Starting phenix.real_space_refine on Sun May 18 04:51:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jnx_61630/05_2025/9jnx_61630.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jnx_61630/05_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_61630/05_2025/9jnx_61630.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jnx_61630/05_2025/9jnx_61630.map" model { file = "/net/cci-nas-00/data/ceres_data/9jnx_61630/05_2025/9jnx_61630.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jnx_61630/05_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-5687/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: 4.16 Conformation dependent library (CDL) restraints added in 1.8 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: 7.52 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: 8.38 Time building geometry restraints manager: 4.87 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: 1.810 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: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 45.040 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.060 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:13.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.400 ------------------------------------------------------------------------------- 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 : 1.347 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: 1.7731 time to fit residues: 364.3407 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 : 1.346 ------------------------------------------------------------------------------- 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 = 0.087938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.061976 restraints weight = 44675.032| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.26 r_work: 0.2874 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.0955 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 0.184 2852 Planarity : 0.005 0.051 2181 Dihedral : 30.186 175.589 4683 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 8.91 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 K 111 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 0.04570 ( 949) hydrogen bonds : angle 3.29725 ( 2433) covalent geometry : bond 0.00471 (17707) covalent geometry : angle 0.64685 (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 : 1.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8848 (tt0) cc_final: 0.8371 (tt0) REVERT: A 76 GLN cc_start: 0.8690 (pp30) cc_final: 0.8388 (pp30) REVERT: A 120 MET cc_start: 0.8794 (mtm) cc_final: 0.8568 (mtt) REVERT: A 133 GLU cc_start: 0.8525 (mp0) cc_final: 0.8219 (mp0) REVERT: C 64 GLU cc_start: 0.8665 (tt0) cc_final: 0.8416 (pt0) REVERT: D 102 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8500 (mm-30) REVERT: E 59 GLU cc_start: 0.8974 (pm20) cc_final: 0.8714 (pm20) REVERT: F 25 ASN cc_start: 0.9185 (m-40) cc_final: 0.8565 (m-40) REVERT: G 92 GLU cc_start: 0.8662 (pt0) cc_final: 0.8422 (mt-10) REVERT: H 65 ASP cc_start: 0.8834 (t0) cc_final: 0.8618 (t0) REVERT: K 93 LYS cc_start: 0.6880 (mttm) cc_final: 0.6393 (pmtt) REVERT: K 377 ASP cc_start: 0.8916 (m-30) cc_final: 0.8716 (m-30) REVERT: K 525 SER cc_start: 0.9036 (t) cc_final: 0.8816 (p) REVERT: K 645 ARG cc_start: 0.8960 (tpp80) cc_final: 0.8425 (tpp80) REVERT: K 717 ASN cc_start: 0.8387 (m-40) cc_final: 0.8184 (t0) REVERT: K 726 TYR cc_start: 0.6443 (t80) cc_final: 0.6074 (t80) outliers start: 14 outliers final: 5 residues processed: 176 average time/residue: 1.7324 time to fit residues: 330.0786 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 : 1.342 ------------------------------------------------------------------------------- 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: 0.0370 chunk 96 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 121 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 overall best weight: 0.9460 ------------------------------------------------------------------------------- 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 = 0.3686 r_free = 0.3686 target = 0.088954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.063163 restraints weight = 44859.555| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.21 r_work: 0.2909 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1406 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= 0.162 Angle : 0.611 7.878 25173 Z= 0.342 Chirality : 0.037 0.160 2852 Planarity : 0.004 0.053 2181 Dihedral : 30.034 175.687 4679 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.84 % Favored : 94.08 % Rotamer: Outliers : 2.25 % Allowed : 12.48 % Favored : 85.27 % 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: 0.84 (0.24), residues: 1318 helix: 1.92 (0.19), residues: 795 sheet: -1.69 (0.74), residues: 65 loop : -1.63 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 364 HIS 0.006 0.001 HIS K 111 PHE 0.019 0.001 PHE K 737 TYR 0.012 0.001 TYR K 545 ARG 0.007 0.000 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.03874 ( 949) hydrogen bonds : angle 3.03535 ( 2433) covalent geometry : bond 0.00362 (17707) covalent geometry : angle 0.61122 (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 198 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 172 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8818 (tt0) cc_final: 0.8348 (tt0) REVERT: A 76 GLN cc_start: 0.8671 (pp30) cc_final: 0.8359 (pp30) REVERT: A 120 MET cc_start: 0.8731 (mtm) cc_final: 0.8509 (mtt) REVERT: A 133 GLU cc_start: 0.8528 (mp0) cc_final: 0.8249 (mp0) REVERT: C 64 GLU cc_start: 0.8706 (tt0) cc_final: 0.8396 (pt0) REVERT: C 95 LYS cc_start: 0.9231 (tttp) cc_final: 0.8938 (ttmm) REVERT: C 110 ASN cc_start: 0.9137 (t0) cc_final: 0.8498 (p0) REVERT: E 59 GLU cc_start: 0.8909 (pm20) cc_final: 0.8624 (pm20) REVERT: F 25 ASN cc_start: 0.9198 (m-40) cc_final: 0.8572 (m-40) REVERT: H 65 ASP cc_start: 0.8833 (t0) cc_final: 0.8574 (t0) REVERT: K 93 LYS cc_start: 0.6847 (mttm) cc_final: 0.6376 (pmtt) REVERT: K 525 SER cc_start: 0.8930 (t) cc_final: 0.8676 (p) REVERT: K 645 ARG cc_start: 0.8932 (tpp80) cc_final: 0.8433 (tpp80) REVERT: K 717 ASN cc_start: 0.8363 (m-40) cc_final: 0.8065 (m-40) outliers start: 26 outliers final: 12 residues processed: 187 average time/residue: 1.6512 time to fit residues: 335.1664 Evaluate side-chains 164 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 1.505 ------------------------------------------------------------------------------- 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 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 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: 0.2980 chunk 41 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 144 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 143 optimal weight: 0.6980 chunk 61 optimal weight: 0.2980 chunk 14 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN E 68 GLN G 38 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 205 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.089988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.063865 restraints weight = 44649.860| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.28 r_work: 0.2928 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17707 Z= 0.145 Angle : 0.600 9.725 25173 Z= 0.335 Chirality : 0.036 0.161 2852 Planarity : 0.004 0.055 2181 Dihedral : 29.949 175.848 4679 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.77 % Favored : 94.16 % Rotamer: Outliers : 2.25 % Allowed : 15.25 % Favored : 82.50 % 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: 1.05 (0.24), residues: 1318 helix: 2.09 (0.19), residues: 799 sheet: -1.57 (0.75), residues: 65 loop : -1.58 (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 0.013 0.001 PHE K 524 TYR 0.011 0.001 TYR K 545 ARG 0.006 0.000 ARG H 83 Details of bonding type rmsd hydrogen bonds : bond 0.03583 ( 949) hydrogen bonds : angle 2.87367 ( 2433) covalent geometry : bond 0.00322 (17707) covalent geometry : angle 0.59974 (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 192 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8811 (tt0) cc_final: 0.8325 (tt0) REVERT: A 76 GLN cc_start: 0.8681 (pp30) cc_final: 0.8357 (pp30) REVERT: A 120 MET cc_start: 0.8650 (mtm) cc_final: 0.8439 (mtt) REVERT: A 133 GLU cc_start: 0.8538 (mp0) cc_final: 0.8219 (mp0) REVERT: C 64 GLU cc_start: 0.8736 (tt0) cc_final: 0.8390 (pt0) REVERT: C 91 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7807 (tm-30) REVERT: C 95 LYS cc_start: 0.9202 (tttp) cc_final: 0.8997 (ttmt) REVERT: C 110 ASN cc_start: 0.9116 (OUTLIER) cc_final: 0.8532 (p0) REVERT: E 59 GLU cc_start: 0.8863 (pm20) cc_final: 0.8573 (pm20) REVERT: E 133 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7797 (mt-10) REVERT: F 25 ASN cc_start: 0.9197 (m-40) cc_final: 0.8543 (m-40) REVERT: H 39 TYR cc_start: 0.8977 (t80) cc_final: 0.8276 (t80) REVERT: H 65 ASP cc_start: 0.8802 (t0) cc_final: 0.8497 (t0) REVERT: K 93 LYS cc_start: 0.6874 (mttm) cc_final: 0.6416 (pmtt) REVERT: K 299 VAL cc_start: 0.9129 (OUTLIER) cc_final: 0.8928 (t) REVERT: K 525 SER cc_start: 0.8896 (t) cc_final: 0.8619 (p) REVERT: K 645 ARG cc_start: 0.8899 (tpp80) cc_final: 0.8359 (tpp80) REVERT: K 717 ASN cc_start: 0.8352 (m-40) cc_final: 0.8059 (m-40) outliers start: 26 outliers final: 10 residues processed: 181 average time/residue: 1.6418 time to fit residues: 324.4145 Evaluate side-chains 164 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 151 time to evaluate : 1.417 ------------------------------------------------------------------------------- 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 E residue 87 SER Chi-restraints excluded: chain E residue 133 GLU 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: 8.9990 chunk 134 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 chunk 105 optimal weight: 0.0570 chunk 29 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 125 optimal weight: 9.9990 overall best weight: 1.1302 ------------------------------------------------------------------------------- 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 = 0.3693 r_free = 0.3693 target = 0.089369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.063495 restraints weight = 44813.837| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.23 r_work: 0.2909 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1823 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= 0.171 Angle : 0.603 8.576 25173 Z= 0.336 Chirality : 0.036 0.152 2852 Planarity : 0.004 0.056 2181 Dihedral : 30.011 176.257 4679 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.07 % Favored : 93.85 % Rotamer: Outliers : 2.34 % Allowed : 16.55 % Favored : 81.11 % 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: 0.98 (0.24), residues: 1318 helix: 2.02 (0.19), residues: 805 sheet: -2.31 (0.75), residues: 53 loop : -1.55 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 364 HIS 0.007 0.001 HIS K 111 PHE 0.019 0.001 PHE K 737 TYR 0.010 0.001 TYR K 596 ARG 0.005 0.000 ARG H 83 Details of bonding type rmsd hydrogen bonds : bond 0.03860 ( 949) hydrogen bonds : angle 2.89694 ( 2433) covalent geometry : bond 0.00388 (17707) covalent geometry : angle 0.60307 (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 185 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8836 (tt0) cc_final: 0.8343 (tt0) REVERT: A 76 GLN cc_start: 0.8664 (pp30) cc_final: 0.8315 (pp30) REVERT: A 120 MET cc_start: 0.8731 (mtm) cc_final: 0.8518 (mtt) REVERT: A 133 GLU cc_start: 0.8523 (mp0) cc_final: 0.8268 (mp0) REVERT: C 91 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7808 (tm-30) REVERT: C 95 LYS cc_start: 0.9185 (tttp) cc_final: 0.8925 (ttmt) REVERT: C 110 ASN cc_start: 0.9118 (t0) cc_final: 0.8517 (p0) REVERT: D 65 ASP cc_start: 0.9089 (t0) cc_final: 0.8861 (t0) REVERT: E 59 GLU cc_start: 0.8852 (pm20) cc_final: 0.8529 (pm20) REVERT: E 133 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7808 (mt-10) REVERT: F 25 ASN cc_start: 0.9199 (m-40) cc_final: 0.8516 (m-40) REVERT: H 65 ASP cc_start: 0.8824 (t0) cc_final: 0.8518 (t0) REVERT: K 93 LYS cc_start: 0.6882 (mttm) cc_final: 0.6438 (pmtt) REVERT: K 525 SER cc_start: 0.8894 (t) cc_final: 0.8558 (p) REVERT: K 717 ASN cc_start: 0.8303 (m-40) cc_final: 0.8017 (m-40) outliers start: 27 outliers final: 15 residues processed: 175 average time/residue: 1.6621 time to fit residues: 316.5531 Evaluate side-chains 168 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 1.423 ------------------------------------------------------------------------------- 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 E residue 133 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 145 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 117 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 18 optimal weight: 0.0270 chunk 147 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 overall best weight: 0.9240 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.089775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.063750 restraints weight = 44393.981| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.26 r_work: 0.2915 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1910 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= 0.158 Angle : 0.601 7.796 25173 Z= 0.335 Chirality : 0.036 0.149 2852 Planarity : 0.004 0.056 2181 Dihedral : 29.981 176.434 4679 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.99 % Favored : 93.93 % Rotamer: Outliers : 2.51 % Allowed : 17.85 % Favored : 79.64 % 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: 1.02 (0.24), residues: 1318 helix: 2.06 (0.19), residues: 805 sheet: -2.34 (0.75), residues: 53 loop : -1.53 (0.28), residues: 460 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 0.011 0.001 PHE E 67 TYR 0.010 0.001 TYR F 51 ARG 0.007 0.000 ARG H 76 Details of bonding type rmsd hydrogen bonds : bond 0.03694 ( 949) hydrogen bonds : angle 2.87009 ( 2433) covalent geometry : bond 0.00355 (17707) covalent geometry : angle 0.60127 (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 187 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8836 (tt0) cc_final: 0.8341 (tt0) REVERT: A 76 GLN cc_start: 0.8657 (pp30) cc_final: 0.8318 (pp30) REVERT: A 120 MET cc_start: 0.8715 (mtm) cc_final: 0.8509 (mtt) REVERT: A 133 GLU cc_start: 0.8515 (mp0) cc_final: 0.8249 (mp0) REVERT: C 91 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7889 (tm-30) REVERT: C 95 LYS cc_start: 0.9195 (tttp) cc_final: 0.8932 (ttmt) REVERT: C 110 ASN cc_start: 0.9104 (OUTLIER) cc_final: 0.8529 (p0) REVERT: D 65 ASP cc_start: 0.9095 (t0) cc_final: 0.8884 (t0) REVERT: E 59 GLU cc_start: 0.8833 (pm20) cc_final: 0.8523 (pm20) REVERT: E 133 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7825 (mt-10) REVERT: F 25 ASN cc_start: 0.9206 (m-40) cc_final: 0.8539 (m-40) REVERT: H 65 ASP cc_start: 0.8824 (t0) cc_final: 0.8524 (t0) REVERT: K 93 LYS cc_start: 0.6887 (mttm) cc_final: 0.6440 (pmtt) REVERT: K 525 SER cc_start: 0.8860 (t) cc_final: 0.8534 (p) REVERT: K 645 ARG cc_start: 0.8771 (tpp80) cc_final: 0.8242 (tpp80) REVERT: K 717 ASN cc_start: 0.8318 (m-40) cc_final: 0.8034 (m-40) outliers start: 29 outliers final: 16 residues processed: 174 average time/residue: 1.6311 time to fit residues: 309.0097 Evaluate side-chains 172 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 1.345 ------------------------------------------------------------------------------- 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 E residue 133 GLU 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 77 LEU 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: 1.9990 chunk 89 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 144 optimal weight: 0.3980 chunk 143 optimal weight: 0.6980 chunk 126 optimal weight: 9.9990 chunk 124 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 153 optimal weight: 7.9990 chunk 111 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.089849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.063839 restraints weight = 44371.239| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.26 r_work: 0.2916 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2044 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= 0.160 Angle : 0.601 12.176 25173 Z= 0.334 Chirality : 0.036 0.147 2852 Planarity : 0.004 0.056 2181 Dihedral : 29.927 176.592 4679 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.99 % Favored : 93.93 % Rotamer: Outliers : 2.51 % Allowed : 17.94 % Favored : 79.55 % 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: 1.12 (0.24), residues: 1318 helix: 2.09 (0.19), residues: 806 sheet: -1.33 (0.88), residues: 41 loop : -1.55 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 364 HIS 0.007 0.001 HIS K 111 PHE 0.019 0.001 PHE K 737 TYR 0.009 0.001 TYR F 51 ARG 0.007 0.000 ARG H 76 Details of bonding type rmsd hydrogen bonds : bond 0.03649 ( 949) hydrogen bonds : angle 2.84345 ( 2433) covalent geometry : bond 0.00360 (17707) covalent geometry : angle 0.60085 (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 187 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8833 (tt0) cc_final: 0.8362 (tt0) REVERT: A 76 GLN cc_start: 0.8667 (pp30) cc_final: 0.8329 (pp30) REVERT: A 120 MET cc_start: 0.8708 (mtm) cc_final: 0.8501 (mtt) REVERT: A 133 GLU cc_start: 0.8553 (mp0) cc_final: 0.8324 (mp0) REVERT: C 91 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7912 (tm-30) REVERT: C 95 LYS cc_start: 0.9200 (tttp) cc_final: 0.8938 (ttmt) REVERT: C 110 ASN cc_start: 0.9100 (OUTLIER) cc_final: 0.8553 (p0) REVERT: D 65 ASP cc_start: 0.9085 (t0) cc_final: 0.8872 (t0) REVERT: D 90 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8138 (mp0) REVERT: E 59 GLU cc_start: 0.8843 (pm20) cc_final: 0.8538 (pm20) REVERT: E 133 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7827 (mt-10) REVERT: F 25 ASN cc_start: 0.9215 (m-40) cc_final: 0.8542 (m-40) REVERT: H 65 ASP cc_start: 0.8821 (t0) cc_final: 0.8530 (t0) REVERT: K 93 LYS cc_start: 0.6835 (mttm) cc_final: 0.6388 (pmtt) REVERT: K 525 SER cc_start: 0.8823 (t) cc_final: 0.8494 (p) REVERT: K 645 ARG cc_start: 0.8713 (tpp80) cc_final: 0.8241 (tpp80) REVERT: K 717 ASN cc_start: 0.8328 (m-40) cc_final: 0.8040 (m-40) outliers start: 29 outliers final: 18 residues processed: 177 average time/residue: 1.6171 time to fit residues: 311.7869 Evaluate side-chains 174 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 79 LYS 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 D residue 90 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 133 GLU 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 77 LEU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 106 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 147 optimal weight: 7.9990 chunk 60 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3706 r_free = 0.3706 target = 0.090047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.064282 restraints weight = 44010.359| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.24 r_work: 0.2926 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2140 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= 0.155 Angle : 0.602 11.694 25173 Z= 0.333 Chirality : 0.035 0.146 2852 Planarity : 0.004 0.056 2181 Dihedral : 29.897 176.721 4679 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.69 % Favored : 94.23 % Rotamer: Outliers : 2.60 % Allowed : 18.72 % Favored : 78.68 % 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: 2.12 (0.19), residues: 806 sheet: -1.34 (0.88), residues: 41 loop : -1.50 (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 0.011 0.001 PHE E 67 TYR 0.011 0.001 TYR H 34 ARG 0.009 0.000 ARG H 76 Details of bonding type rmsd hydrogen bonds : bond 0.03567 ( 949) hydrogen bonds : angle 2.82732 ( 2433) covalent geometry : bond 0.00348 (17707) covalent geometry : angle 0.60156 (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 185 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 1.508 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8830 (tt0) cc_final: 0.8361 (tt0) REVERT: A 76 GLN cc_start: 0.8654 (pp30) cc_final: 0.8313 (pp30) REVERT: C 91 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7927 (tm-30) REVERT: C 95 LYS cc_start: 0.9202 (tttp) cc_final: 0.8939 (ttmt) REVERT: C 110 ASN cc_start: 0.9097 (t0) cc_final: 0.8581 (p0) REVERT: D 65 ASP cc_start: 0.9065 (t0) cc_final: 0.8846 (t0) REVERT: D 90 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8143 (mp0) REVERT: E 59 GLU cc_start: 0.8815 (pm20) cc_final: 0.8526 (pm20) REVERT: F 25 ASN cc_start: 0.9219 (m-40) cc_final: 0.8553 (m-40) REVERT: H 39 TYR cc_start: 0.8931 (t80) cc_final: 0.8281 (t80) REVERT: H 65 ASP cc_start: 0.8817 (t0) cc_final: 0.8532 (t0) REVERT: K 93 LYS cc_start: 0.6861 (mttm) cc_final: 0.6450 (pmtt) REVERT: K 525 SER cc_start: 0.8813 (t) cc_final: 0.8474 (p) REVERT: K 645 ARG cc_start: 0.8718 (tpp80) cc_final: 0.8267 (tpp80) REVERT: K 717 ASN cc_start: 0.8345 (m-40) cc_final: 0.8056 (m-40) outliers start: 30 outliers final: 18 residues processed: 174 average time/residue: 1.7076 time to fit residues: 324.0430 Evaluate side-chains 169 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 79 LYS 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 D residue 90 GLU 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 77 LEU 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 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: 10.0000 chunk 109 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 72 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN E 68 GLN G 38 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.088122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.062153 restraints weight = 44361.066| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.25 r_work: 0.2868 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2021 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= 0.230 Angle : 0.638 10.663 25173 Z= 0.352 Chirality : 0.038 0.147 2852 Planarity : 0.004 0.054 2181 Dihedral : 30.148 176.357 4679 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.22 % Favored : 93.70 % Rotamer: Outliers : 2.69 % Allowed : 18.72 % Favored : 78.60 % 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: 0.97 (0.24), residues: 1318 helix: 1.96 (0.18), residues: 806 sheet: -2.55 (0.71), residues: 53 loop : -1.41 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 364 HIS 0.006 0.001 HIS K 111 PHE 0.022 0.001 PHE K 737 TYR 0.029 0.002 TYR K 545 ARG 0.008 0.000 ARG H 76 Details of bonding type rmsd hydrogen bonds : bond 0.04399 ( 949) hydrogen bonds : angle 3.02045 ( 2433) covalent geometry : bond 0.00529 (17707) covalent geometry : angle 0.63790 (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 174 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8846 (tt0) cc_final: 0.8378 (tt0) REVERT: A 76 GLN cc_start: 0.8715 (pp30) cc_final: 0.8367 (pp30) REVERT: C 91 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7968 (tm-30) REVERT: C 95 LYS cc_start: 0.9236 (tttp) cc_final: 0.8958 (ttmt) REVERT: C 110 ASN cc_start: 0.9143 (OUTLIER) cc_final: 0.8600 (p0) REVERT: D 65 ASP cc_start: 0.9092 (t0) cc_final: 0.8866 (t0) REVERT: D 90 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8161 (mp0) REVERT: E 59 GLU cc_start: 0.8869 (pm20) cc_final: 0.8561 (pm20) REVERT: F 25 ASN cc_start: 0.9236 (m-40) cc_final: 0.8575 (m-40) REVERT: H 65 ASP cc_start: 0.8903 (t0) cc_final: 0.8604 (t0) REVERT: K 93 LYS cc_start: 0.6808 (mttm) cc_final: 0.6446 (pmtt) REVERT: K 525 SER cc_start: 0.8885 (t) cc_final: 0.8543 (p) REVERT: K 645 ARG cc_start: 0.8758 (tpp80) cc_final: 0.8188 (tpp80) REVERT: K 717 ASN cc_start: 0.8396 (m-40) cc_final: 0.8158 (t0) outliers start: 31 outliers final: 19 residues processed: 159 average time/residue: 1.8782 time to fit residues: 323.6600 Evaluate side-chains 162 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 64 GLU 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 D residue 90 GLU 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 77 LEU 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 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=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: 2.9990 chunk 23 optimal weight: 0.5980 chunk 56 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 1 optimal weight: 0.1980 chunk 9 optimal weight: 6.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN G 38 ASN ** 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 = 0.3685 r_free = 0.3685 target = 0.089126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.063090 restraints weight = 43729.589| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.25 r_work: 0.2896 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17707 Z= 0.149 Angle : 0.621 10.854 25173 Z= 0.344 Chirality : 0.036 0.147 2852 Planarity : 0.004 0.055 2181 Dihedral : 30.119 176.235 4679 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.07 % Favored : 93.85 % Rotamer: Outliers : 1.91 % Allowed : 19.67 % Favored : 78.42 % 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: 1.08 (0.24), residues: 1318 helix: 2.01 (0.18), residues: 806 sheet: -1.50 (0.87), residues: 41 loop : -1.44 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 364 HIS 0.006 0.001 HIS K 111 PHE 0.010 0.001 PHE E 67 TYR 0.019 0.001 TYR K 545 ARG 0.008 0.000 ARG H 76 Details of bonding type rmsd hydrogen bonds : bond 0.04016 ( 949) hydrogen bonds : angle 2.92387 ( 2433) covalent geometry : bond 0.00330 (17707) covalent geometry : angle 0.62084 (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 172 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 1.536 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8838 (tt0) cc_final: 0.8366 (tt0) REVERT: A 76 GLN cc_start: 0.8692 (pp30) cc_final: 0.8347 (pp30) REVERT: C 91 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7955 (tm-30) REVERT: C 95 LYS cc_start: 0.9214 (tttp) cc_final: 0.8942 (ttmt) REVERT: C 110 ASN cc_start: 0.9119 (t0) cc_final: 0.8590 (p0) REVERT: D 65 ASP cc_start: 0.9087 (t0) cc_final: 0.8863 (t0) REVERT: D 90 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8135 (mp0) REVERT: E 59 GLU cc_start: 0.8811 (pm20) cc_final: 0.8512 (pm20) REVERT: F 25 ASN cc_start: 0.9224 (m-40) cc_final: 0.8548 (m-40) REVERT: H 48 ASP cc_start: 0.8812 (p0) cc_final: 0.8484 (p0) REVERT: H 65 ASP cc_start: 0.8877 (t0) cc_final: 0.8548 (t0) REVERT: K 93 LYS cc_start: 0.6798 (mttm) cc_final: 0.6442 (pmtt) REVERT: K 525 SER cc_start: 0.8851 (t) cc_final: 0.8512 (p) REVERT: K 645 ARG cc_start: 0.8736 (tpp80) cc_final: 0.8164 (tpp80) REVERT: K 717 ASN cc_start: 0.8391 (m-40) cc_final: 0.8161 (t0) outliers start: 22 outliers final: 16 residues processed: 163 average time/residue: 1.6752 time to fit residues: 296.6803 Evaluate side-chains 164 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 90 GLU 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 77 LEU 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: 4.9990 chunk 113 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 chunk 144 optimal weight: 0.0670 chunk 46 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 135 optimal weight: 0.5980 chunk 105 optimal weight: 0.8980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN D 46 HIS E 68 GLN G 38 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.089547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.063718 restraints weight = 43883.034| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.23 r_work: 0.2908 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17707 Z= 0.148 Angle : 0.619 10.537 25173 Z= 0.343 Chirality : 0.036 0.145 2852 Planarity : 0.004 0.056 2181 Dihedral : 29.995 176.608 4679 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.07 % Favored : 93.85 % Rotamer: Outliers : 2.17 % Allowed : 19.41 % Favored : 78.42 % 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: 1.16 (0.24), residues: 1318 helix: 2.07 (0.18), residues: 807 sheet: -1.46 (0.87), residues: 41 loop : -1.42 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 364 HIS 0.006 0.001 HIS K 111 PHE 0.021 0.001 PHE K 737 TYR 0.015 0.001 TYR K 545 ARG 0.008 0.000 ARG H 76 Details of bonding type rmsd hydrogen bonds : bond 0.03671 ( 949) hydrogen bonds : angle 2.87999 ( 2433) covalent geometry : bond 0.00330 (17707) covalent geometry : angle 0.61941 (25173) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10512.00 seconds wall clock time: 181 minutes 31.08 seconds (10891.08 seconds total)