Starting phenix.real_space_refine on Fri Jul 3 20:18:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jnu_61627/07_2026/9jnu_61627.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jnu_61627/07_2026/9jnu_61627.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jnu_61627/07_2026/9jnu_61627.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jnu_61627/07_2026/9jnu_61627.map" model { file = "/net/cci-nas-00/data/ceres_data/9jnu_61627/07_2026/9jnu_61627.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jnu_61627/07_2026/9jnu_61627.cif" } resolution = 2.5 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= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 294 5.49 5 Mg 1 5.21 5 S 25 5.16 5 C 9382 2.51 5 N 2993 2.21 5 O 3615 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 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: 16310 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: 4271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4271 Classifications: {'peptide': 520} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 500} Chain breaks: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.35, per 1000 atoms: 0.21 Number of scatterers: 16310 At special positions: 0 Unit cell: (95.26, 116.91, 158.045, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 25 16.00 P 294 15.00 Mg 1 11.99 O 3615 8.00 N 2993 7.00 C 9382 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: 1.25 Conformation dependent library (CDL) restraints added in 545.1 milliseconds 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2434 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 10 sheets defined 65.2% alpha, 4.7% beta 145 base pairs and 274 stacking pairs defined. Time for finding SS restraints: 2.29 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.631A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' 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: 3.800A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (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: 3.520A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.612A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.571A pdb=" N GLN D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.851A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.625A pdb=" N ASP E 106 " --> pdb=" O ALA E 102 " (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: 3.879A 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 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.487A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) 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: 3.668A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.627A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 91 removed outlier: 3.688A pdb=" N LEU K 91 " --> pdb=" O LYS K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 116 Processing helix chain 'K' and resid 119 through 127 Processing helix chain 'K' and resid 130 through 143 removed outlier: 3.876A pdb=" N ARG K 134 " --> pdb=" O ASP K 130 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 213 Processing helix chain 'K' and resid 227 through 242 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 310 through 315 removed outlier: 3.703A pdb=" N LYS K 315 " --> pdb=" O SER K 311 " (cutoff:3.500A) Processing helix chain 'K' and resid 326 through 329 Processing helix chain 'K' and resid 334 through 343 removed outlier: 3.632A pdb=" N PHE K 343 " --> pdb=" O VAL K 339 " (cutoff:3.500A) Processing helix chain 'K' and resid 359 through 371 removed outlier: 3.999A pdb=" N LEU K 363 " --> pdb=" O ASN K 359 " (cutoff:3.500A) Processing helix chain 'K' and resid 377 through 386 removed outlier: 3.756A pdb=" N PHE K 381 " --> pdb=" O ASP K 377 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE K 385 " --> pdb=" O PHE K 381 " (cutoff:3.500A) Processing helix chain 'K' and resid 396 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: 3.777A 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 501 removed outlier: 3.938A pdb=" N ALA K 501 " --> pdb=" O LEU K 497 " (cutoff:3.500A) Processing helix chain 'K' and resid 501 through 518 removed outlier: 3.609A pdb=" N GLU K 517 " --> pdb=" O LYS K 513 " (cutoff:3.500A) Processing helix chain 'K' and resid 528 through 541 Processing helix chain 'K' and resid 553 through 565 Processing helix chain 'K' and resid 601 through 614 removed outlier: 3.853A pdb=" N ASP K 605 " --> pdb=" O ASN K 601 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA K 612 " --> pdb=" O ALA K 608 " (cutoff:3.500A) Processing helix chain 'K' and resid 631 through 651 removed outlier: 4.012A pdb=" N LYS K 635 " --> pdb=" O SER K 631 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.999A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.697A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.172A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.758A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.958A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.988A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'K' and resid 273 through 275 removed outlier: 6.567A pdb=" N PHE K 274 " --> pdb=" O ILE K 300 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N SER K 302 " --> pdb=" O PHE K 274 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N PHE K 248 " --> pdb=" O VAL K 299 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ALA K 301 " --> pdb=" O PHE K 248 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N VAL K 250 " --> pdb=" O ALA K 301 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ILE K 321 " --> pdb=" O LEU K 349 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ILE K 351 " --> pdb=" O ILE K 321 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE K 323 " --> pdb=" O ILE K 351 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLY K 217 " --> pdb=" O ARG K 348 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE K 218 " --> pdb=" O LEU K 410 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 425 through 431 removed outlier: 6.375A pdb=" N LYS K 425 " --> pdb=" O VAL K 623 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ARG K 625 " --> pdb=" O LYS K 425 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU K 427 " --> pdb=" O ARG K 625 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL K 627 " --> pdb=" O LEU K 427 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N LEU K 429 " --> pdb=" O VAL K 627 " (cutoff:3.500A) 589 hydrogen bonds defined for protein. 1725 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 371 hydrogen bonds 738 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 274 stacking parallelities Total time for adding SS restraints: 3.33 Time building geometry restraints manager: 1.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2128 1.32 - 1.44: 5959 1.44 - 1.56: 8484 1.56 - 1.69: 588 1.69 - 1.81: 43 Bond restraints: 17202 Sorted by residual: bond pdb=" CG PRO K 489 " pdb=" CD PRO K 489 " ideal model delta sigma weight residual 1.503 1.333 0.170 3.40e-02 8.65e+02 2.51e+01 bond pdb=" C3' DT I 142 " pdb=" C2' DT I 142 " ideal model delta sigma weight residual 1.516 1.554 -0.038 8.00e-03 1.56e+04 2.28e+01 bond pdb=" CA LEU K 421 " pdb=" C LEU K 421 " ideal model delta sigma weight residual 1.523 1.466 0.057 1.34e-02 5.57e+03 1.80e+01 bond pdb=" CA LEU K 422 " pdb=" C LEU K 422 " ideal model delta sigma weight residual 1.528 1.484 0.045 1.11e-02 8.12e+03 1.61e+01 bond pdb=" C1' DC I 143 " pdb=" N1 DC I 143 " ideal model delta sigma weight residual 1.468 1.524 -0.056 1.40e-02 5.10e+03 1.58e+01 ... (remaining 17197 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.00: 24283 3.00 - 6.00: 192 6.00 - 9.00: 15 9.00 - 12.00: 3 12.00 - 15.00: 2 Bond angle restraints: 24495 Sorted by residual: angle pdb=" CA PRO K 490 " pdb=" N PRO K 490 " pdb=" CD PRO K 490 " ideal model delta sigma weight residual 112.00 101.27 10.73 1.40e+00 5.10e-01 5.87e+01 angle pdb=" CA PRO K 489 " pdb=" N PRO K 489 " pdb=" CD PRO K 489 " ideal model delta sigma weight residual 112.00 102.10 9.90 1.40e+00 5.10e-01 5.00e+01 angle pdb=" N LEU K 421 " pdb=" CA LEU K 421 " pdb=" C LEU K 421 " ideal model delta sigma weight residual 110.80 95.80 15.00 2.13e+00 2.20e-01 4.96e+01 angle pdb=" N PRO K 489 " pdb=" CD PRO K 489 " pdb=" CG PRO K 489 " ideal model delta sigma weight residual 103.20 94.31 8.89 1.50e+00 4.44e-01 3.52e+01 angle pdb=" O4' DG I 121 " pdb=" C4' DG I 121 " pdb=" C3' DG I 121 " ideal model delta sigma weight residual 106.00 102.85 3.15 6.00e-01 2.78e+00 2.76e+01 ... (remaining 24490 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 8029 35.81 - 71.61: 1558 71.61 - 107.42: 20 107.42 - 143.22: 7 143.22 - 179.03: 9 Dihedral angle restraints: 9623 sinusoidal: 5867 harmonic: 3756 Sorted by residual: dihedral pdb=" O2A ADP K1202 " pdb=" O3A ADP K1202 " pdb=" PA ADP K1202 " pdb=" PB ADP K1202 " ideal model delta sinusoidal sigma weight residual -60.00 108.23 -168.23 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C4' ADP K1202 " pdb=" C5' ADP K1202 " pdb=" O5' ADP K1202 " pdb=" PA ADP K1202 " ideal model delta sinusoidal sigma weight residual 180.00 92.29 87.71 1 2.00e+01 2.50e-03 2.30e+01 dihedral pdb=" C2' ADP K1202 " pdb=" C1' ADP K1202 " pdb=" N9 ADP K1202 " pdb=" C4 ADP K1202 " ideal model delta sinusoidal sigma weight residual 91.55 169.49 -77.95 1 2.00e+01 2.50e-03 1.90e+01 ... (remaining 9620 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2323 0.064 - 0.129: 428 0.129 - 0.193: 24 0.193 - 0.257: 2 0.257 - 0.322: 2 Chirality restraints: 2779 Sorted by residual: chirality pdb=" CB ILE K 329 " pdb=" CA ILE K 329 " pdb=" CG1 ILE K 329 " pdb=" CG2 ILE K 329 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CA PRO K 489 " pdb=" N PRO K 489 " pdb=" C PRO K 489 " pdb=" CB PRO K 489 " both_signs ideal model delta sigma weight residual False 2.72 2.40 0.32 2.00e-01 2.50e+01 2.54e+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 -2.53 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 2776 not shown) Planarity restraints: 2092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP K 416 " 0.024 2.00e-02 2.50e+03 4.93e-02 2.43e+01 pdb=" C ASP K 416 " -0.085 2.00e-02 2.50e+03 pdb=" O ASP K 416 " 0.032 2.00e-02 2.50e+03 pdb=" N VAL K 417 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO K 489 " 0.075 5.00e-02 4.00e+02 1.07e-01 1.82e+01 pdb=" N PRO K 490 " -0.184 5.00e-02 4.00e+02 pdb=" CA PRO K 490 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO K 490 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY K 488 " -0.061 5.00e-02 4.00e+02 8.69e-02 1.21e+01 pdb=" N PRO K 489 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO K 489 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO K 489 " -0.047 5.00e-02 4.00e+02 ... (remaining 2089 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 128 2.56 - 3.15: 12109 3.15 - 3.73: 28252 3.73 - 4.32: 40308 4.32 - 4.90: 59641 Nonbonded interactions: 140438 Sorted by model distance: nonbonded pdb="MG MG K1201 " pdb=" O2B ADP K1202 " model vdw 1.978 2.170 nonbonded pdb="MG MG K1201 " pdb=" O1B ADP K1202 " model vdw 2.080 2.170 nonbonded pdb=" O2 DC I 92 " pdb=" N2 DG J 56 " model vdw 2.145 2.496 nonbonded pdb=" OG1 THR D 87 " pdb=" OE1 GLU D 90 " model vdw 2.176 3.040 nonbonded pdb=" OH TYR K 199 " pdb=" O LEU K 225 " model vdw 2.178 3.040 ... (remaining 140433 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: 1.230 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 16.690 Find NCS groups from input model: 0.150 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:6.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 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 : 0.007 0.170 17202 Z= 0.553 Angle : 0.819 15.000 24495 Z= 0.658 Chirality : 0.048 0.322 2779 Planarity : 0.005 0.107 2092 Dihedral : 27.461 179.031 7189 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.25 % Favored : 96.59 % Rotamer: Outliers : 2.55 % Allowed : 21.51 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.87 (0.24), residues: 1262 helix: 1.57 (0.18), residues: 788 sheet: -0.89 (0.64), residues: 69 loop : -1.12 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 35 TYR 0.012 0.002 TYR D 37 PHE 0.011 0.001 PHE A 67 TRP 0.018 0.002 TRP K 364 HIS 0.004 0.001 HIS K 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00693 / 0.55 (17202) covalent geometry : angle 0.81945 / 0.66 (24495) hydrogen bonds : bond 0.09810 / 6.35 ( 960) hydrogen bonds : angle 4.09487 / 3.03 ( 2463) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 167 time to evaluate : 0.522 Fit side-chains revert: symmetry clash REVERT: E 129 ARG cc_start: 0.8351 (tmt170) cc_final: 0.8067 (tpt90) REVERT: F 92 ARG cc_start: 0.8927 (ptm-80) cc_final: 0.8693 (ptm-80) outliers start: 28 outliers final: 20 residues processed: 192 average time/residue: 0.8416 time to fit residues: 174.2027 Evaluate side-chains 181 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 398 VAL Chi-restraints excluded: chain K residue 405 LEU Chi-restraints excluded: chain K residue 493 THR Chi-restraints excluded: chain K residue 498 VAL Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain K residue 576 LEU 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: 9.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 8.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN H 81 ASN ** K 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 554 HIS ** K 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.094234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.066170 restraints weight = 34029.647| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.13 r_work: 0.2865 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.0562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17202 Z= 0.255 Angle : 0.723 10.599 24495 Z= 0.400 Chirality : 0.051 0.336 2779 Planarity : 0.005 0.049 2092 Dihedral : 30.575 179.753 4642 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.37 % Allowed : 19.78 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 1.00 (0.23), residues: 1262 helix: 1.68 (0.18), residues: 785 sheet: -0.74 (0.65), residues: 69 loop : -1.09 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 83 TYR 0.012 0.002 TYR D 37 PHE 0.010 0.002 PHE K 109 TRP 0.016 0.001 TRP K 364 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.25 (17202) covalent geometry : angle 0.72263 / 0.40 (24495) hydrogen bonds : bond 0.06360 / 4.12 ( 960) hydrogen bonds : angle 3.72827 / 2.76 ( 2463) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 165 time to evaluate : 0.509 Fit side-chains REVERT: A 131 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.8703 (mtp85) REVERT: D 30 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7572 (mtp-110) REVERT: E 79 LYS cc_start: 0.9264 (tttt) cc_final: 0.9037 (tttp) REVERT: E 129 ARG cc_start: 0.8502 (tmt170) cc_final: 0.8162 (tpt90) REVERT: G 35 ARG cc_start: 0.8681 (mtm110) cc_final: 0.8421 (mtm110) outliers start: 37 outliers final: 20 residues processed: 190 average time/residue: 0.8398 time to fit residues: 171.4247 Evaluate side-chains 180 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 398 VAL Chi-restraints excluded: chain K residue 492 THR Chi-restraints excluded: chain K residue 493 THR Chi-restraints excluded: chain K residue 498 VAL Chi-restraints excluded: chain K residue 538 CYS Chi-restraints excluded: chain K residue 546 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 34 optimal weight: 0.7980 chunk 73 optimal weight: 20.0000 chunk 30 optimal weight: 0.8980 chunk 105 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN ** K 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 554 HIS K 620 GLN ** K 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.095813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.067812 restraints weight = 34324.904| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.18 r_work: 0.2908 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.0841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17202 Z= 0.160 Angle : 0.661 8.690 24495 Z= 0.370 Chirality : 0.047 0.330 2779 Planarity : 0.004 0.034 2092 Dihedral : 30.449 179.055 4632 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.19 % Allowed : 19.87 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 1.36 (0.24), residues: 1262 helix: 1.96 (0.18), residues: 785 sheet: -0.50 (0.64), residues: 69 loop : -0.96 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 83 TYR 0.011 0.001 TYR D 37 PHE 0.008 0.001 PHE A 67 TRP 0.017 0.001 TRP K 364 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.16 (17202) covalent geometry : angle 0.66145 / 0.37 (24495) hydrogen bonds : bond 0.05077 / 3.20 ( 960) hydrogen bonds : angle 3.49058 / 2.58 ( 2463) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 166 time to evaluate : 0.500 Fit side-chains revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.8629 (mtp85) REVERT: D 30 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7448 (mtp-110) REVERT: D 68 GLU cc_start: 0.8114 (pt0) cc_final: 0.7905 (tp30) REVERT: D 90 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8140 (mp0) REVERT: E 79 LYS cc_start: 0.9283 (tttt) cc_final: 0.9043 (tttp) REVERT: E 129 ARG cc_start: 0.8480 (tmt170) cc_final: 0.8191 (tpt90) REVERT: H 83 ARG cc_start: 0.8590 (mmt90) cc_final: 0.8364 (mmt90) REVERT: H 90 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8149 (mp0) outliers start: 35 outliers final: 16 residues processed: 188 average time/residue: 0.8453 time to fit residues: 170.5906 Evaluate side-chains 181 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain K residue 185 PHE Chi-restraints excluded: chain K residue 398 VAL Chi-restraints excluded: chain K residue 420 SER Chi-restraints excluded: chain K residue 493 THR Chi-restraints excluded: chain K residue 498 VAL Chi-restraints excluded: chain K residue 538 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 132 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 73 optimal weight: 20.0000 chunk 130 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 554 HIS ** K 654 ASN ** 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 = 0.3611 r_free = 0.3611 target = 0.094836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.066806 restraints weight = 34028.030| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.14 r_work: 0.2883 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.0900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 17202 Z= 0.228 Angle : 0.684 8.773 24495 Z= 0.378 Chirality : 0.049 0.319 2779 Planarity : 0.004 0.049 2092 Dihedral : 30.449 179.821 4627 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.01 % Allowed : 19.69 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 1.30 (0.24), residues: 1262 helix: 1.91 (0.18), residues: 791 sheet: -0.50 (0.63), residues: 71 loop : -1.03 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 645 TYR 0.011 0.001 TYR D 37 PHE 0.014 0.001 PHE K 109 TRP 0.014 0.001 TRP K 364 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.23 (17202) covalent geometry : angle 0.68423 / 0.38 (24495) hydrogen bonds : bond 0.05853 / 3.79 ( 960) hydrogen bonds : angle 3.51760 / 2.59 ( 2463) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 161 time to evaluate : 0.486 Fit side-chains revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.8666 (mtp85) REVERT: B 91 LYS cc_start: 0.9264 (OUTLIER) cc_final: 0.8988 (ttmm) REVERT: D 30 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7620 (mtp-110) REVERT: D 90 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8099 (mp0) REVERT: E 79 LYS cc_start: 0.9287 (tttt) cc_final: 0.9072 (tttp) REVERT: E 129 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.8151 (tpt90) REVERT: G 35 ARG cc_start: 0.8616 (mtm110) cc_final: 0.8337 (mtm110) REVERT: H 82 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.8949 (mttm) REVERT: H 90 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8079 (mp0) REVERT: K 320 TYR cc_start: 0.8248 (OUTLIER) cc_final: 0.7284 (m-10) outliers start: 44 outliers final: 23 residues processed: 185 average time/residue: 0.8888 time to fit residues: 176.2358 Evaluate side-chains 190 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 159 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain K residue 185 PHE Chi-restraints excluded: chain K residue 196 LEU Chi-restraints excluded: chain K residue 320 TYR Chi-restraints excluded: chain K residue 398 VAL Chi-restraints excluded: chain K residue 493 THR Chi-restraints excluded: chain K residue 498 VAL Chi-restraints excluded: chain K residue 538 CYS Chi-restraints excluded: chain K residue 576 LEU Chi-restraints excluded: chain K residue 623 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 80 optimal weight: 10.0000 chunk 73 optimal weight: 20.0000 chunk 61 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 92 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 82 optimal weight: 20.0000 chunk 13 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 96 optimal weight: 10.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 554 HIS ** K 654 ASN ** 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 = 0.3623 r_free = 0.3623 target = 0.095565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.067502 restraints weight = 33964.558| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.15 r_work: 0.2899 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17202 Z= 0.163 Angle : 0.664 8.738 24495 Z= 0.368 Chirality : 0.047 0.321 2779 Planarity : 0.004 0.040 2092 Dihedral : 30.428 179.583 4627 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.46 % Allowed : 20.42 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 1.46 (0.24), residues: 1262 helix: 2.02 (0.18), residues: 791 sheet: -0.21 (0.63), residues: 69 loop : -0.99 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 83 TYR 0.010 0.001 TYR D 37 PHE 0.008 0.001 PHE A 67 TRP 0.015 0.001 TRP K 364 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.16 (17202) covalent geometry : angle 0.66386 / 0.37 (24495) hydrogen bonds : bond 0.05273 / 3.36 ( 960) hydrogen bonds : angle 3.44780 / 2.54 ( 2463) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 161 time to evaluate : 0.534 Fit side-chains revert: symmetry clash REVERT: D 30 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7558 (mtp-110) REVERT: D 90 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8088 (mp0) REVERT: E 79 LYS cc_start: 0.9278 (tttt) cc_final: 0.9066 (tttp) REVERT: E 129 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8156 (tpt90) REVERT: G 35 ARG cc_start: 0.8614 (mtm110) cc_final: 0.8283 (mtm110) REVERT: H 82 LYS cc_start: 0.9219 (OUTLIER) cc_final: 0.8944 (mttm) REVERT: H 90 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8094 (mp0) REVERT: K 320 TYR cc_start: 0.8238 (OUTLIER) cc_final: 0.7260 (m-10) REVERT: K 348 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.8137 (mtm-85) outliers start: 38 outliers final: 20 residues processed: 181 average time/residue: 0.8810 time to fit residues: 170.9327 Evaluate side-chains 184 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain K residue 185 PHE Chi-restraints excluded: chain K residue 320 TYR Chi-restraints excluded: chain K residue 335 MET Chi-restraints excluded: chain K residue 348 ARG Chi-restraints excluded: chain K residue 398 VAL Chi-restraints excluded: chain K residue 493 THR Chi-restraints excluded: chain K residue 498 VAL Chi-restraints excluded: chain K residue 538 CYS Chi-restraints excluded: chain K residue 576 LEU Chi-restraints excluded: chain K residue 623 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 132 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 chunk 105 optimal weight: 30.0000 chunk 8 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 24 optimal weight: 0.7980 chunk 112 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 554 HIS ** K 654 ASN ** 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 = 0.3630 r_free = 0.3630 target = 0.095982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.068035 restraints weight = 33996.415| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.14 r_work: 0.2907 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17202 Z= 0.166 Angle : 0.660 9.883 24495 Z= 0.365 Chirality : 0.047 0.319 2779 Planarity : 0.004 0.040 2092 Dihedral : 30.377 179.272 4626 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.46 % Allowed : 20.42 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 1.57 (0.24), residues: 1262 helix: 2.10 (0.18), residues: 785 sheet: -0.15 (0.63), residues: 69 loop : -0.87 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 83 TYR 0.010 0.001 TYR D 37 PHE 0.012 0.001 PHE K 109 TRP 0.015 0.001 TRP K 364 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.17 (17202) covalent geometry : angle 0.65958 / 0.37 (24495) hydrogen bonds : bond 0.05054 / 3.20 ( 960) hydrogen bonds : angle 3.40195 / 2.50 ( 2463) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 162 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: B 93 GLN cc_start: 0.8771 (mm-40) cc_final: 0.8554 (mp10) REVERT: D 30 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7597 (mtp-110) REVERT: D 68 GLU cc_start: 0.8271 (tp30) cc_final: 0.7997 (tp30) REVERT: D 90 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8088 (mp0) REVERT: E 79 LYS cc_start: 0.9269 (tttt) cc_final: 0.9061 (tttp) REVERT: E 129 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.8158 (tpt90) REVERT: H 31 LYS cc_start: 0.8204 (mppt) cc_final: 0.7947 (mppt) REVERT: H 82 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8951 (mttm) REVERT: H 90 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8084 (mp0) REVERT: K 320 TYR cc_start: 0.8240 (OUTLIER) cc_final: 0.7239 (m-10) outliers start: 38 outliers final: 22 residues processed: 183 average time/residue: 0.8182 time to fit residues: 161.0720 Evaluate side-chains 188 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 160 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain K residue 185 PHE Chi-restraints excluded: chain K residue 196 LEU Chi-restraints excluded: chain K residue 320 TYR Chi-restraints excluded: chain K residue 398 VAL Chi-restraints excluded: chain K residue 493 THR Chi-restraints excluded: chain K residue 498 VAL Chi-restraints excluded: chain K residue 531 LEU 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 70 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 114 optimal weight: 0.7980 chunk 26 optimal weight: 0.4980 chunk 116 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 85 optimal weight: 20.0000 chunk 2 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 402 HIS K 554 HIS K 654 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.096630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.068516 restraints weight = 34035.074| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.21 r_work: 0.2920 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17202 Z= 0.144 Angle : 0.645 8.691 24495 Z= 0.360 Chirality : 0.046 0.319 2779 Planarity : 0.004 0.084 2092 Dihedral : 30.335 179.065 4626 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.01 % Allowed : 21.33 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 1.64 (0.24), residues: 1262 helix: 2.16 (0.18), residues: 785 sheet: -0.13 (0.63), residues: 69 loop : -0.84 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG K 645 TYR 0.010 0.001 TYR D 37 PHE 0.010 0.001 PHE K 119 TRP 0.016 0.001 TRP K 364 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.14 (17202) covalent geometry : angle 0.64469 / 0.36 (24495) hydrogen bonds : bond 0.04810 / 3.02 ( 960) hydrogen bonds : angle 3.37234 / 2.47 ( 2463) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 164 time to evaluate : 0.481 Fit side-chains revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.8674 (mtp85) REVERT: B 93 GLN cc_start: 0.8740 (mm-40) cc_final: 0.8514 (mp10) REVERT: D 30 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7543 (mtp-110) REVERT: D 68 GLU cc_start: 0.8304 (tp30) cc_final: 0.8019 (tp30) REVERT: D 90 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8066 (mp0) REVERT: E 79 LYS cc_start: 0.9205 (tttt) cc_final: 0.8977 (tttp) REVERT: E 129 ARG cc_start: 0.8459 (tmt170) cc_final: 0.8151 (tpt90) REVERT: H 31 LYS cc_start: 0.8206 (mppt) cc_final: 0.7941 (mmtt) REVERT: H 82 LYS cc_start: 0.9168 (OUTLIER) cc_final: 0.8929 (mttm) REVERT: H 90 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8067 (mp0) REVERT: H 102 GLU cc_start: 0.8959 (tp30) cc_final: 0.8739 (tp30) REVERT: K 320 TYR cc_start: 0.8252 (OUTLIER) cc_final: 0.7254 (m-10) REVERT: K 348 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.8147 (mtm-85) outliers start: 33 outliers final: 20 residues processed: 183 average time/residue: 0.8373 time to fit residues: 164.3205 Evaluate side-chains 186 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain K residue 185 PHE Chi-restraints excluded: chain K residue 320 TYR Chi-restraints excluded: chain K residue 348 ARG Chi-restraints excluded: chain K residue 398 VAL Chi-restraints excluded: chain K residue 493 THR Chi-restraints excluded: chain K residue 498 VAL Chi-restraints excluded: chain K residue 531 LEU Chi-restraints excluded: chain K residue 538 CYS Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain K residue 623 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 4 optimal weight: 2.9990 chunk 53 optimal weight: 0.0980 chunk 101 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 148 optimal weight: 0.9980 chunk 102 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 23 optimal weight: 0.0060 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.096951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.069010 restraints weight = 34201.334| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.19 r_work: 0.2937 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 17202 Z= 0.143 Angle : 0.637 8.654 24495 Z= 0.356 Chirality : 0.046 0.317 2779 Planarity : 0.004 0.074 2092 Dihedral : 30.278 178.737 4625 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.28 % Allowed : 21.70 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 1.71 (0.24), residues: 1262 helix: 2.21 (0.18), residues: 785 sheet: -0.09 (0.63), residues: 69 loop : -0.81 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG K 645 TYR 0.010 0.001 TYR D 37 PHE 0.009 0.001 PHE K 119 TRP 0.015 0.001 TRP K 364 HIS 0.004 0.001 HIS K 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.14 (17202) covalent geometry : angle 0.63664 / 0.36 (24495) hydrogen bonds : bond 0.04688 / 2.93 ( 960) hydrogen bonds : angle 3.33051 / 2.43 ( 2463) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 163 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.8686 (mtp85) REVERT: B 93 GLN cc_start: 0.8741 (mm-40) cc_final: 0.8415 (mp10) REVERT: D 30 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7547 (mtp-110) REVERT: D 68 GLU cc_start: 0.8313 (tp30) cc_final: 0.8020 (tp30) REVERT: D 90 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8097 (mp0) REVERT: E 79 LYS cc_start: 0.9200 (tttt) cc_final: 0.8967 (tttp) REVERT: E 129 ARG cc_start: 0.8459 (tmt170) cc_final: 0.8160 (tpt90) REVERT: H 31 LYS cc_start: 0.8255 (mppt) cc_final: 0.8023 (mppt) REVERT: H 82 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8916 (mttm) REVERT: H 90 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8070 (mp0) REVERT: H 105 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7941 (mtmm) REVERT: K 89 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.7605 (ptt180) REVERT: K 320 TYR cc_start: 0.8284 (OUTLIER) cc_final: 0.7284 (m-10) REVERT: K 645 ARG cc_start: 0.8561 (tmm160) cc_final: 0.8309 (ttp80) outliers start: 36 outliers final: 24 residues processed: 183 average time/residue: 0.8031 time to fit residues: 158.1627 Evaluate side-chains 194 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 162 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 105 LYS Chi-restraints excluded: chain K residue 89 ARG Chi-restraints excluded: chain K residue 185 PHE Chi-restraints excluded: chain K residue 320 TYR Chi-restraints excluded: chain K residue 398 VAL Chi-restraints excluded: chain K residue 493 THR Chi-restraints excluded: chain K residue 498 VAL Chi-restraints excluded: chain K residue 531 LEU Chi-restraints excluded: chain K residue 538 CYS Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain K residue 623 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 5 optimal weight: 1.9990 chunk 126 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 40 optimal weight: 0.0980 chunk 43 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 87 optimal weight: 20.0000 chunk 111 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 554 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.096577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.068542 restraints weight = 33801.334| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.18 r_work: 0.2927 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17202 Z= 0.162 Angle : 0.639 8.617 24495 Z= 0.356 Chirality : 0.046 0.307 2779 Planarity : 0.004 0.032 2092 Dihedral : 30.223 179.032 4625 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.92 % Allowed : 22.15 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 1.66 (0.24), residues: 1262 helix: 2.18 (0.18), residues: 791 sheet: -0.25 (0.63), residues: 71 loop : -0.86 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 645 TYR 0.010 0.001 TYR D 37 PHE 0.007 0.001 PHE A 67 TRP 0.014 0.001 TRP K 364 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.16 (17202) covalent geometry : angle 0.63931 / 0.36 (24495) hydrogen bonds : bond 0.04938 / 3.13 ( 960) hydrogen bonds : angle 3.32466 / 2.43 ( 2463) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 163 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8701 (mtp85) REVERT: B 93 GLN cc_start: 0.8741 (mm-40) cc_final: 0.8401 (mp10) REVERT: D 68 GLU cc_start: 0.8298 (tp30) cc_final: 0.8003 (tp30) REVERT: D 90 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8107 (mp0) REVERT: E 79 LYS cc_start: 0.9182 (tttt) cc_final: 0.8960 (tttp) REVERT: E 129 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.8144 (tpt90) REVERT: H 31 LYS cc_start: 0.8247 (mppt) cc_final: 0.7945 (mppt) REVERT: H 82 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8911 (mttm) REVERT: H 90 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8090 (mp0) REVERT: K 89 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7647 (ptt180) REVERT: K 320 TYR cc_start: 0.8260 (OUTLIER) cc_final: 0.7387 (m-10) REVERT: K 348 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.8160 (mtm-85) REVERT: K 645 ARG cc_start: 0.8583 (tmm160) cc_final: 0.8232 (tmm-80) outliers start: 32 outliers final: 20 residues processed: 182 average time/residue: 0.8254 time to fit residues: 161.4976 Evaluate side-chains 190 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain K residue 89 ARG Chi-restraints excluded: chain K residue 185 PHE Chi-restraints excluded: chain K residue 320 TYR Chi-restraints excluded: chain K residue 348 ARG Chi-restraints excluded: chain K residue 398 VAL Chi-restraints excluded: chain K residue 493 THR Chi-restraints excluded: chain K residue 498 VAL Chi-restraints excluded: chain K residue 531 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 68 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 137 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 554 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.096738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.068565 restraints weight = 33873.617| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.22 r_work: 0.2925 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17202 Z= 0.150 Angle : 0.641 8.621 24495 Z= 0.357 Chirality : 0.045 0.308 2779 Planarity : 0.004 0.031 2092 Dihedral : 30.221 178.996 4625 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.55 % Allowed : 22.70 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 1.67 (0.24), residues: 1262 helix: 2.18 (0.18), residues: 791 sheet: -0.24 (0.63), residues: 71 loop : -0.85 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 645 TYR 0.010 0.001 TYR D 37 PHE 0.007 0.001 PHE A 67 TRP 0.014 0.001 TRP K 364 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.15 (17202) covalent geometry : angle 0.64091 / 0.36 (24495) hydrogen bonds : bond 0.04845 / 3.07 ( 960) hydrogen bonds : angle 3.31696 / 2.42 ( 2463) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 0.492 Fit side-chains revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.8694 (mtp85) REVERT: B 93 GLN cc_start: 0.8738 (mm-40) cc_final: 0.8395 (mp10) REVERT: D 68 GLU cc_start: 0.8303 (tp30) cc_final: 0.8007 (tp30) REVERT: D 90 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8101 (mp0) REVERT: E 79 LYS cc_start: 0.9176 (tttt) cc_final: 0.8959 (tttp) REVERT: E 129 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8147 (tpt90) REVERT: H 31 LYS cc_start: 0.8240 (mppt) cc_final: 0.7933 (mppt) REVERT: H 82 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8908 (mttm) REVERT: H 90 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8079 (mp0) REVERT: K 89 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7647 (ptt180) REVERT: K 320 TYR cc_start: 0.8254 (OUTLIER) cc_final: 0.7381 (m-10) REVERT: K 348 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.8155 (mtm-85) REVERT: K 645 ARG cc_start: 0.8580 (tmm160) cc_final: 0.8246 (tmm-80) outliers start: 28 outliers final: 19 residues processed: 181 average time/residue: 0.9240 time to fit residues: 179.4691 Evaluate side-chains 191 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain K residue 89 ARG Chi-restraints excluded: chain K residue 185 PHE Chi-restraints excluded: chain K residue 320 TYR Chi-restraints excluded: chain K residue 348 ARG Chi-restraints excluded: chain K residue 398 VAL Chi-restraints excluded: chain K residue 493 THR Chi-restraints excluded: chain K residue 498 VAL Chi-restraints excluded: chain K residue 531 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 122 optimal weight: 2.9990 chunk 127 optimal weight: 20.0000 chunk 21 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 79 optimal weight: 10.0000 chunk 101 optimal weight: 0.2980 chunk 48 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 554 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.096896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.068821 restraints weight = 33758.126| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.15 r_work: 0.2925 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17202 Z= 0.139 Angle : 0.640 8.614 24495 Z= 0.356 Chirality : 0.045 0.308 2779 Planarity : 0.004 0.060 2092 Dihedral : 30.216 179.032 4625 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.73 % Allowed : 22.33 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 1.69 (0.24), residues: 1262 helix: 2.20 (0.18), residues: 791 sheet: -0.24 (0.63), residues: 71 loop : -0.84 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG G 35 TYR 0.010 0.001 TYR D 37 PHE 0.008 0.001 PHE A 67 TRP 0.015 0.001 TRP K 364 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.14 (17202) covalent geometry : angle 0.64024 / 0.36 (24495) hydrogen bonds : bond 0.04766 / 3.01 ( 960) hydrogen bonds : angle 3.30826 / 2.42 ( 2463) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6020.38 seconds wall clock time: 103 minutes 1.70 seconds (6181.70 seconds total)