERT: A 76 GLN cc_start: 0.8317 (pp30) cc_final: 0.8080 (pp30) REVERT: F 25 ASN cc_start: 0.9039 (m-40) cc_final: 0.8460 (m-40) REVERT: F 79 LYS cc_start: 0.8847 (mttp) cc_final: 0.8615 (mttm) REVERT: K 93 LYS cc_start: 0.6321 (mttm) cc_final: 0.5905 (pmtt) REVERT: K 377 ASP cc_start: 0.8612 (m-30) cc_final: 0.8279 (m-30) REVERT: K 418 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6896 (mp0) REVERT: K 525 SER cc_start: 0.8821 (t) cc_final: 0.8604 (p) REVERT: K 645 ARG cc_start: 0.8595 (tpp80) cc_final: 0.8140 (tpp80) REVERT: K 717 ASN cc_start: 0.8213 (m-40) cc_final: 0.8013 (t0) outliers start: 2 outliers final: 1 residues processed: 190 average time/residue: 1.9022 time to fit residues: 389.6038 Evaluate side-chains 147 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 145 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 418 GLU Chi-restraints excluded: chain K residue 420 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN B 25 ASN E 68 GLN F 93 GLN G 38 ASN K 86 ASN ** K 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 774 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.087874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.061924 restraints weight = 44703.329| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.26 r_work: 0.2873 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.0956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 17707 Z= 0.207 Angle : 0.647 7.052 25173 Z= 0.361 Chirality : 0.039 0.183 2852 Planarity : 0.005 0.051 2181 Dihedral : 30.185 175.590 4683 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.53 % Favored : 93.40 % Rotamer: Outliers : 1.21 % Allowed : 10.40 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.50 (0.24), residues: 1318 helix: 1.62 (0.18), residues: 792 sheet: -1.64 (0.73), residues: 63 loop : -1.72 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 364 HIS 0.007 0.001 HIS A 39 PHE 0.020 0.001 PHE K 524 TYR 0.013 0.002 TYR F 51 ARG 0.006 0.000 ARG H 76 Details of bonding type rmsd hydrogen bonds : bond 0.04569 ( 949) hydrogen bonds : angle 3.29660 ( 2433) covalent geometry : bond 0.00471 (17707) covalent geometry : angle 0.64675 (25173) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 170 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8852 (tt0) cc_final: 0.8375 (tt0) REVERT: A 76 GLN cc_start: 0.8691 (pp30) cc_final: 0.8389 (pp30) REVERT: A 120 MET cc_start: 0.8793 (mtm) cc_final: 0.8567 (mtt) REVERT: A 133 GLU cc_start: 0.8528 (mp0) cc_final: 0.8222 (mp0) REVERT: C 64 GLU cc_start: 0.8667 (tt0) cc_final: 0.8417 (pt0) REVERT: D 102 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8499 (mm-30) REVERT: E 59 GLU cc_start: 0.8975 (pm20) cc_final: 0.8716 (pm20) REVERT: F 25 ASN cc_start: 0.9185 (m-40) cc_final: 0.8564 (m-40) REVERT: G 92 GLU cc_start: 0.8659 (pt0) cc_final: 0.8421 (mt-10) REVERT: H 65 ASP cc_start: 0.8835 (t0) cc_final: 0.8619 (t0) REVERT: K 93 LYS cc_start: 0.6884 (mttm) cc_final: 0.6396 (pmtt) REVERT: K 525 SER cc_start: 0.9038 (t) cc_final: 0.8818 (p) REVERT: K 645 ARG cc_start: 0.8964 (tpp80) cc_final: 0.8429 (tpp80) REVERT: K 717 ASN cc_start: 0.8395 (m-40) cc_final: 0.8191 (t0) REVERT: K 726 TYR cc_start: 0.6441 (t80) cc_final: 0.6074 (t80) outliers start: 14 outliers final: 5 residues processed: 176 average time/residue: 1.8559 time to fit residues: 352.5912 Evaluate side-chains 152 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 146 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain K residue 538 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 126 optimal weight: 0.4980 chunk 96 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 121 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 137 optimal weight: 9.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN E 68 GLN G 38 ASN K 617 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.088247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.062171 restraints weight = 44082.324| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.24 r_work: 0.2879 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17707 Z= 0.195 Angle : 0.627 7.935 25173 Z= 0.351 Chirality : 0.038 0.164 2852 Planarity : 0.004 0.053 2181 Dihedral : 30.165 175.754 4679 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.30 % Favored : 93.63 % Rotamer: Outliers : 2.34 % Allowed : 12.91 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.70 (0.24), residues: 1318 helix: 1.80 (0.19), residues: 797 sheet: -1.72 (0.73), residues: 65 loop : -1.69 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 364 HIS 0.007 0.001 HIS K 111 PHE 0.019 0.001 PHE K 737 TYR 0.013 0.001 TYR K 545 ARG 0.007 0.000 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.04271 ( 949) hydrogen bonds : angle 3.14021 ( 2433) covalent geometry : bond 0.00444 (17707) covalent geometry : angle 0.62730 (25173) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8860 (tt0) cc_final: 0.8386 (tt0) REVERT: A 76 GLN cc_start: 0.8690 (pp30) cc_final: 0.8367 (pp30) REVERT: A 120 MET cc_start: 0.8782 (mtm) cc_final: 0.8529 (mtt) REVERT: A 133 GLU cc_start: 0.8488 (mp0) cc_final: 0.8174 (mp0) REVERT: C 64 GLU cc_start: 0.8687 (tt0) cc_final: 0.8369 (pt0) REVERT: C 95 LYS cc_start: 0.9224 (tttp) cc_final: 0.8935 (ttmm) REVERT: C 110 ASN cc_start: 0.9170 (OUTLIER) cc_final: 0.8503 (p0) REVERT: E 59 GLU cc_start: 0.8947 (pm20) cc_final: 0.8652 (pm20) REVERT: F 25 ASN cc_start: 0.9180 (m-40) cc_final: 0.8533 (m-40) REVERT: H 65 ASP cc_start: 0.8848 (t0) cc_final: 0.8588 (t0) REVERT: K 93 LYS cc_start: 0.6917 (mttm) cc_final: 0.6449 (pmtt) REVERT: K 525 SER cc_start: 0.8967 (t) cc_final: 0.8696 (p) REVERT: K 645 ARG cc_start: 0.8943 (tpp80) cc_final: 0.8434 (tpp80) REVERT: K 717 ASN cc_start: 0.8383 (m-40) cc_final: 0.8091 (m-40) outliers start: 27 outliers final: 13 residues processed: 177 average time/residue: 1.7073 time to fit residues: 327.7138 Evaluate side-chains 159 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 133 PHE Chi-restraints excluded: chain K residue 386 SER Chi-restraints excluded: chain K residue 538 CYS Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain K residue 647 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 34 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 61 optimal weight: 0.0970 chunk 14 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN E 68 GLN G 38 ASN ** K 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.089804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.063675 restraints weight = 44161.662| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.25 r_work: 0.2919 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17707 Z= 0.149 Angle : 0.600 10.033 25173 Z= 0.336 Chirality : 0.036 0.156 2852 Planarity : 0.004 0.055 2181 Dihedral : 29.987 175.825 4679 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.92 % Favored : 94.01 % Rotamer: Outliers : 2.34 % Allowed : 14.47 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.99 (0.24), residues: 1318 helix: 2.04 (0.19), residues: 799 sheet: -1.63 (0.75), residues: 65 loop : -1.60 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 364 HIS 0.009 0.001 HIS K 111 PHE 0.012 0.001 PHE K 524 TYR 0.010 0.001 TYR K 545 ARG 0.005 0.000 ARG K 108 Details of bonding type rmsd hydrogen bonds : bond 0.03652 ( 949) hydrogen bonds : angle 2.90576 ( 2433) covalent geometry : bond 0.00331 (17707) covalent geometry : angle 0.60036 (25173) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 167 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8829 (tt0) cc_final: 0.8339 (tt0) REVERT: A 76 GLN cc_start: 0.8646 (pp30) cc_final: 0.8326 (pp30) REVERT: A 120 MET cc_start: 0.8693 (mtm) cc_final: 0.8489 (mtt) REVERT: A 133 GLU cc_start: 0.8564 (mp0) cc_final: 0.8233 (mp0) REVERT: C 64 GLU cc_start: 0.8699 (tt0) cc_final: 0.8370 (pt0) REVERT: C 91 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7826 (tm-30) REVERT: C 95 LYS cc_start: 0.9191 (tttp) cc_final: 0.8988 (ttmt) REVERT: C 110 ASN cc_start: 0.9133 (t0) cc_final: 0.8510 (p0) REVERT: E 59 GLU cc_start: 0.8867 (pm20) cc_final: 0.8565 (pm20) REVERT: F 25 ASN cc_start: 0.9195 (m-40) cc_final: 0.8543 (m-40) REVERT: H 65 ASP cc_start: 0.8803 (t0) cc_final: 0.8499 (t0) REVERT: K 93 LYS cc_start: 0.6906 (mttm) cc_final: 0.6483 (pmtt) REVERT: K 299 VAL cc_start: 0.9121 (OUTLIER) cc_final: 0.8916 (t) REVERT: K 525 SER cc_start: 0.8914 (t) cc_final: 0.8639 (p) REVERT: K 645 ARG cc_start: 0.8922 (tpp80) cc_final: 0.8362 (tpp80) REVERT: K 717 ASN cc_start: 0.8368 (m-40) cc_final: 0.8078 (m-40) outliers start: 27 outliers final: 11 residues processed: 184 average time/residue: 1.8196 time to fit residues: 364.1370 Evaluate side-chains 161 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 133 PHE Chi-restraints excluded: chain K residue 299 VAL Chi-restraints excluded: chain K residue 386 SER Chi-restraints excluded: chain K residue 538 CYS Chi-restraints excluded: chain K residue 546 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 151 optimal weight: 0.0870 chunk 134 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 105 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 125 optimal weight: 9.9990 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN E 68 GLN G 38 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 505 GLN K 723 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.086303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.060001 restraints weight = 45054.323| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.29 r_work: 0.2826 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 17707 Z= 0.309 Angle : 0.680 7.627 25173 Z= 0.376 Chirality : 0.041 0.164 2852 Planarity : 0.005 0.054 2181 Dihedral : 30.437 176.005 4679 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.90 % Favored : 93.02 % Rotamer: Outliers : 2.95 % Allowed : 16.20 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.68 (0.24), residues: 1318 helix: 1.77 (0.18), residues: 798 sheet: -1.87 (0.72), residues: 65 loop : -1.64 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 384 HIS 0.008 0.001 HIS K 111 PHE 0.022 0.002 PHE K 737 TYR 0.013 0.002 TYR G 50 ARG 0.005 0.001 ARG H 83 Details of bonding type rmsd hydrogen bonds : bond 0.05244 ( 949) hydrogen bonds : angle 3.23050 ( 2433) covalent geometry : bond 0.00714 (17707) covalent geometry : angle 0.67968 (25173) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 152 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8841 (tt0) cc_final: 0.8371 (tt0) REVERT: A 76 GLN cc_start: 0.8764 (pp30) cc_final: 0.8425 (pp30) REVERT: A 120 MET cc_start: 0.8884 (mtm) cc_final: 0.8663 (mtt) REVERT: A 133 GLU cc_start: 0.8545 (mp0) cc_final: 0.8087 (mp0) REVERT: C 91 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7923 (tm-30) REVERT: C 95 LYS cc_start: 0.9229 (tttp) cc_final: 0.8965 (ttmt) REVERT: C 110 ASN cc_start: 0.9177 (OUTLIER) cc_final: 0.8454 (p0) REVERT: E 59 GLU cc_start: 0.8891 (pm20) cc_final: 0.8579 (pm20) REVERT: F 25 ASN cc_start: 0.9197 (m-40) cc_final: 0.8559 (m-40) REVERT: H 65 ASP cc_start: 0.8945 (t0) cc_final: 0.8656 (t0) REVERT: K 93 LYS cc_start: 0.6862 (mttm) cc_final: 0.6469 (pmtt) REVERT: K 525 SER cc_start: 0.8983 (t) cc_final: 0.8666 (p) REVERT: K 717 ASN cc_start: 0.8415 (m-40) cc_final: 0.8128 (m-40) outliers start: 34 outliers final: 17 residues processed: 172 average time/residue: 1.9090 time to fit residues: 356.6805 Evaluate side-chains 165 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 3.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 133 PHE Chi-restraints excluded: chain K residue 263 GLU Chi-restraints excluded: chain K residue 475 CYS Chi-restraints excluded: chain K residue 538 CYS Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain K residue 548 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 145 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 18 optimal weight: 0.4980 chunk 147 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN E 68 GLN G 38 ASN K 205 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.088038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.061827 restraints weight = 44300.997| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.24 r_work: 0.2872 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17707 Z= 0.183 Angle : 0.620 7.452 25173 Z= 0.347 Chirality : 0.037 0.155 2852 Planarity : 0.004 0.055 2181 Dihedral : 30.171 176.214 4679 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.07 % Favored : 93.85 % Rotamer: Outliers : 2.51 % Allowed : 17.59 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.82 (0.24), residues: 1318 helix: 1.85 (0.18), residues: 806 sheet: -1.87 (0.72), residues: 65 loop : -1.56 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 364 HIS 0.007 0.001 HIS K 111 PHE 0.012 0.001 PHE E 67 TYR 0.014 0.001 TYR K 545 ARG 0.005 0.000 ARG H 83 Details of bonding type rmsd hydrogen bonds : bond 0.04078 ( 949) hydrogen bonds : angle 3.01168 ( 2433) covalent geometry : bond 0.00416 (17707) covalent geometry : angle 0.62014 (25173) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 155 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8834 (tt0) cc_final: 0.8364 (tt0) REVERT: A 76 GLN cc_start: 0.8710 (pp30) cc_final: 0.8363 (pp30) REVERT: A 120 MET cc_start: 0.8762 (mtm) cc_final: 0.8528 (mtt) REVERT: A 133 GLU cc_start: 0.8519 (mp0) cc_final: 0.8089 (mp0) REVERT: C 64 GLU cc_start: 0.8701 (tt0) cc_final: 0.8432 (pt0) REVERT: C 91 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7954 (tm-30) REVERT: C 95 LYS cc_start: 0.9214 (tttp) cc_final: 0.8956 (ttmt) REVERT: C 110 ASN cc_start: 0.9147 (OUTLIER) cc_final: 0.8514 (p0) REVERT: E 59 GLU cc_start: 0.8864 (pm20) cc_final: 0.8559 (pm20) REVERT: F 25 ASN cc_start: 0.9190 (m-40) cc_final: 0.8552 (m-40) REVERT: H 65 ASP cc_start: 0.8871 (t0) cc_final: 0.8594 (t0) REVERT: K 93 LYS cc_start: 0.6813 (mttm) cc_final: 0.6444 (pmtt) REVERT: K 525 SER cc_start: 0.8971 (t) cc_final: 0.8657 (p) REVERT: K 645 ARG cc_start: 0.8716 (tpp80) cc_final: 0.8464 (tpp80) REVERT: K 717 ASN cc_start: 0.8351 (m-40) cc_final: 0.8123 (t0) outliers start: 29 outliers final: 15 residues processed: 171 average time/residue: 2.0083 time to fit residues: 372.4053 Evaluate side-chains 163 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 133 PHE Chi-restraints excluded: chain K residue 538 CYS Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain K residue 548 ILE Chi-restraints excluded: chain K residue 706 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 16 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 55 optimal weight: 0.3980 chunk 144 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 126 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 153 optimal weight: 9.9990 chunk 111 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN E 68 GLN G 38 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.089479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.063281 restraints weight = 44156.174| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.26 r_work: 0.2909 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17707 Z= 0.152 Angle : 0.613 11.983 25173 Z= 0.340 Chirality : 0.036 0.148 2852 Planarity : 0.004 0.057 2181 Dihedral : 29.998 176.144 4679 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.92 % Favored : 94.01 % Rotamer: Outliers : 2.34 % Allowed : 18.11 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.10 (0.24), residues: 1318 helix: 2.03 (0.19), residues: 806 sheet: -0.91 (0.82), residues: 53 loop : -1.52 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 364 HIS 0.007 0.001 HIS K 111 PHE 0.025 0.001 PHE K 737 TYR 0.010 0.001 TYR K 726 ARG 0.006 0.000 ARG H 83 Details of bonding type rmsd hydrogen bonds : bond 0.03588 ( 949) hydrogen bonds : angle 2.88950 ( 2433) covalent geometry : bond 0.00340 (17707) covalent geometry : angle 0.61343 (25173) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8818 (tt0) cc_final: 0.8356 (tt0) REVERT: A 76 GLN cc_start: 0.8661 (pp30) cc_final: 0.8323 (pp30) REVERT: A 120 MET cc_start: 0.8675 (mtm) cc_final: 0.8459 (mtt) REVERT: A 133 GLU cc_start: 0.8554 (mp0) cc_final: 0.8276 (mp0) REVERT: C 64 GLU cc_start: 0.8704 (tt0) cc_final: 0.8433 (pt0) REVERT: C 91 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7944 (tm-30) REVERT: C 95 LYS cc_start: 0.9194 (tttp) cc_final: 0.8932 (ttmt) REVERT: C 110 ASN cc_start: 0.9143 (t0) cc_final: 0.8576 (p0) REVERT: E 59 GLU cc_start: 0.8800 (pm20) cc_final: 0.8474 (pm20) REVERT: F 25 ASN cc_start: 0.9194 (m-40) cc_final: 0.8542 (m-40) REVERT: H 48 ASP cc_start: 0.8831 (p0) cc_final: 0.8506 (p0) REVERT: H 65 ASP cc_start: 0.8827 (t0) cc_final: 0.8547 (t0) REVERT: K 93 LYS cc_start: 0.6789 (mttm) cc_final: 0.6419 (pmtt) REVERT: K 525 SER cc_start: 0.8911 (t) cc_final: 0.8584 (p) REVERT: K 645 ARG cc_start: 0.8674 (tpp80) cc_final: 0.8228 (tpp80) REVERT: K 717 ASN cc_start: 0.8351 (m-40) cc_final: 0.8064 (m-40) outliers start: 27 outliers final: 16 residues processed: 174 average time/residue: 1.7337 time to fit residues: 327.4139 Evaluate side-chains 167 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 133 PHE Chi-restraints excluded: chain K residue 386 SER Chi-restraints excluded: chain K residue 538 CYS Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain K residue 548 ILE Chi-restraints excluded: chain K residue 706 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 106 optimal weight: 0.7980 chunk 99 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 59 optimal weight: 0.4980 chunk 19 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 147 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 chunk 119 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN E 68 GLN G 38 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.090315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.064423 restraints weight = 44000.233| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.25 r_work: 0.2934 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17707 Z= 0.145 Angle : 0.601 12.008 25173 Z= 0.334 Chirality : 0.036 0.146 2852 Planarity : 0.004 0.057 2181 Dihedral : 29.865 176.376 4679 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.46 % Favored : 94.46 % Rotamer: Outliers : 1.91 % Allowed : 19.06 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.18 (0.24), residues: 1318 helix: 2.11 (0.18), residues: 807 sheet: -1.34 (0.88), residues: 41 loop : -1.47 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 364 HIS 0.007 0.001 HIS K 111 PHE 0.012 0.001 PHE E 67 TYR 0.009 0.001 TYR C 57 ARG 0.010 0.000 ARG H 83 Details of bonding type rmsd hydrogen bonds : bond 0.03479 ( 949) hydrogen bonds : angle 2.82234 ( 2433) covalent geometry : bond 0.00322 (17707) covalent geometry : angle 0.60097 (25173) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8790 (tt0) cc_final: 0.8297 (tt0) REVERT: A 76 GLN cc_start: 0.8645 (pp30) cc_final: 0.8305 (pp30) REVERT: A 120 MET cc_start: 0.8657 (mtm) cc_final: 0.8444 (mtt) REVERT: A 133 GLU cc_start: 0.8472 (mp0) cc_final: 0.8236 (mp0) REVERT: C 64 GLU cc_start: 0.8734 (tt0) cc_final: 0.8439 (pt0) REVERT: C 72 ASP cc_start: 0.8619 (m-30) cc_final: 0.8389 (t0) REVERT: C 91 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7958 (tm-30) REVERT: C 95 LYS cc_start: 0.9189 (tttp) cc_final: 0.8933 (ttmt) REVERT: C 110 ASN cc_start: 0.9102 (t0) cc_final: 0.8607 (p0) REVERT: E 59 GLU cc_start: 0.8754 (pm20) cc_final: 0.8419 (pm20) REVERT: F 25 ASN cc_start: 0.9199 (m-40) cc_final: 0.8546 (m-40) REVERT: H 65 ASP cc_start: 0.8819 (t0) cc_final: 0.8539 (t0) REVERT: K 93 LYS cc_start: 0.6821 (mttm) cc_final: 0.6411 (pmtt) REVERT: K 525 SER cc_start: 0.8864 (t) cc_final: 0.8526 (p) REVERT: K 645 ARG cc_start: 0.8701 (tpp80) cc_final: 0.8116 (tpp80) REVERT: K 717 ASN cc_start: 0.8357 (m-40) cc_final: 0.8129 (t0) outliers start: 22 outliers final: 13 residues processed: 175 average time/residue: 1.7590 time to fit residues: 334.6690 Evaluate side-chains 161 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 133 PHE Chi-restraints excluded: chain K residue 538 CYS Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain K residue 548 ILE Chi-restraints excluded: chain K residue 706 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 81 optimal weight: 4.9990 chunk 125 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 chunk 127 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 126 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 122 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN E 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.089575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.063503 restraints weight = 44296.476| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.26 r_work: 0.2908 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17707 Z= 0.168 Angle : 0.619 10.779 25173 Z= 0.341 Chirality : 0.036 0.144 2852 Planarity : 0.004 0.057 2181 Dihedral : 29.882 176.558 4679 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.84 % Favored : 94.08 % Rotamer: Outliers : 1.82 % Allowed : 19.67 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.17 (0.24), residues: 1318 helix: 2.09 (0.18), residues: 806 sheet: -1.38 (0.88), residues: 41 loop : -1.42 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 364 HIS 0.007 0.001 HIS K 111 PHE 0.021 0.001 PHE K 737 TYR 0.010 0.001 TYR K 726 ARG 0.006 0.000 ARG D 83 Details of bonding type rmsd hydrogen bonds : bond 0.03742 ( 949) hydrogen bonds : angle 2.87437 ( 2433) covalent geometry : bond 0.00381 (17707) covalent geometry : angle 0.61858 (25173) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8806 (tt0) cc_final: 0.8341 (tt0) REVERT: A 76 GLN cc_start: 0.8681 (pp30) cc_final: 0.8349 (pp30) REVERT: A 120 MET cc_start: 0.8710 (mtm) cc_final: 0.8499 (mtt) REVERT: A 133 GLU cc_start: 0.8384 (mp0) cc_final: 0.8170 (mp0) REVERT: C 72 ASP cc_start: 0.8630 (m-30) cc_final: 0.8393 (t0) REVERT: C 91 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7953 (tm-30) REVERT: C 92 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8412 (mm-30) REVERT: C 95 LYS cc_start: 0.9192 (tttp) cc_final: 0.8927 (ttmt) REVERT: C 110 ASN cc_start: 0.9119 (t0) cc_final: 0.8657 (p0) REVERT: E 59 GLU cc_start: 0.8789 (pm20) cc_final: 0.8426 (pm20) REVERT: F 25 ASN cc_start: 0.9211 (m-40) cc_final: 0.8560 (m-40) REVERT: H 65 ASP cc_start: 0.8862 (t0) cc_final: 0.8535 (t0) REVERT: H 83 ARG cc_start: 0.8950 (mmt90) cc_final: 0.8719 (mpt-90) REVERT: K 93 LYS cc_start: 0.6839 (mttm) cc_final: 0.6433 (pmtt) REVERT: K 525 SER cc_start: 0.8871 (t) cc_final: 0.8539 (p) REVERT: K 645 ARG cc_start: 0.8727 (tpp80) cc_final: 0.8167 (tpp80) REVERT: K 717 ASN cc_start: 0.8413 (m-40) cc_final: 0.8186 (t0) outliers start: 21 outliers final: 13 residues processed: 165 average time/residue: 1.7148 time to fit residues: 307.1597 Evaluate side-chains 162 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 149 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 133 PHE Chi-restraints excluded: chain K residue 538 CYS Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain K residue 548 ILE Chi-restraints excluded: chain K residue 706 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 121 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 149 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 61 optimal weight: 0.0670 chunk 21 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN E 68 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.089944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.063672 restraints weight = 44111.938| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.27 r_work: 0.2915 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17707 Z= 0.157 Angle : 0.624 11.050 25173 Z= 0.343 Chirality : 0.036 0.144 2852 Planarity : 0.004 0.056 2181 Dihedral : 29.854 176.661 4679 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.77 % Favored : 94.16 % Rotamer: Outliers : 1.56 % Allowed : 19.93 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.14 (0.24), residues: 1318 helix: 2.10 (0.18), residues: 806 sheet: -2.42 (0.73), residues: 53 loop : -1.37 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 364 HIS 0.007 0.001 HIS K 111 PHE 0.014 0.001 PHE E 67 TYR 0.018 0.001 TYR K 545 ARG 0.006 0.000 ARG D 83 Details of bonding type rmsd hydrogen bonds : bond 0.03631 ( 949) hydrogen bonds : angle 2.85808 ( 2433) covalent geometry : bond 0.00355 (17707) covalent geometry : angle 0.62367 (25173) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 1.461 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8818 (tt0) cc_final: 0.8328 (tt0) REVERT: A 76 GLN cc_start: 0.8672 (pp30) cc_final: 0.8338 (pp30) REVERT: A 133 GLU cc_start: 0.8367 (mp0) cc_final: 0.8154 (mp0) REVERT: C 72 ASP cc_start: 0.8631 (m-30) cc_final: 0.8398 (t0) REVERT: C 95 LYS cc_start: 0.9206 (tttp) cc_final: 0.8946 (ttmt) REVERT: C 110 ASN cc_start: 0.9107 (t0) cc_final: 0.8659 (p0) REVERT: E 59 GLU cc_start: 0.8760 (pm20) cc_final: 0.8410 (pm20) REVERT: F 25 ASN cc_start: 0.9212 (m-40) cc_final: 0.8569 (m-40) REVERT: H 39 TYR cc_start: 0.8954 (t80) cc_final: 0.8346 (t80) REVERT: H 65 ASP cc_start: 0.8847 (t0) cc_final: 0.8561 (t0) REVERT: H 83 ARG cc_start: 0.8941 (mmt90) cc_final: 0.8715 (mpt-90) REVERT: K 93 LYS cc_start: 0.6835 (mttm) cc_final: 0.6432 (pmtt) REVERT: K 525 SER cc_start: 0.8855 (t) cc_final: 0.8517 (p) REVERT: K 645 ARG cc_start: 0.8722 (tpp80) cc_final: 0.8163 (tpp80) REVERT: K 717 ASN cc_start: 0.8419 (m-40) cc_final: 0.8187 (t0) outliers start: 18 outliers final: 13 residues processed: 161 average time/residue: 1.8537 time to fit residues: 322.9293 Evaluate side-chains 162 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 149 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 133 PHE Chi-restraints excluded: chain K residue 538 CYS Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain K residue 548 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 145 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 152 optimal weight: 4.9990 chunk 144 optimal weight: 0.0070 chunk 46 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 135 optimal weight: 0.0770 chunk 105 optimal weight: 0.0030 overall best weight: 0.3366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN E 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.090423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.064614 restraints weight = 43959.391| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.24 r_work: 0.2932 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17707 Z= 0.141 Angle : 0.620 10.893 25173 Z= 0.342 Chirality : 0.036 0.146 2852 Planarity : 0.004 0.056 2181 Dihedral : 29.839 176.602 4679 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.61 % Favored : 94.31 % Rotamer: Outliers : 1.56 % Allowed : 20.10 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.24 (0.24), residues: 1318 helix: 2.13 (0.18), residues: 806 sheet: -1.34 (0.88), residues: 41 loop : -1.39 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 364 HIS 0.007 0.001 HIS K 111 PHE 0.028 0.001 PHE K 737 TYR 0.013 0.001 TYR K 545 ARG 0.007 0.000 ARG D 83 Details of bonding type rmsd hydrogen bonds : bond 0.03516 ( 949) hydrogen bonds : angle 2.83214 ( 2433) covalent geometry : bond 0.00312 (17707) covalent geometry : angle 0.62002 (25173) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10977.17 seconds wall clock time: 189 minutes 47.95 seconds (11387.95 seconds total)