Starting phenix.real_space_refine on Thu Aug 6 15:38:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jnz_61632/08_2026/9jnz_61632.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jnz_61632/08_2026/9jnz_61632.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 { model { file = "/net/cci-nas-00/data/ceres_data/9jnz_61632/08_2026/9jnz_61632.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jnz_61632/08_2026/9jnz_61632.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jnz_61632/08_2026/9jnz_61632.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jnz_61632/08_2026/9jnz_61632.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 sd= 0.010 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 292 5.49 5 S 25 5.16 5 Cl 1 4.86 5 C 9394 2.51 5 N 2993 2.21 5 O 3618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16323 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: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} 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: 4311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4311 Classifications: {'peptide': 525} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 505} Chain breaks: 2 Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.74, per 1000 atoms: 0.23 Number of scatterers: 16323 At special positions: 0 Unit cell: (96.3425, 116.91, 156.962, 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) Cl 1 17.00 S 25 16.00 P 292 15.00 O 3618 8.00 N 2993 7.00 C 9394 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: 1.42 Conformation dependent library (CDL) restraints added in 699.7 milliseconds 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2444 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 10 sheets defined 64.4% alpha, 4.0% beta 144 base pairs and 254 stacking pairs defined. Time for finding SS restraints: 2.23 Creating SS restraints... Processing helix chain 'A' and resid 46 through 55 Processing helix chain 'A' and resid 63 through 74 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.333A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 36 removed outlier: 3.588A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.442A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.563A pdb=" N LYS D 40 " --> pdb=" O ILE D 36 " (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 121 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.920A pdb=" N GLN E 76 " --> pdb=" O ARG E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.509A pdb=" N ASP E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.051A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 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 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: 3.975A pdb=" N LYS H 40 " --> pdb=" O ILE H 36 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N LYS H 43 " --> pdb=" O TYR H 39 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.532A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 Processing helix chain 'K' and resid 82 through 91 removed outlier: 3.518A pdb=" N ARG K 89 " --> pdb=" O SER K 85 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU K 91 " --> pdb=" O LYS K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 116 removed outlier: 3.989A pdb=" N THR K 105 " --> pdb=" O ASP K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 119 through 127 Processing helix chain 'K' and resid 131 through 143 removed outlier: 3.829A pdb=" N ASN K 143 " --> pdb=" O VAL K 139 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 213 Processing helix chain 'K' and resid 228 through 241 Processing helix chain 'K' and resid 253 through 255 No H-bonds generated for 'chain 'K' and resid 253 through 255' Processing helix chain 'K' and resid 256 through 268 Processing helix chain 'K' and resid 279 through 290 Processing helix chain 'K' and resid 303 through 309 Processing helix chain 'K' and resid 309 through 315 removed outlier: 3.775A pdb=" N LEU K 313 " --> pdb=" O GLU K 309 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS K 315 " --> pdb=" O SER K 311 " (cutoff:3.500A) Processing helix chain 'K' and resid 325 through 329 Processing helix chain 'K' and resid 334 through 343 Processing helix chain 'K' and resid 360 through 371 removed outlier: 3.578A pdb=" N TRP K 364 " --> pdb=" O LEU K 360 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE K 369 " --> pdb=" O ALA K 365 " (cutoff:3.500A) Processing helix chain 'K' and resid 377 through 385 removed outlier: 3.810A pdb=" N PHE K 381 " --> pdb=" O ASP K 377 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N PHE K 385 " --> pdb=" O PHE K 381 " (cutoff:3.500A) Processing helix chain 'K' and resid 391 through 394 Processing helix chain 'K' and resid 395 through 401 Processing helix chain 'K' and resid 402 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 495 through 500 removed outlier: 3.892A pdb=" N TYR K 499 " --> pdb=" O GLU K 495 " (cutoff:3.500A) Processing helix chain 'K' and resid 502 through 518 removed outlier: 3.821A pdb=" N VAL K 506 " --> pdb=" O ALA K 502 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLU K 516 " --> pdb=" O LYS K 512 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLU K 517 " --> pdb=" O LYS K 513 " (cutoff:3.500A) Processing helix chain 'K' and resid 527 through 541 removed outlier: 3.752A pdb=" N ILE K 533 " --> pdb=" O ARG K 529 " (cutoff:3.500A) Processing helix chain 'K' and resid 553 through 565 Processing helix chain 'K' and resid 601 through 614 removed outlier: 3.740A pdb=" N ASP K 605 " --> pdb=" O ASN K 601 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA K 612 " --> pdb=" O ALA K 608 " (cutoff:3.500A) Processing helix chain 'K' and resid 631 through 651 removed outlier: 4.140A pdb=" N LYS K 635 " --> pdb=" O SER K 631 " (cutoff:3.500A) Processing helix chain 'K' and resid 652 through 656 removed outlier: 3.943A pdb=" N THR K 656 " --> pdb=" O GLN K 653 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.548A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.899A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.796A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.074A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.856A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'K' and resid 273 through 275 removed outlier: 6.104A pdb=" N PHE K 274 " --> pdb=" O ILE K 300 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N SER K 302 " --> pdb=" O PHE K 274 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N PHE K 248 " --> pdb=" O VAL K 299 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ALA K 301 " --> pdb=" O PHE K 248 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N VAL K 250 " --> pdb=" O ALA K 301 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N ILE K 321 " --> pdb=" O LEU K 349 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ILE K 351 " --> pdb=" O ILE K 321 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE K 323 " --> pdb=" O ILE K 351 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE K 218 " --> pdb=" O LEU K 410 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 427 through 431 removed outlier: 6.254A pdb=" N LEU K 427 " --> pdb=" O ARG K 625 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N VAL K 627 " --> pdb=" O LEU K 427 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N LEU K 429 " --> pdb=" O VAL K 627 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU K 626 " --> pdb=" O LEU K 595 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL K 521 " --> pdb=" O PHE K 574 " (cutoff:3.500A) 570 hydrogen bonds defined for protein. 1659 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 370 hydrogen bonds 740 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 254 stacking parallelities Total time for adding SS restraints: 4.03 Time building geometry restraints manager: 1.92 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: 3027 1.33 - 1.45: 5220 1.45 - 1.57: 8342 1.57 - 1.69: 582 1.69 - 1.81: 43 Bond restraints: 17214 Sorted by residual: bond pdb=" CA ASP K 416 " pdb=" C ASP K 416 " ideal model delta sigma weight residual 1.523 1.454 0.069 1.34e-02 5.57e+03 2.63e+01 bond pdb=" CA SER K 415 " pdb=" C SER K 415 " ideal model delta sigma weight residual 1.523 1.455 0.069 1.34e-02 5.57e+03 2.62e+01 bond pdb=" N ASP K 416 " pdb=" CA ASP K 416 " ideal model delta sigma weight residual 1.457 1.402 0.055 1.29e-02 6.01e+03 1.84e+01 bond pdb=" C3' DT I 142 " pdb=" C2' DT I 142 " ideal model delta sigma weight residual 1.516 1.549 -0.033 8.00e-03 1.56e+04 1.75e+01 bond pdb=" N SER K 415 " pdb=" CA SER K 415 " ideal model delta sigma weight residual 1.457 1.405 0.053 1.29e-02 6.01e+03 1.66e+01 ... (remaining 17209 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 23934 2.32 - 4.65: 532 4.65 - 6.97: 34 6.97 - 9.30: 5 9.30 - 11.62: 2 Bond angle restraints: 24507 Sorted by residual: angle pdb=" O4' DA I 61 " pdb=" C4' DA I 61 " pdb=" C3' DA I 61 " ideal model delta sigma weight residual 106.00 102.59 3.41 6.00e-01 2.78e+00 3.24e+01 angle pdb=" N SER K 415 " pdb=" CA SER K 415 " pdb=" C SER K 415 " ideal model delta sigma weight residual 110.80 99.18 11.62 2.13e+00 2.20e-01 2.98e+01 angle pdb=" O4' DG J 106 " pdb=" C4' DG J 106 " pdb=" C3' DG J 106 " ideal model delta sigma weight residual 106.00 102.87 3.13 6.00e-01 2.78e+00 2.72e+01 angle pdb=" O4' DG I 76 " pdb=" C4' DG I 76 " pdb=" C3' DG I 76 " ideal model delta sigma weight residual 106.00 103.01 2.99 6.00e-01 2.78e+00 2.48e+01 angle pdb=" O4' DA I 69 " pdb=" C4' DA I 69 " pdb=" C3' DA I 69 " ideal model delta sigma weight residual 106.00 103.13 2.87 6.00e-01 2.78e+00 2.28e+01 ... (remaining 24502 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.11: 8162 35.11 - 70.23: 1427 70.23 - 105.34: 33 105.34 - 140.45: 9 140.45 - 175.56: 8 Dihedral angle restraints: 9639 sinusoidal: 5867 harmonic: 3772 Sorted by residual: dihedral pdb=" CA PRO K 489 " pdb=" C PRO K 489 " pdb=" N PRO K 490 " pdb=" CA PRO K 490 " ideal model delta harmonic sigma weight residual 180.00 138.66 41.34 0 5.00e+00 4.00e-02 6.83e+01 dihedral pdb=" CA VAL A 71 " pdb=" C VAL A 71 " pdb=" N ARG A 72 " pdb=" CA ARG A 72 " ideal model delta harmonic sigma weight residual 180.00 139.88 40.12 0 5.00e+00 4.00e-02 6.44e+01 dihedral pdb=" CA GLU C 92 " pdb=" C GLU C 92 " pdb=" N LEU C 93 " pdb=" CA LEU C 93 " ideal model delta harmonic sigma weight residual 180.00 155.76 24.24 0 5.00e+00 4.00e-02 2.35e+01 ... (remaining 9636 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1882 0.042 - 0.083: 629 0.083 - 0.125: 230 0.125 - 0.167: 36 0.167 - 0.209: 4 Chirality restraints: 2781 Sorted by residual: chirality pdb=" CB ILE K 323 " pdb=" CA ILE K 323 " pdb=" CG1 ILE K 323 " pdb=" CG2 ILE K 323 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" C3' DA I 20 " pdb=" C4' DA I 20 " pdb=" O3' DA I 20 " pdb=" C2' DA I 20 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 9.04e-01 chirality pdb=" CB ILE H 86 " pdb=" CA ILE H 86 " pdb=" CG1 ILE H 86 " pdb=" CG2 ILE H 86 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.61e-01 ... (remaining 2778 not shown) Planarity restraints: 2100 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO K 489 " 0.073 5.00e-02 4.00e+02 1.12e-01 2.01e+01 pdb=" N PRO K 490 " -0.194 5.00e-02 4.00e+02 pdb=" CA PRO K 490 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO K 490 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY K 488 " 0.056 5.00e-02 4.00e+02 8.59e-02 1.18e+01 pdb=" N PRO K 489 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO K 489 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO K 489 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS K 414 " 0.015 2.00e-02 2.50e+03 3.12e-02 9.71e+00 pdb=" C LYS K 414 " -0.054 2.00e-02 2.50e+03 pdb=" O LYS K 414 " 0.021 2.00e-02 2.50e+03 pdb=" N SER K 415 " 0.019 2.00e-02 2.50e+03 ... (remaining 2097 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1017 2.72 - 3.26: 15625 3.26 - 3.81: 30691 3.81 - 4.35: 37233 4.35 - 4.90: 55144 Nonbonded interactions: 139710 Sorted by model distance: nonbonded pdb=" OD2 ASP A 106 " pdb=" NH2 ARG A 131 " model vdw 2.171 3.120 nonbonded pdb=" OH TYR E 99 " pdb=" OE1 GLU E 133 " model vdw 2.177 3.040 nonbonded pdb=" OD2 ASP D 65 " pdb=" OH TYR F 98 " model vdw 2.197 3.040 nonbonded pdb=" OD1 ASP K 494 " pdb=" ND1 HIS K 496 " model vdw 2.203 3.120 nonbonded pdb=" OE2 GLU K 638 " pdb=" NE2 GLN K 642 " model vdw 2.204 3.120 ... (remaining 139705 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: 1.130 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.720 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 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:7.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 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 0.077 17214 Z= 0.512 Angle : 0.814 11.622 24507 Z= 0.656 Chirality : 0.047 0.209 2781 Planarity : 0.005 0.112 2100 Dihedral : 26.602 175.564 7195 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.20 % Favored : 94.72 % Rotamer: Outliers : 0.54 % Allowed : 0.36 % Favored : 99.09 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.24), residues: 1269 helix: 1.17 (0.19), residues: 764 sheet: -2.65 (0.62), residues: 73 loop : -1.93 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 83 TYR 0.016 0.002 TYR K 441 PHE 0.019 0.002 PHE C 25 TRP 0.037 0.002 TRP K 267 HIS 0.005 0.001 HIS K 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00636 / 0.51 (17214) covalent geometry : angle 0.81364 / 0.66 (24507) hydrogen bonds : bond 0.09697 / 6.79 ( 940) hydrogen bonds : angle 4.21842 / 3.05 ( 2399) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 211 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 72 ASP cc_start: 0.8436 (t70) cc_final: 0.8206 (t0) REVERT: C 90 ASP cc_start: 0.8651 (t0) cc_final: 0.8394 (t0) REVERT: D 68 GLU cc_start: 0.7861 (tp30) cc_final: 0.7610 (tp30) REVERT: G 15 LYS cc_start: 0.8690 (tptm) cc_final: 0.8437 (tptm) REVERT: H 65 ASP cc_start: 0.8512 (t0) cc_final: 0.8295 (t0) REVERT: K 133 PHE cc_start: 0.9042 (m-80) cc_final: 0.8506 (m-80) outliers start: 6 outliers final: 3 residues processed: 217 average time/residue: 0.7610 time to fit residues: 179.7146 Evaluate side-chains 169 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 166 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 415 SER Chi-restraints excluded: chain K residue 416 ASP Chi-restraints excluded: chain K residue 417 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 10.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 84 GLN C 110 ASN D 60 ASN D 106 HIS E 76 GLN G 73 ASN G 104 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.085827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.060254 restraints weight = 45230.957| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.15 r_work: 0.2924 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 17214 Z= 0.185 Angle : 0.710 8.314 24507 Z= 0.396 Chirality : 0.049 0.323 2781 Planarity : 0.005 0.099 2100 Dihedral : 30.486 171.946 4615 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.09 % Allowed : 10.62 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.24), residues: 1269 helix: 1.39 (0.19), residues: 771 sheet: -2.42 (0.64), residues: 65 loop : -1.88 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 134 TYR 0.016 0.002 TYR K 191 PHE 0.013 0.001 PHE K 183 TRP 0.012 0.001 TRP K 267 HIS 0.026 0.002 HIS K 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.18 (17214) covalent geometry : angle 0.70985 / 0.40 (24507) hydrogen bonds : bond 0.05335 / 3.61 ( 940) hydrogen bonds : angle 3.69201 / 2.66 ( 2399) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 177 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.8874 (mmm) cc_final: 0.8479 (tmm) REVERT: C 72 ASP cc_start: 0.8824 (t70) cc_final: 0.8609 (t0) REVERT: C 90 ASP cc_start: 0.8795 (t0) cc_final: 0.8456 (t0) REVERT: D 68 GLU cc_start: 0.8647 (tp30) cc_final: 0.8316 (tp30) REVERT: F 92 ARG cc_start: 0.8615 (ttp80) cc_final: 0.8391 (ttp80) REVERT: H 65 ASP cc_start: 0.9019 (t0) cc_final: 0.8745 (OUTLIER) REVERT: K 133 PHE cc_start: 0.9141 (m-80) cc_final: 0.8775 (m-80) REVERT: K 527 MET cc_start: 0.8829 (mtm) cc_final: 0.8483 (mtt) outliers start: 23 outliers final: 13 residues processed: 187 average time/residue: 0.7406 time to fit residues: 150.7788 Evaluate side-chains 176 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 164 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 415 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 50 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 76 optimal weight: 20.0000 chunk 78 optimal weight: 20.0000 chunk 0 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 118 optimal weight: 8.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 84 GLN C 104 GLN C 110 ASN G 73 ASN G 104 GLN ** K 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.085431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.059591 restraints weight = 45711.015| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.16 r_work: 0.2910 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 17214 Z= 0.193 Angle : 0.691 9.710 24507 Z= 0.385 Chirality : 0.048 0.335 2781 Planarity : 0.005 0.092 2100 Dihedral : 30.565 171.180 4612 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.90 % Allowed : 13.25 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.24), residues: 1269 helix: 1.44 (0.19), residues: 778 sheet: -2.24 (0.64), residues: 65 loop : -1.81 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 134 TYR 0.013 0.001 TYR K 191 PHE 0.011 0.001 PHE C 25 TRP 0.010 0.001 TRP K 267 HIS 0.017 0.001 HIS K 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.19 (17214) covalent geometry : angle 0.69068 / 0.38 (24507) hydrogen bonds : bond 0.05154 / 3.48 ( 940) hydrogen bonds : angle 3.59447 / 2.58 ( 2399) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 172 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8842 (t0) cc_final: 0.8468 (t0) REVERT: D 68 GLU cc_start: 0.8650 (tp30) cc_final: 0.8326 (tp30) REVERT: D 102 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7627 (tp30) REVERT: F 68 ASP cc_start: 0.8580 (m-30) cc_final: 0.7914 (m-30) REVERT: F 92 ARG cc_start: 0.8617 (ttp80) cc_final: 0.8271 (ttp80) REVERT: G 15 LYS cc_start: 0.8626 (tptm) cc_final: 0.8203 (tmtt) REVERT: H 65 ASP cc_start: 0.9065 (t0) cc_final: 0.8766 (t0) REVERT: K 133 PHE cc_start: 0.9079 (m-80) cc_final: 0.8759 (m-80) REVERT: K 527 MET cc_start: 0.8814 (mtm) cc_final: 0.8498 (mtt) outliers start: 32 outliers final: 13 residues processed: 186 average time/residue: 0.6803 time to fit residues: 137.8521 Evaluate side-chains 175 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 162 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 137 LEU 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: 152 random chunks: chunk 95 optimal weight: 20.0000 chunk 69 optimal weight: 0.6980 chunk 91 optimal weight: 10.0000 chunk 104 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 chunk 76 optimal weight: 20.0000 chunk 109 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 110 optimal weight: 9.9990 chunk 140 optimal weight: 8.9990 chunk 129 optimal weight: 0.0020 overall best weight: 2.1192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 84 GLN C 110 ASN G 73 ASN ** K 648 GLN ** 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 = 0.3683 r_free = 0.3683 target = 0.085519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.059882 restraints weight = 45688.644| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.15 r_work: 0.2918 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 17214 Z= 0.182 Angle : 0.685 10.069 24507 Z= 0.379 Chirality : 0.047 0.334 2781 Planarity : 0.004 0.084 2100 Dihedral : 30.596 171.253 4611 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.72 % Allowed : 15.70 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.24), residues: 1269 helix: 1.60 (0.19), residues: 771 sheet: -2.04 (0.67), residues: 63 loop : -1.79 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 134 TYR 0.012 0.001 TYR K 191 PHE 0.008 0.001 PHE K 296 TRP 0.008 0.001 TRP K 267 HIS 0.013 0.001 HIS K 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.18 (17214) covalent geometry : angle 0.68523 / 0.38 (24507) hydrogen bonds : bond 0.04964 / 3.35 ( 940) hydrogen bonds : angle 3.55079 / 2.55 ( 2399) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8862 (t0) cc_final: 0.8471 (t0) REVERT: D 68 GLU cc_start: 0.8625 (tp30) cc_final: 0.8299 (tp30) REVERT: D 102 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7637 (tp30) REVERT: F 68 ASP cc_start: 0.8637 (m-30) cc_final: 0.7894 (m-30) REVERT: F 92 ARG cc_start: 0.8624 (ttp80) cc_final: 0.8208 (ttp80) REVERT: G 15 LYS cc_start: 0.8585 (tptm) cc_final: 0.8153 (tmtt) REVERT: H 65 ASP cc_start: 0.9066 (t0) cc_final: 0.8775 (t0) REVERT: K 120 LYS cc_start: 0.9151 (pttm) cc_final: 0.8930 (tmmt) REVERT: K 133 PHE cc_start: 0.9122 (m-80) cc_final: 0.8812 (m-80) REVERT: K 527 MET cc_start: 0.8785 (mtm) cc_final: 0.8467 (mtt) outliers start: 30 outliers final: 15 residues processed: 185 average time/residue: 0.6774 time to fit residues: 136.6778 Evaluate side-chains 177 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 207 LEU 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: 152 random chunks: chunk 25 optimal weight: 0.0770 chunk 35 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 151 optimal weight: 6.9990 chunk 76 optimal weight: 20.0000 chunk 107 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 84 GLN C 104 GLN C 110 ASN D 81 ASN G 73 ASN ** K 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.086615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.061166 restraints weight = 45325.261| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.19 r_work: 0.2951 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 17214 Z= 0.140 Angle : 0.665 11.111 24507 Z= 0.369 Chirality : 0.046 0.313 2781 Planarity : 0.004 0.076 2100 Dihedral : 30.498 171.893 4611 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.18 % Allowed : 17.06 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.24), residues: 1269 helix: 1.71 (0.19), residues: 777 sheet: -1.79 (0.68), residues: 63 loop : -1.70 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 134 TYR 0.014 0.001 TYR H 39 PHE 0.008 0.001 PHE B 61 TRP 0.008 0.001 TRP K 267 HIS 0.011 0.001 HIS K 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.14 (17214) covalent geometry : angle 0.66543 / 0.37 (24507) hydrogen bonds : bond 0.04419 / 2.99 ( 940) hydrogen bonds : angle 3.41807 / 2.46 ( 2399) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 185 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: A 125 GLN cc_start: 0.9180 (OUTLIER) cc_final: 0.8843 (mp10) REVERT: C 90 ASP cc_start: 0.8860 (t0) cc_final: 0.8461 (t0) REVERT: C 110 ASN cc_start: 0.8871 (t0) cc_final: 0.8660 (t0) REVERT: D 68 GLU cc_start: 0.8647 (tp30) cc_final: 0.8335 (tp30) REVERT: D 102 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7535 (tp30) REVERT: F 30 THR cc_start: 0.8022 (OUTLIER) cc_final: 0.7817 (p) REVERT: F 68 ASP cc_start: 0.8618 (m-30) cc_final: 0.7764 (m-30) REVERT: F 92 ARG cc_start: 0.8630 (ttp80) cc_final: 0.8165 (ttp80) REVERT: G 15 LYS cc_start: 0.8605 (tptm) cc_final: 0.8364 (tmtt) REVERT: G 104 GLN cc_start: 0.8744 (tp40) cc_final: 0.8368 (mm110) REVERT: H 65 ASP cc_start: 0.9017 (t0) cc_final: 0.8738 (t0) REVERT: K 120 LYS cc_start: 0.9095 (pttm) cc_final: 0.8887 (tmmt) REVERT: K 133 PHE cc_start: 0.9110 (m-80) cc_final: 0.8797 (m-80) REVERT: K 263 GLU cc_start: 0.9390 (tp30) cc_final: 0.9098 (tp30) REVERT: K 433 MET cc_start: 0.8141 (mmm) cc_final: 0.7833 (tpt) REVERT: K 527 MET cc_start: 0.8758 (mtm) cc_final: 0.8455 (mtt) outliers start: 24 outliers final: 15 residues processed: 196 average time/residue: 0.6148 time to fit residues: 131.2749 Evaluate side-chains 185 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 168 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain K residue 538 CYS Chi-restraints excluded: chain K residue 546 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 47 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 95 optimal weight: 20.0000 chunk 58 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 127 optimal weight: 0.0030 overall best weight: 0.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 84 GLN G 73 ASN ** K 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.086545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.061138 restraints weight = 45975.909| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.18 r_work: 0.2955 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17214 Z= 0.143 Angle : 0.667 11.573 24507 Z= 0.370 Chirality : 0.047 0.323 2781 Planarity : 0.004 0.069 2100 Dihedral : 30.483 171.720 4611 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.09 % Allowed : 18.33 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.24), residues: 1269 helix: 1.80 (0.19), residues: 778 sheet: -1.65 (0.69), residues: 63 loop : -1.67 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG K 134 TYR 0.011 0.001 TYR C 57 PHE 0.008 0.001 PHE A 67 TRP 0.010 0.001 TRP K 267 HIS 0.009 0.001 HIS K 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.14 (17214) covalent geometry : angle 0.66731 / 0.37 (24507) hydrogen bonds : bond 0.04415 / 2.98 ( 940) hydrogen bonds : angle 3.39259 / 2.44 ( 2399) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 0.473 Fit side-chains revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8889 (t0) cc_final: 0.8466 (t0) REVERT: C 91 GLU cc_start: 0.8355 (tp30) cc_final: 0.8073 (tp30) REVERT: D 68 GLU cc_start: 0.8614 (tp30) cc_final: 0.8294 (tp30) REVERT: F 68 ASP cc_start: 0.8630 (m-30) cc_final: 0.8113 (m-30) REVERT: F 92 ARG cc_start: 0.8638 (ttp80) cc_final: 0.8304 (ttp80) REVERT: G 15 LYS cc_start: 0.8594 (tptm) cc_final: 0.8340 (tmtt) REVERT: G 104 GLN cc_start: 0.8721 (tp40) cc_final: 0.8340 (mm110) REVERT: H 65 ASP cc_start: 0.9030 (t0) cc_final: 0.8751 (t0) REVERT: K 133 PHE cc_start: 0.9062 (m-80) cc_final: 0.8763 (m-80) REVERT: K 527 MET cc_start: 0.8763 (mtm) cc_final: 0.8485 (mtt) REVERT: K 638 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8226 (tm-30) REVERT: K 642 GLN cc_start: 0.8859 (mt0) cc_final: 0.8417 (mt0) outliers start: 23 outliers final: 14 residues processed: 185 average time/residue: 0.6413 time to fit residues: 129.2837 Evaluate side-chains 178 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain K residue 538 CYS Chi-restraints excluded: chain K residue 546 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 17 optimal weight: 4.9990 chunk 106 optimal weight: 20.0000 chunk 24 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 75 optimal weight: 20.0000 chunk 107 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 45 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 84 GLN C 110 ASN G 73 ASN ** K 648 GLN ** 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 = 0.3695 r_free = 0.3695 target = 0.086145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.060587 restraints weight = 45348.088| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.15 r_work: 0.2936 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 17214 Z= 0.172 Angle : 0.686 12.382 24507 Z= 0.376 Chirality : 0.047 0.343 2781 Planarity : 0.004 0.066 2100 Dihedral : 30.555 171.348 4611 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.09 % Allowed : 18.87 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.24), residues: 1269 helix: 1.81 (0.19), residues: 778 sheet: -1.59 (0.64), residues: 70 loop : -1.64 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG K 134 TYR 0.015 0.001 TYR H 39 PHE 0.010 0.001 PHE B 61 TRP 0.012 0.001 TRP K 267 HIS 0.008 0.001 HIS K 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.17 (17214) covalent geometry : angle 0.68617 / 0.38 (24507) hydrogen bonds : bond 0.04627 / 3.11 ( 940) hydrogen bonds : angle 3.41684 / 2.46 ( 2399) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 169 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8936 (t0) cc_final: 0.8535 (t0) REVERT: C 91 GLU cc_start: 0.8419 (tp30) cc_final: 0.8216 (tp30) REVERT: D 68 GLU cc_start: 0.8630 (tp30) cc_final: 0.8320 (tp30) REVERT: F 92 ARG cc_start: 0.8636 (ttp80) cc_final: 0.8292 (ttp80) REVERT: G 15 LYS cc_start: 0.8598 (tptm) cc_final: 0.8341 (tmtt) REVERT: G 104 GLN cc_start: 0.8696 (tp40) cc_final: 0.8209 (mm110) REVERT: H 65 ASP cc_start: 0.9021 (t0) cc_final: 0.8749 (t0) REVERT: K 133 PHE cc_start: 0.9053 (m-80) cc_final: 0.8758 (m-80) REVERT: K 433 MET cc_start: 0.8040 (tmm) cc_final: 0.7805 (tpt) REVERT: K 499 TYR cc_start: 0.8656 (OUTLIER) cc_final: 0.8449 (t80) REVERT: K 527 MET cc_start: 0.8828 (mtm) cc_final: 0.8509 (mtt) REVERT: K 642 GLN cc_start: 0.8919 (mt0) cc_final: 0.8523 (mt0) outliers start: 23 outliers final: 18 residues processed: 178 average time/residue: 0.6363 time to fit residues: 123.7798 Evaluate side-chains 187 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 223 MET Chi-restraints excluded: chain K residue 335 MET Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain K residue 499 TYR Chi-restraints excluded: chain K residue 538 CYS Chi-restraints excluded: chain K residue 546 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 120 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 93 optimal weight: 20.0000 chunk 143 optimal weight: 0.0770 chunk 49 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 102 optimal weight: 20.0000 chunk 148 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 84 GLN G 73 ASN ** K 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.086760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.061186 restraints weight = 45748.684| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.15 r_work: 0.2959 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17214 Z= 0.146 Angle : 0.677 12.522 24507 Z= 0.372 Chirality : 0.046 0.325 2781 Planarity : 0.004 0.059 2100 Dihedral : 30.512 171.743 4611 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.63 % Allowed : 20.15 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.24), residues: 1269 helix: 1.84 (0.19), residues: 776 sheet: -1.39 (0.65), residues: 70 loop : -1.56 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG K 134 TYR 0.010 0.001 TYR C 57 PHE 0.009 0.001 PHE A 67 TRP 0.014 0.001 TRP K 267 HIS 0.007 0.001 HIS K 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.15 (17214) covalent geometry : angle 0.67745 / 0.37 (24507) hydrogen bonds : bond 0.04345 / 2.94 ( 940) hydrogen bonds : angle 3.38994 / 2.45 ( 2399) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 177 time to evaluate : 0.500 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7967 (mp0) REVERT: C 90 ASP cc_start: 0.8969 (t0) cc_final: 0.8597 (t0) REVERT: D 68 GLU cc_start: 0.8614 (tp30) cc_final: 0.8307 (tp30) REVERT: F 92 ARG cc_start: 0.8658 (ttp80) cc_final: 0.8290 (ttp80) REVERT: G 15 LYS cc_start: 0.8609 (tptm) cc_final: 0.8348 (tmtt) REVERT: G 104 GLN cc_start: 0.8697 (tp40) cc_final: 0.8229 (mm110) REVERT: H 65 ASP cc_start: 0.9008 (t0) cc_final: 0.8734 (t0) REVERT: K 133 PHE cc_start: 0.9052 (m-80) cc_final: 0.8783 (m-80) REVERT: K 263 GLU cc_start: 0.9386 (tp30) cc_final: 0.9132 (tp30) REVERT: K 433 MET cc_start: 0.8021 (mmm) cc_final: 0.7691 (tpt) REVERT: K 499 TYR cc_start: 0.8652 (OUTLIER) cc_final: 0.8446 (t80) REVERT: K 527 MET cc_start: 0.8795 (mtm) cc_final: 0.8498 (mtt) REVERT: K 638 GLU cc_start: 0.8819 (tm-30) cc_final: 0.8494 (tm-30) REVERT: K 642 GLN cc_start: 0.8951 (mt0) cc_final: 0.8638 (mt0) outliers start: 18 outliers final: 14 residues processed: 185 average time/residue: 0.6673 time to fit residues: 134.4215 Evaluate side-chains 178 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 163 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain K residue 499 TYR Chi-restraints excluded: chain K residue 538 CYS Chi-restraints excluded: chain K residue 546 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 50 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 105 optimal weight: 10.0000 chunk 114 optimal weight: 0.1980 chunk 138 optimal weight: 9.9990 chunk 13 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 144 optimal weight: 6.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 73 ASN ** K 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.087608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.062075 restraints weight = 45499.564| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.22 r_work: 0.2983 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 17214 Z= 0.137 Angle : 0.683 17.337 24507 Z= 0.373 Chirality : 0.045 0.318 2781 Planarity : 0.004 0.056 2100 Dihedral : 30.423 172.084 4611 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.63 % Allowed : 20.96 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.25), residues: 1269 helix: 1.88 (0.19), residues: 781 sheet: -1.26 (0.62), residues: 79 loop : -1.49 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG K 134 TYR 0.015 0.001 TYR H 39 PHE 0.015 0.001 PHE K 119 TRP 0.016 0.001 TRP K 267 HIS 0.007 0.001 HIS K 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.14 (17214) covalent geometry : angle 0.68263 / 0.37 (24507) hydrogen bonds : bond 0.04117 / 2.80 ( 940) hydrogen bonds : angle 3.29898 / 2.38 ( 2399) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 174 time to evaluate : 0.516 Fit side-chains REVERT: A 50 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7973 (mp0) REVERT: C 90 ASP cc_start: 0.8938 (t0) cc_final: 0.8584 (t0) REVERT: C 91 GLU cc_start: 0.8496 (tp30) cc_final: 0.8205 (tp30) REVERT: D 68 GLU cc_start: 0.8632 (tp30) cc_final: 0.8328 (tp30) REVERT: F 68 ASP cc_start: 0.8500 (m-30) cc_final: 0.8248 (m-30) REVERT: F 92 ARG cc_start: 0.8649 (ttp80) cc_final: 0.8417 (ttp80) REVERT: G 15 LYS cc_start: 0.8580 (tptm) cc_final: 0.8320 (tmtt) REVERT: H 65 ASP cc_start: 0.9008 (t0) cc_final: 0.8759 (t0) REVERT: K 133 PHE cc_start: 0.9063 (m-80) cc_final: 0.8762 (m-80) REVERT: K 357 GLN cc_start: 0.8962 (mt0) cc_final: 0.8657 (mm-40) REVERT: K 433 MET cc_start: 0.7907 (mmm) cc_final: 0.7518 (tpt) REVERT: K 527 MET cc_start: 0.8814 (mtm) cc_final: 0.8559 (mtt) REVERT: K 642 GLN cc_start: 0.8983 (mt0) cc_final: 0.8588 (mt0) outliers start: 18 outliers final: 12 residues processed: 183 average time/residue: 0.6650 time to fit residues: 132.8627 Evaluate side-chains 177 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 165 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain K residue 538 CYS Chi-restraints excluded: chain K residue 546 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 105 optimal weight: 20.0000 chunk 48 optimal weight: 0.9980 chunk 97 optimal weight: 20.0000 chunk 43 optimal weight: 0.8980 chunk 102 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 135 optimal weight: 0.0980 chunk 116 optimal weight: 9.9990 chunk 142 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 84 GLN G 73 ASN ** K 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.087722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.062179 restraints weight = 45653.069| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.22 r_work: 0.2983 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 17214 Z= 0.143 Angle : 0.699 17.344 24507 Z= 0.380 Chirality : 0.046 0.323 2781 Planarity : 0.004 0.057 2100 Dihedral : 30.416 171.726 4611 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.27 % Allowed : 22.05 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.24), residues: 1269 helix: 1.86 (0.19), residues: 779 sheet: -1.25 (0.62), residues: 79 loop : -1.43 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 76 TYR 0.025 0.001 TYR F 88 PHE 0.016 0.001 PHE K 119 TRP 0.015 0.001 TRP K 267 HIS 0.007 0.001 HIS K 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.14 (17214) covalent geometry : angle 0.69911 / 0.38 (24507) hydrogen bonds : bond 0.04184 / 2.84 ( 940) hydrogen bonds : angle 3.34058 / 2.42 ( 2399) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 165 time to evaluate : 0.427 Fit side-chains REVERT: A 50 GLU cc_start: 0.8290 (mt-10) cc_final: 0.8001 (mp0) REVERT: C 90 ASP cc_start: 0.8976 (t0) cc_final: 0.8619 (t0) REVERT: C 91 GLU cc_start: 0.8524 (tp30) cc_final: 0.8267 (tp30) REVERT: D 68 GLU cc_start: 0.8606 (tp30) cc_final: 0.8304 (tp30) REVERT: F 68 ASP cc_start: 0.8506 (m-30) cc_final: 0.7786 (m-30) REVERT: F 92 ARG cc_start: 0.8657 (ttp80) cc_final: 0.8220 (ttp80) REVERT: G 15 LYS cc_start: 0.8545 (tptm) cc_final: 0.8279 (tmtt) REVERT: G 104 GLN cc_start: 0.8627 (tp40) cc_final: 0.8181 (mm110) REVERT: H 65 ASP cc_start: 0.8989 (t0) cc_final: 0.8742 (t0) REVERT: K 133 PHE cc_start: 0.9119 (m-80) cc_final: 0.8874 (m-80) REVERT: K 357 GLN cc_start: 0.8968 (mt0) cc_final: 0.8620 (mm-40) REVERT: K 433 MET cc_start: 0.7885 (mmm) cc_final: 0.7514 (tpt) REVERT: K 436 MET cc_start: 0.7850 (tpp) cc_final: 0.7549 (tpt) REVERT: K 527 MET cc_start: 0.8832 (mtm) cc_final: 0.8508 (mtt) REVERT: K 642 GLN cc_start: 0.9031 (mt0) cc_final: 0.8629 (mt0) outliers start: 14 outliers final: 13 residues processed: 173 average time/residue: 0.6884 time to fit residues: 129.6326 Evaluate side-chains 174 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 161 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain K residue 538 CYS Chi-restraints excluded: chain K residue 546 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 82 optimal weight: 20.0000 chunk 107 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 109 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 146 optimal weight: 8.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 73 ASN ** K 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.086827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.061130 restraints weight = 45572.149| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.19 r_work: 0.2954 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 17214 Z= 0.188 Angle : 0.713 15.897 24507 Z= 0.385 Chirality : 0.046 0.337 2781 Planarity : 0.004 0.056 2100 Dihedral : 30.489 172.214 4611 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.72 % Allowed : 21.69 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.24), residues: 1269 helix: 1.82 (0.19), residues: 780 sheet: -1.02 (0.68), residues: 66 loop : -1.44 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG K 134 TYR 0.034 0.001 TYR F 88 PHE 0.009 0.001 PHE B 61 TRP 0.018 0.002 TRP K 267 HIS 0.007 0.001 HIS K 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.19 (17214) covalent geometry : angle 0.71251 / 0.39 (24507) hydrogen bonds : bond 0.04516 / 3.04 ( 940) hydrogen bonds : angle 3.37564 / 2.44 ( 2399) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4567.14 seconds wall clock time: 78 minutes 33.55 seconds (4713.55 seconds total)