Starting phenix.real_space_refine on Fri Jul 3 20:10:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jnz_61632/07_2026/9jnz_61632.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jnz_61632/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9jnz_61632/07_2026/9jnz_61632.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jnz_61632/07_2026/9jnz_61632.map" model { file = "/net/cci-nas-00/data/ceres_data/9jnz_61632/07_2026/9jnz_61632.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jnz_61632/07_2026/9jnz_61632.cif" } 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-dev-6108/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, 0 Ad-hoc single atom residues: {' CL': 1} Chain breaks: 1 Time building chain proxies: 3.73, 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: 1.36 Conformation dependent library (CDL) restraints added in 566.5 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: 2.38 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: 3.79 Time building geometry restraints manager: 1.91 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: 23944 2.32 - 4.65: 522 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: 1.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 19.070 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 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:7.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.610 ------------------------------------------------------------------------------- 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 : 0.808 11.622 24507 Z= 0.651 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 0.80839 / 0.65 (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 : 0.544 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: 0.8436 (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: 0.7528 time to fit residues: 177.8437 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 : 0.506 ------------------------------------------------------------------------------- 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 = 0.3689 r_free = 0.3689 target = 0.085841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.060266 restraints weight = 45208.535| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.15 r_work: 0.2923 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.0901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 17214 Z= 0.184 Angle : 0.692 8.063 24507 Z= 0.392 Chirality : 0.048 0.294 2781 Planarity : 0.005 0.100 2100 Dihedral : 30.558 172.933 4615 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.00 % Allowed : 10.98 % Favored : 87.02 % 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: -2.44 (0.64), residues: 65 loop : -1.88 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 83 TYR 0.016 0.002 TYR K 191 PHE 0.012 0.001 PHE K 183 TRP 0.012 0.001 TRP K 267 HIS 0.025 0.002 HIS K 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.18 (17214) covalent geometry : angle 0.69195 / 0.39 (24507) hydrogen bonds : bond 0.05307 / 3.59 ( 940) hydrogen bonds : angle 3.67789 / 2.65 ( 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 199 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 177 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8812 (t0) cc_final: 0.8464 (t0) REVERT: D 68 GLU cc_start: 0.8647 (tp30) cc_final: 0.8321 (tp30) REVERT: F 92 ARG cc_start: 0.8590 (ttp80) cc_final: 0.8314 (ttp80) REVERT: H 65 ASP cc_start: 0.9017 (t0) cc_final: 0.8749 (OUTLIER) REVERT: H 83 ARG cc_start: 0.8903 (mmt90) cc_final: 0.8674 (mmt90) REVERT: K 133 PHE cc_start: 0.9117 (m-80) cc_final: 0.8756 (m-80) REVERT: K 527 MET cc_start: 0.8830 (mtm) cc_final: 0.8488 (mtt) outliers start: 22 outliers final: 11 residues processed: 187 average time/residue: 0.7422 time to fit residues: 151.1646 Evaluate side-chains 173 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 163 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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 113 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: 0.6980 chunk 46 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 151 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 chunk 76 optimal weight: 20.0000 chunk 78 optimal weight: 9.9990 chunk 0 optimal weight: 2.9990 chunk 116 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 118 optimal weight: 7.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 = 0.3678 r_free = 0.3678 target = 0.085298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.059434 restraints weight = 45684.507| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.20 r_work: 0.2906 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 17214 Z= 0.202 Angle : 0.682 9.474 24507 Z= 0.383 Chirality : 0.047 0.311 2781 Planarity : 0.005 0.091 2100 Dihedral : 30.668 171.959 4612 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.72 % Allowed : 13.61 % Favored : 83.67 % 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: 0.27 (0.24), residues: 1269 helix: 1.44 (0.19), residues: 778 sheet: -2.26 (0.64), residues: 65 loop : -1.82 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 134 TYR 0.012 0.001 TYR K 191 PHE 0.011 0.001 PHE K 185 TRP 0.009 0.001 TRP K 267 HIS 0.017 0.001 HIS K 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.20 (17214) covalent geometry : angle 0.68172 / 0.38 (24507) hydrogen bonds : bond 0.05239 / 3.53 ( 940) hydrogen bonds : angle 3.59306 / 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: 30 poor density : 174 time to evaluate : 0.494 Fit side-chains revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8845 (t0) cc_final: 0.8469 (t0) REVERT: D 68 GLU cc_start: 0.8652 (tp30) cc_final: 0.8333 (tp30) REVERT: D 102 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7730 (tp30) REVERT: F 68 ASP cc_start: 0.8494 (m-30) cc_final: 0.8018 (m-30) REVERT: F 92 ARG cc_start: 0.8628 (ttp80) cc_final: 0.8300 (ttp80) REVERT: H 65 ASP cc_start: 0.9065 (t0) cc_final: 0.8764 (t0) REVERT: H 83 ARG cc_start: 0.8945 (mmt90) cc_final: 0.8705 (mmt90) REVERT: K 133 PHE cc_start: 0.9111 (m-80) cc_final: 0.8785 (m-80) REVERT: K 527 MET cc_start: 0.8802 (mtm) cc_final: 0.8484 (mtt) outliers start: 30 outliers final: 15 residues processed: 187 average time/residue: 0.7386 time to fit residues: 150.3268 Evaluate side-chains 175 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 160 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 62 ILE 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: 0.9990 chunk 91 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 chunk 76 optimal weight: 20.0000 chunk 109 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 110 optimal weight: 0.8980 chunk 140 optimal weight: 7.9990 chunk 129 optimal weight: 10.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- 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 = 0.3652 r_free = 0.3652 target = 0.084497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.058301 restraints weight = 46299.791| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.25 r_work: 0.2865 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.127 17214 Z= 0.296 Angle : 0.741 9.535 24507 Z= 0.406 Chirality : 0.050 0.350 2781 Planarity : 0.005 0.084 2100 Dihedral : 30.884 171.502 4611 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.36 % Allowed : 15.43 % Favored : 81.22 % 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: 0.24 (0.24), residues: 1269 helix: 1.41 (0.19), residues: 773 sheet: -2.02 (0.65), residues: 66 loop : -1.83 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 134 TYR 0.016 0.002 TYR H 39 PHE 0.013 0.002 PHE G 25 TRP 0.009 0.002 TRP K 267 HIS 0.013 0.001 HIS K 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00645 / 0.30 (17214) covalent geometry : angle 0.74085 / 0.41 (24507) hydrogen bonds : bond 0.05914 / 3.98 ( 940) hydrogen bonds : angle 3.74130 / 2.69 ( 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 202 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 165 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8865 (t0) cc_final: 0.8516 (t0) REVERT: D 68 GLU cc_start: 0.8672 (tp30) cc_final: 0.8347 (tp30) REVERT: D 90 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8344 (mp0) REVERT: D 102 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7800 (tp30) REVERT: F 68 ASP cc_start: 0.8649 (m-30) cc_final: 0.8085 (m-30) REVERT: F 92 ARG cc_start: 0.8657 (ttp80) cc_final: 0.8250 (ttp80) REVERT: H 65 ASP cc_start: 0.9095 (t0) cc_final: 0.8766 (t0) REVERT: H 83 ARG cc_start: 0.8995 (mmt90) cc_final: 0.8651 (mmp80) REVERT: K 133 PHE cc_start: 0.9141 (m-80) cc_final: 0.8804 (m-80) REVERT: K 527 MET cc_start: 0.8862 (mtm) cc_final: 0.8583 (mtt) outliers start: 37 outliers final: 20 residues processed: 183 average time/residue: 0.7502 time to fit residues: 149.2859 Evaluate side-chains 177 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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 113 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 80 THR 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 53 SER Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 335 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 25 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 151 optimal weight: 3.9990 chunk 76 optimal weight: 20.0000 chunk 107 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 84 GLN C 104 GLN C 110 ASN G 73 ASN ** K 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.085921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.059854 restraints weight = 45883.665| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.24 r_work: 0.2907 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 17214 Z= 0.161 Angle : 0.676 10.860 24507 Z= 0.375 Chirality : 0.047 0.298 2781 Planarity : 0.004 0.078 2100 Dihedral : 30.793 172.188 4611 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.45 % Allowed : 17.70 % Favored : 79.85 % 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: 0.49 (0.24), residues: 1269 helix: 1.57 (0.19), residues: 780 sheet: -1.81 (0.67), residues: 64 loop : -1.73 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 134 TYR 0.012 0.001 TYR K 191 PHE 0.009 0.001 PHE B 61 TRP 0.008 0.001 TRP K 267 HIS 0.010 0.001 HIS K 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.16 (17214) covalent geometry : angle 0.67616 / 0.38 (24507) hydrogen bonds : bond 0.04816 / 3.24 ( 940) hydrogen bonds : angle 3.51576 / 2.53 ( 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 199 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 0.513 Fit side-chains revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8857 (t0) cc_final: 0.8490 (t0) REVERT: C 110 ASN cc_start: 0.8900 (t0) cc_final: 0.8690 (t0) REVERT: D 68 GLU cc_start: 0.8642 (tp30) cc_final: 0.8322 (tp30) REVERT: D 102 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7782 (tp30) REVERT: F 68 ASP cc_start: 0.8620 (m-30) cc_final: 0.7862 (m-30) REVERT: F 92 ARG cc_start: 0.8659 (ttp80) cc_final: 0.8247 (ttp80) REVERT: H 65 ASP cc_start: 0.9074 (t0) cc_final: 0.8772 (t0) REVERT: K 133 PHE cc_start: 0.9161 (m-80) cc_final: 0.8832 (m-80) REVERT: K 527 MET cc_start: 0.8798 (mtm) cc_final: 0.8391 (mtt) outliers start: 27 outliers final: 12 residues processed: 184 average time/residue: 0.7591 time to fit residues: 151.6372 Evaluate side-chains 175 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 163 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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 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 86 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 47 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 95 optimal weight: 20.0000 chunk 58 optimal weight: 5.9990 chunk 128 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 7 optimal weight: 0.1980 chunk 127 optimal weight: 0.0070 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN C 84 GLN D 81 ASN F 93 GLN 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 = 0.3708 r_free = 0.3708 target = 0.086758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.061190 restraints weight = 45820.153| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.24 r_work: 0.2956 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17214 Z= 0.136 Angle : 0.658 11.849 24507 Z= 0.367 Chirality : 0.045 0.285 2781 Planarity : 0.004 0.070 2100 Dihedral : 30.621 173.062 4611 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.72 % Allowed : 18.69 % Favored : 78.58 % 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: 0.72 (0.24), residues: 1269 helix: 1.76 (0.19), residues: 774 sheet: -1.54 (0.68), residues: 64 loop : -1.65 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 134 TYR 0.018 0.001 TYR H 39 PHE 0.010 0.001 PHE A 67 TRP 0.013 0.001 TRP K 267 HIS 0.008 0.001 HIS K 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.14 (17214) covalent geometry : angle 0.65833 / 0.37 (24507) hydrogen bonds : bond 0.04326 / 2.95 ( 940) hydrogen bonds : angle 3.37774 / 2.43 ( 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 217 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 187 time to evaluate : 0.498 Fit side-chains revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8892 (t0) cc_final: 0.8493 (t0) REVERT: D 68 GLU cc_start: 0.8644 (tp30) cc_final: 0.8328 (tp30) REVERT: F 68 ASP cc_start: 0.8630 (m-30) cc_final: 0.7842 (m-30) REVERT: F 92 ARG cc_start: 0.8657 (ttp80) cc_final: 0.8197 (ttp80) REVERT: G 15 LYS cc_start: 0.8584 (tptm) cc_final: 0.8382 (tmtt) REVERT: H 60 ASN cc_start: 0.9042 (t0) cc_final: 0.8840 (t0) REVERT: H 65 ASP cc_start: 0.9019 (t0) cc_final: 0.8749 (t0) REVERT: K 133 PHE cc_start: 0.9114 (m-80) cc_final: 0.8827 (m-80) REVERT: K 263 GLU cc_start: 0.9362 (tp30) cc_final: 0.9067 (tp30) REVERT: K 433 MET cc_start: 0.7977 (tmm) cc_final: 0.7755 (tpt) REVERT: K 527 MET cc_start: 0.8788 (mtm) cc_final: 0.8472 (mtt) REVERT: K 642 GLN cc_start: 0.8958 (mt0) cc_final: 0.8584 (mt0) outliers start: 30 outliers final: 11 residues processed: 201 average time/residue: 0.7418 time to fit residues: 162.5206 Evaluate side-chains 177 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 166 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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 G residue 113 SER Chi-restraints excluded: chain H residue 70 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: 6.9990 chunk 106 optimal weight: 20.0000 chunk 24 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 75 optimal weight: 20.0000 chunk 107 optimal weight: 0.3980 chunk 124 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.3705 r_free = 0.3705 target = 0.086492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.061100 restraints weight = 45439.476| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.19 r_work: 0.2954 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17214 Z= 0.148 Angle : 0.673 12.306 24507 Z= 0.372 Chirality : 0.046 0.303 2781 Planarity : 0.004 0.062 2100 Dihedral : 30.632 172.499 4611 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.00 % Allowed : 20.60 % 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: 0.82 (0.24), residues: 1269 helix: 1.84 (0.19), residues: 775 sheet: -1.38 (0.70), residues: 64 loop : -1.63 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG K 134 TYR 0.010 0.001 TYR C 57 PHE 0.010 0.001 PHE A 67 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 0.00281 / 0.15 (17214) covalent geometry : angle 0.67339 / 0.37 (24507) hydrogen bonds : bond 0.04374 / 2.96 ( 940) hydrogen bonds : angle 3.38142 / 2.43 ( 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 198 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 176 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8931 (t0) cc_final: 0.8537 (t0) REVERT: C 91 GLU cc_start: 0.8452 (tp30) cc_final: 0.8008 (tp30) REVERT: D 68 GLU cc_start: 0.8628 (tp30) cc_final: 0.8323 (tp30) REVERT: F 92 ARG cc_start: 0.8666 (ttp80) cc_final: 0.8191 (ttp80) REVERT: G 15 LYS cc_start: 0.8600 (tptm) cc_final: 0.8351 (tmtt) REVERT: G 104 GLN cc_start: 0.8693 (tp40) cc_final: 0.8235 (mm110) REVERT: H 60 ASN cc_start: 0.9053 (t0) cc_final: 0.8845 (t0) REVERT: H 65 ASP cc_start: 0.9021 (t0) cc_final: 0.8745 (t0) REVERT: K 133 PHE cc_start: 0.9113 (m-80) cc_final: 0.8831 (m-80) REVERT: K 433 MET cc_start: 0.8105 (mmm) cc_final: 0.7726 (tpt) REVERT: K 527 MET cc_start: 0.8795 (mtm) cc_final: 0.8555 (mtt) REVERT: K 642 GLN cc_start: 0.8918 (mt0) cc_final: 0.8514 (mt0) outliers start: 22 outliers final: 12 residues processed: 187 average time/residue: 0.7570 time to fit residues: 154.0585 Evaluate side-chains 178 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 166 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 C residue 113 SER Chi-restraints excluded: chain E residue 124 ILE 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 404 VAL 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: 6.9990 chunk 93 optimal weight: 20.0000 chunk 143 optimal weight: 9.9990 chunk 49 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 102 optimal weight: 20.0000 chunk 148 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 = 0.3687 r_free = 0.3687 target = 0.086287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.060666 restraints weight = 46730.880| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.18 r_work: 0.2917 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 17214 Z= 0.199 Angle : 0.698 12.047 24507 Z= 0.382 Chirality : 0.047 0.327 2781 Planarity : 0.004 0.058 2100 Dihedral : 30.746 171.788 4611 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.00 % Allowed : 21.78 % Favored : 76.23 % 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: 0.77 (0.24), residues: 1269 helix: 1.75 (0.19), residues: 785 sheet: -1.52 (0.67), residues: 70 loop : -1.60 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG K 134 TYR 0.016 0.001 TYR H 39 PHE 0.010 0.001 PHE B 61 TRP 0.017 0.002 TRP K 267 HIS 0.007 0.001 HIS K 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.20 (17214) covalent geometry : angle 0.69795 / 0.38 (24507) hydrogen bonds : bond 0.04883 / 3.28 ( 940) hydrogen bonds : angle 3.47998 / 2.50 ( 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 190 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8958 (t0) cc_final: 0.8592 (t0) REVERT: D 68 GLU cc_start: 0.8633 (tp30) cc_final: 0.8314 (tp30) REVERT: F 92 ARG cc_start: 0.8702 (ttp80) cc_final: 0.8298 (ttp80) REVERT: G 13 LYS cc_start: 0.8815 (tppp) cc_final: 0.8596 (tmtt) REVERT: G 15 LYS cc_start: 0.8577 (tptm) cc_final: 0.8353 (tmtt) REVERT: H 65 ASP cc_start: 0.9060 (t0) cc_final: 0.8769 (t0) REVERT: K 133 PHE cc_start: 0.9066 (m-80) cc_final: 0.8751 (m-80) REVERT: K 527 MET cc_start: 0.8868 (mtm) cc_final: 0.8552 (mtt) REVERT: K 642 GLN cc_start: 0.8987 (mt0) cc_final: 0.8593 (mt0) outliers start: 22 outliers final: 12 residues processed: 178 average time/residue: 0.7597 time to fit residues: 147.1488 Evaluate side-chains 173 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 161 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 50 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 105 optimal weight: 20.0000 chunk 114 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 144 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3712 r_free = 0.3712 target = 0.087530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.062140 restraints weight = 46406.000| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.17 r_work: 0.2956 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17214 Z= 0.141 Angle : 0.695 15.757 24507 Z= 0.377 Chirality : 0.046 0.295 2781 Planarity : 0.004 0.057 2100 Dihedral : 30.637 172.759 4611 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.63 % Allowed : 22.41 % Favored : 75.95 % 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: 0.84 (0.24), residues: 1269 helix: 1.79 (0.19), residues: 784 sheet: -1.40 (0.65), residues: 70 loop : -1.54 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG K 134 TYR 0.010 0.001 TYR C 57 PHE 0.009 0.001 PHE B 61 TRP 0.019 0.001 TRP K 267 HIS 0.008 0.001 HIS B 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.14 (17214) covalent geometry : angle 0.69526 / 0.38 (24507) hydrogen bonds : bond 0.04316 / 2.92 ( 940) hydrogen bonds : angle 3.35435 / 2.43 ( 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 185 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 167 time to evaluate : 0.517 Fit side-chains REVERT: C 90 ASP cc_start: 0.8973 (t0) cc_final: 0.8613 (t0) REVERT: C 91 GLU cc_start: 0.8303 (tp30) cc_final: 0.7980 (tp30) REVERT: D 68 GLU cc_start: 0.8622 (tp30) cc_final: 0.8315 (tp30) REVERT: F 68 ASP cc_start: 0.8438 (m-30) cc_final: 0.7773 (m-30) REVERT: F 92 ARG cc_start: 0.8664 (ttp80) cc_final: 0.8377 (ttp80) REVERT: G 13 LYS cc_start: 0.8801 (tppp) cc_final: 0.8589 (tmtt) REVERT: G 15 LYS cc_start: 0.8545 (tptm) cc_final: 0.8312 (tmtt) REVERT: G 104 GLN cc_start: 0.8680 (tp40) cc_final: 0.8218 (mm110) REVERT: H 60 ASN cc_start: 0.9089 (t0) cc_final: 0.8884 (t0) REVERT: H 65 ASP cc_start: 0.9009 (t0) cc_final: 0.8734 (t0) REVERT: K 133 PHE cc_start: 0.9117 (m-80) cc_final: 0.8842 (m-80) REVERT: K 433 MET cc_start: 0.7976 (tmm) cc_final: 0.7695 (tpt) REVERT: K 527 MET cc_start: 0.8835 (mtm) cc_final: 0.8530 (mtt) REVERT: K 642 GLN cc_start: 0.8979 (mt0) cc_final: 0.8593 (mt0) outliers start: 18 outliers final: 14 residues processed: 177 average time/residue: 0.7562 time to fit residues: 145.6879 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 : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU 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 E residue 87 SER Chi-restraints excluded: chain E residue 124 ILE 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 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: 0.0040 chunk 48 optimal weight: 0.7980 chunk 97 optimal weight: 20.0000 chunk 43 optimal weight: 0.9980 chunk 102 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 116 optimal weight: 8.9990 chunk 142 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 overall best weight: 1.3596 ------------------------------------------------------------------------------- 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 = 0.3708 r_free = 0.3708 target = 0.086712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.061218 restraints weight = 45394.685| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.13 r_work: 0.2956 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17214 Z= 0.155 Angle : 0.702 14.739 24507 Z= 0.381 Chirality : 0.046 0.305 2781 Planarity : 0.004 0.056 2100 Dihedral : 30.619 172.594 4611 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.45 % Allowed : 22.50 % Favored : 76.04 % 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: 0.89 (0.24), residues: 1269 helix: 1.82 (0.19), residues: 782 sheet: -1.28 (0.66), residues: 70 loop : -1.50 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 71 TYR 0.016 0.001 TYR H 39 PHE 0.010 0.001 PHE A 67 TRP 0.022 0.002 TRP K 267 HIS 0.007 0.001 HIS B 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 (17214) covalent geometry : angle 0.70217 / 0.38 (24507) hydrogen bonds : bond 0.04401 / 2.97 ( 940) hydrogen bonds : angle 3.33186 / 2.41 ( 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 182 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 0.534 Fit side-chains REVERT: C 90 ASP cc_start: 0.8984 (t0) cc_final: 0.8619 (t0) REVERT: C 91 GLU cc_start: 0.8303 (tp30) cc_final: 0.8037 (tp30) REVERT: D 68 GLU cc_start: 0.8608 (tp30) cc_final: 0.8295 (tp30) REVERT: F 68 ASP cc_start: 0.8453 (m-30) cc_final: 0.7777 (m-30) REVERT: F 92 ARG cc_start: 0.8693 (ttp80) cc_final: 0.8410 (ttp80) REVERT: G 13 LYS cc_start: 0.8852 (tppp) cc_final: 0.8633 (tmtt) REVERT: G 15 LYS cc_start: 0.8536 (tptm) cc_final: 0.8298 (tmtt) REVERT: H 60 ASN cc_start: 0.9100 (t0) cc_final: 0.8898 (t0) REVERT: H 65 ASP cc_start: 0.9004 (t0) cc_final: 0.8740 (t0) REVERT: K 133 PHE cc_start: 0.9030 (m-80) cc_final: 0.8752 (m-80) REVERT: K 433 MET cc_start: 0.8016 (tmm) cc_final: 0.7744 (tpt) REVERT: K 436 MET cc_start: 0.7835 (tpp) cc_final: 0.7483 (tpt) REVERT: K 527 MET cc_start: 0.8833 (mtm) cc_final: 0.8551 (mtt) REVERT: K 642 GLN cc_start: 0.9019 (mt0) cc_final: 0.8622 (mt0) outliers start: 16 outliers final: 13 residues processed: 173 average time/residue: 0.7609 time to fit residues: 143.0457 Evaluate side-chains 173 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 0.475 ------------------------------------------------------------------------------- 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 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 207 LEU Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain K residue 409 LEU 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: 7.9990 chunk 35 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 109 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 91 optimal weight: 10.0000 chunk 108 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.3710 r_free = 0.3710 target = 0.086769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.061313 restraints weight = 45465.950| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.15 r_work: 0.2956 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17214 Z= 0.156 Angle : 0.695 13.978 24507 Z= 0.379 Chirality : 0.046 0.303 2781 Planarity : 0.004 0.056 2100 Dihedral : 30.599 172.569 4611 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.18 % Allowed : 23.23 % Favored : 75.59 % 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: 0.89 (0.24), residues: 1269 helix: 1.80 (0.19), residues: 782 sheet: -1.24 (0.63), residues: 79 loop : -1.47 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 99 TYR 0.010 0.001 TYR C 57 PHE 0.013 0.001 PHE A 67 TRP 0.019 0.002 TRP K 267 HIS 0.007 0.001 HIS K 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.16 (17214) covalent geometry : angle 0.69519 / 0.38 (24507) hydrogen bonds : bond 0.04388 / 2.96 ( 940) hydrogen bonds : angle 3.29328 / 2.38 ( 2399) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5087.51 seconds wall clock time: 87 minutes 41.26 seconds (5261.26 seconds total)