Starting phenix.real_space_refine on Thu Aug 6 15:46:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jnu_61627/08_2026/9jnu_61627.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jnu_61627/08_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_61627/08_2026/9jnu_61627.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jnu_61627/08_2026/9jnu_61627.map" model { file = "/net/cci-nas-00/data/ceres_data/9jnu_61627/08_2026/9jnu_61627.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jnu_61627/08_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-2.2rc3-6140/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: 2.98, per 1000 atoms: 0.18 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: 1.20 Conformation dependent library (CDL) restraints added in 507.9 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: 2.01 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: 3.56 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: 24279 3.00 - 6.00: 196 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: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.740 Find NCS groups from input model: 0.120 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:6.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.490 ------------------------------------------------------------------------------- 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 : 0.825 15.000 24495 Z= 0.664 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 0.82524 / 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 : 0.461 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: 0.7959 time to fit residues: 164.6905 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 : 0.323 ------------------------------------------------------------------------------- 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 = 0.3600 r_free = 0.3600 target = 0.094224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.066172 restraints weight = 34051.757| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.14 r_work: 0.2864 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.0548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 17202 Z= 0.252 Angle : 0.738 10.799 24495 Z= 0.404 Chirality : 0.052 0.355 2779 Planarity : 0.005 0.049 2092 Dihedral : 30.516 178.894 4642 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.19 % Allowed : 20.15 % Favored : 76.66 % 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: 1.00 (0.23), residues: 1262 helix: 1.68 (0.18), residues: 785 sheet: -0.75 (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 0.00536 / 0.25 (17202) covalent geometry : angle 0.73845 / 0.40 (24495) hydrogen bonds : bond 0.06413 / 4.16 ( 960) hydrogen bonds : angle 3.73608 / 2.77 ( 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 200 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 165 time to evaluate : 0.497 Fit side-chains REVERT: A 131 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.8692 (mtp85) REVERT: D 30 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7571 (mtp-110) REVERT: E 79 LYS cc_start: 0.9261 (tttt) cc_final: 0.9034 (tttp) REVERT: E 129 ARG cc_start: 0.8494 (tmt170) cc_final: 0.8154 (tpt90) REVERT: G 35 ARG cc_start: 0.8678 (mtm110) cc_final: 0.8418 (mtm110) outliers start: 35 outliers final: 18 residues processed: 190 average time/residue: 0.8840 time to fit residues: 180.6092 Evaluate side-chains 178 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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 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 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: 2.9990 chunk 73 optimal weight: 20.0000 chunk 30 optimal weight: 0.6980 chunk 105 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 chunk 147 optimal weight: 7.9990 chunk 44 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.3622 r_free = 0.3622 target = 0.095483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.067505 restraints weight = 34333.993| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.15 r_work: 0.2898 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.0755 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= 0.162 Angle : 0.691 12.139 24495 Z= 0.381 Chirality : 0.049 0.348 2779 Planarity : 0.004 0.037 2092 Dihedral : 30.431 179.907 4632 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.10 % Allowed : 19.96 % 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: 1.30 (0.24), residues: 1262 helix: 1.91 (0.18), residues: 785 sheet: -0.51 (0.64), residues: 69 loop : -0.98 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 83 TYR 0.010 0.001 TYR B 51 PHE 0.009 0.001 PHE A 67 TRP 0.016 0.001 TRP K 364 HIS 0.004 0.001 HIS K 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.16 (17202) covalent geometry : angle 0.69113 / 0.38 (24495) hydrogen bonds : bond 0.05303 / 3.36 ( 960) hydrogen bonds : angle 3.55732 / 2.63 ( 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 202 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 168 time to evaluate : 0.493 Fit side-chains revert: symmetry clash REVERT: D 30 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7448 (mtp-110) REVERT: E 79 LYS cc_start: 0.9274 (tttt) cc_final: 0.9037 (tttp) REVERT: E 129 ARG cc_start: 0.8488 (tmt170) cc_final: 0.8166 (tpt90) REVERT: H 83 ARG cc_start: 0.8587 (mmt90) cc_final: 0.8355 (mmt90) REVERT: H 90 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8176 (mp0) outliers start: 34 outliers final: 18 residues processed: 189 average time/residue: 0.8780 time to fit residues: 178.1022 Evaluate side-chains 182 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain D residue 30 ARG 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 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 335 MET Chi-restraints excluded: chain K residue 398 VAL Chi-restraints excluded: chain K residue 468 ILE 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 132 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 26 optimal weight: 0.5980 chunk 73 optimal weight: 20.0000 chunk 130 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3633 r_free = 0.3633 target = 0.096123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.068147 restraints weight = 34091.213| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.18 r_work: 0.2918 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17202 Z= 0.160 Angle : 0.657 9.267 24495 Z= 0.365 Chirality : 0.048 0.344 2779 Planarity : 0.004 0.052 2092 Dihedral : 30.282 179.866 4630 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.56 % Allowed : 20.15 % 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: 1.50 (0.24), residues: 1262 helix: 2.06 (0.18), residues: 791 sheet: -0.23 (0.64), residues: 69 loop : -0.97 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 645 TYR 0.011 0.001 TYR D 37 PHE 0.016 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 0.00305 / 0.16 (17202) covalent geometry : angle 0.65723 / 0.37 (24495) hydrogen bonds : bond 0.05013 / 3.17 ( 960) hydrogen bonds : angle 3.41660 / 2.52 ( 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 201 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 162 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.8715 (mtp85) REVERT: D 68 GLU cc_start: 0.8315 (tp30) cc_final: 0.8011 (tt0) REVERT: D 90 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8044 (mp0) REVERT: E 79 LYS cc_start: 0.9271 (tttt) cc_final: 0.9039 (tttp) REVERT: E 129 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.8168 (tpt90) REVERT: G 35 ARG cc_start: 0.8606 (mtm110) cc_final: 0.8304 (mtm110) REVERT: H 90 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8079 (mp0) REVERT: K 320 TYR cc_start: 0.8231 (OUTLIER) cc_final: 0.7259 (m-10) REVERT: K 348 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8126 (mtm-85) outliers start: 39 outliers final: 16 residues processed: 185 average time/residue: 0.8345 time to fit residues: 166.1071 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 : 0.486 ------------------------------------------------------------------------------- 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 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 129 ARG 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 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 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 538 CYS 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: 0.6980 chunk 57 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 130 optimal weight: 0.7980 chunk 82 optimal weight: 20.0000 chunk 13 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 96 optimal weight: 10.0000 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3646 r_free = 0.3646 target = 0.096855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.068976 restraints weight = 34074.785| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.16 r_work: 0.2931 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 17202 Z= 0.139 Angle : 0.658 9.229 24495 Z= 0.364 Chirality : 0.047 0.343 2779 Planarity : 0.004 0.040 2092 Dihedral : 30.248 179.563 4627 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.19 % Allowed : 20.69 % 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: 1.63 (0.24), residues: 1262 helix: 2.14 (0.18), residues: 785 sheet: -0.12 (0.64), residues: 69 loop : -0.84 (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 C 57 PHE 0.009 0.001 PHE K 119 TRP 0.015 0.001 TRP K 364 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.14 (17202) covalent geometry : angle 0.65773 / 0.36 (24495) hydrogen bonds : bond 0.04704 / 2.94 ( 960) hydrogen bonds : angle 3.35475 / 2.47 ( 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 203 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 168 time to evaluate : 0.473 Fit side-chains revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.8705 (mtp85) REVERT: B 93 GLN cc_start: 0.8753 (mm-40) cc_final: 0.8546 (mp10) REVERT: D 30 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7406 (mtp-110) REVERT: D 68 GLU cc_start: 0.8338 (tp30) cc_final: 0.8003 (tt0) REVERT: D 83 ARG cc_start: 0.8633 (mmt90) cc_final: 0.8428 (mmt90) REVERT: D 90 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8105 (mp0) REVERT: E 79 LYS cc_start: 0.9259 (tttt) cc_final: 0.9039 (tttp) REVERT: E 129 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.8181 (tpt90) REVERT: G 35 ARG cc_start: 0.8638 (mtm110) cc_final: 0.8290 (mtm110) REVERT: H 31 LYS cc_start: 0.8246 (mppt) cc_final: 0.8025 (mppt) REVERT: H 90 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8079 (mp0) REVERT: H 102 GLU cc_start: 0.9110 (tp30) cc_final: 0.8731 (tp30) REVERT: H 105 LYS cc_start: 0.8161 (mtpp) cc_final: 0.7928 (mtmm) REVERT: K 320 TYR cc_start: 0.8243 (OUTLIER) cc_final: 0.7272 (m-10) REVERT: K 348 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.8129 (mtm-85) outliers start: 35 outliers final: 20 residues processed: 188 average time/residue: 0.8646 time to fit residues: 174.4351 Evaluate side-chains 188 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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 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 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 196 LEU Chi-restraints excluded: chain K residue 215 ILE 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 546 CYS 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: 3.9990 chunk 57 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 105 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 112 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.096058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.067965 restraints weight = 34071.877| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.19 r_work: 0.2906 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17202 Z= 0.180 Angle : 0.662 9.240 24495 Z= 0.365 Chirality : 0.047 0.332 2779 Planarity : 0.004 0.057 2092 Dihedral : 30.238 179.992 4625 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.65 % Allowed : 20.60 % Favored : 75.75 % 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: 1.56 (0.24), residues: 1262 helix: 2.10 (0.18), residues: 791 sheet: -0.26 (0.64), residues: 71 loop : -0.90 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG K 645 TYR 0.010 0.001 TYR D 37 PHE 0.007 0.001 PHE F 61 TRP 0.013 0.001 TRP K 364 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.18 (17202) covalent geometry : angle 0.66206 / 0.36 (24495) hydrogen bonds : bond 0.05211 / 3.33 ( 960) hydrogen bonds : angle 3.35985 / 2.46 ( 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 203 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 163 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8692 (mtp85) REVERT: B 93 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8514 (mp10) REVERT: D 30 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7546 (mtp-110) REVERT: D 68 GLU cc_start: 0.8338 (tp30) cc_final: 0.8020 (tp30) REVERT: D 83 ARG cc_start: 0.8689 (mmt90) cc_final: 0.8475 (mmt90) REVERT: D 90 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8114 (mp0) REVERT: E 79 LYS cc_start: 0.9256 (tttt) cc_final: 0.9039 (tttp) REVERT: E 129 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.8144 (tpt90) REVERT: H 31 LYS cc_start: 0.8197 (mppt) cc_final: 0.7886 (mppt) REVERT: H 82 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8880 (mttm) REVERT: H 90 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8090 (mp0) REVERT: K 320 TYR cc_start: 0.8280 (OUTLIER) cc_final: 0.7278 (m-10) outliers start: 40 outliers final: 21 residues processed: 188 average time/residue: 0.7970 time to fit residues: 161.1890 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 : 0.299 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 52 optimal weight: 0.6980 chunk 91 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 114 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 85 optimal weight: 20.0000 chunk 2 optimal weight: 0.9990 chunk 139 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.096396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.068366 restraints weight = 33906.023| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.19 r_work: 0.2924 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 17202 Z= 0.157 Angle : 0.662 9.548 24495 Z= 0.365 Chirality : 0.047 0.333 2779 Planarity : 0.004 0.036 2092 Dihedral : 30.229 179.914 4625 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.73 % Allowed : 21.79 % Favored : 75.48 % 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: 2.17 (0.18), residues: 785 sheet: -0.23 (0.64), residues: 71 loop : -0.82 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 645 TYR 0.010 0.001 TYR C 57 PHE 0.007 0.001 PHE F 61 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 0.00305 / 0.16 (17202) covalent geometry : angle 0.66214 / 0.36 (24495) hydrogen bonds : bond 0.04974 / 3.16 ( 960) hydrogen bonds : angle 3.35345 / 2.45 ( 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 194 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 164 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8695 (mtp85) REVERT: B 93 GLN cc_start: 0.8736 (mm-40) cc_final: 0.8490 (mp10) REVERT: D 30 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7525 (mtp-110) REVERT: D 68 GLU cc_start: 0.8325 (tp30) cc_final: 0.8009 (tp30) REVERT: D 83 ARG cc_start: 0.8653 (mmt90) cc_final: 0.8434 (mmt90) REVERT: D 90 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8064 (mp0) REVERT: E 79 LYS cc_start: 0.9190 (tttt) cc_final: 0.8977 (tttp) REVERT: E 129 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.8145 (tpt90) REVERT: H 31 LYS cc_start: 0.8245 (mppt) cc_final: 0.8015 (mppt) REVERT: H 82 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8878 (mttm) REVERT: H 90 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8070 (mp0) REVERT: H 102 GLU cc_start: 0.8952 (tp30) cc_final: 0.8741 (tp30) REVERT: K 320 TYR cc_start: 0.8278 (OUTLIER) cc_final: 0.7296 (m-10) outliers start: 30 outliers final: 21 residues processed: 179 average time/residue: 0.7642 time to fit residues: 146.8539 Evaluate side-chains 189 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR 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 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 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 185 PHE Chi-restraints excluded: chain K residue 320 TYR Chi-restraints excluded: chain K residue 335 MET 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 546 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 4 optimal weight: 0.0980 chunk 53 optimal weight: 7.9990 chunk 101 optimal weight: 8.9990 chunk 75 optimal weight: 9.9990 chunk 148 optimal weight: 9.9990 chunk 102 optimal weight: 20.0000 chunk 44 optimal weight: 1.9990 chunk 95 optimal weight: 20.0000 chunk 1 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.096593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.068536 restraints weight = 34206.634| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.21 r_work: 0.2919 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17202 Z= 0.155 Angle : 0.660 9.226 24495 Z= 0.364 Chirality : 0.047 0.332 2779 Planarity : 0.004 0.034 2092 Dihedral : 30.208 179.601 4625 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.28 % Allowed : 21.51 % Favored : 75.21 % 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: 2.21 (0.18), residues: 785 sheet: -0.24 (0.64), residues: 71 loop : -0.81 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 35 TYR 0.009 0.001 TYR C 57 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 0.00297 / 0.15 (17202) covalent geometry : angle 0.66049 / 0.36 (24495) hydrogen bonds : bond 0.04836 / 3.05 ( 960) hydrogen bonds : angle 3.33443 / 2.44 ( 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 201 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 165 time to evaluate : 0.474 Fit side-chains revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8695 (mtp85) REVERT: B 93 GLN cc_start: 0.8739 (mm-40) cc_final: 0.8487 (mp10) REVERT: D 30 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7517 (mtp-110) REVERT: D 68 GLU cc_start: 0.8325 (tp30) cc_final: 0.8012 (tp30) REVERT: D 83 ARG cc_start: 0.8681 (mmt90) cc_final: 0.8432 (mmt90) REVERT: D 90 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8071 (mp0) REVERT: E 79 LYS cc_start: 0.9185 (tttt) cc_final: 0.8970 (tttp) REVERT: E 129 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.8152 (tpt90) REVERT: H 31 LYS cc_start: 0.8257 (mppt) cc_final: 0.8013 (mppt) REVERT: H 82 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8877 (mttm) REVERT: H 90 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8081 (mp0) REVERT: K 320 TYR cc_start: 0.8284 (OUTLIER) cc_final: 0.7295 (m-10) outliers start: 36 outliers final: 23 residues processed: 183 average time/residue: 0.8024 time to fit residues: 158.3884 Evaluate side-chains 192 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 87 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 105 GLU 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 215 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 5 optimal weight: 1.9990 chunk 126 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 87 optimal weight: 20.0000 chunk 111 optimal weight: 0.8980 chunk 53 optimal weight: 7.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.3644 r_free = 0.3644 target = 0.096793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.068703 restraints weight = 33918.946| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.16 r_work: 0.2926 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17202 Z= 0.161 Angle : 0.657 9.390 24495 Z= 0.361 Chirality : 0.046 0.326 2779 Planarity : 0.004 0.032 2092 Dihedral : 30.128 179.737 4625 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.10 % Allowed : 21.79 % Favored : 75.11 % 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: -0.21 (0.64), residues: 71 loop : -0.87 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 35 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 0.00314 / 0.16 (17202) covalent geometry : angle 0.65687 / 0.36 (24495) hydrogen bonds : bond 0.04825 / 3.04 ( 960) hydrogen bonds : angle 3.30851 / 2.42 ( 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 198 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 164 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8683 (mtp85) REVERT: B 93 GLN cc_start: 0.8739 (mm-40) cc_final: 0.8385 (mp10) REVERT: D 30 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7520 (mtp-110) REVERT: D 68 GLU cc_start: 0.8326 (tp30) cc_final: 0.8043 (tp30) REVERT: D 83 ARG cc_start: 0.8695 (mmt90) cc_final: 0.8436 (mmt90) REVERT: D 90 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8075 (mp0) REVERT: E 79 LYS cc_start: 0.9192 (tttt) cc_final: 0.8976 (tttp) REVERT: E 129 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.8151 (tpt90) REVERT: H 31 LYS cc_start: 0.8273 (mppt) cc_final: 0.7964 (mppt) REVERT: H 82 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8887 (mttm) REVERT: H 90 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8078 (mp0) REVERT: K 320 TYR cc_start: 0.8275 (OUTLIER) cc_final: 0.7401 (m-10) REVERT: K 348 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8166 (mtm-85) outliers start: 34 outliers final: 21 residues processed: 183 average time/residue: 0.8334 time to fit residues: 163.6047 Evaluate side-chains 192 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR 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 77 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 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 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: 4.9990 chunk 2 optimal weight: 0.9990 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: 7.9990 chunk 35 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 137 optimal weight: 0.1980 chunk 53 optimal weight: 7.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN 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 = 0.096870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.068750 restraints weight = 33839.081| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.20 r_work: 0.2925 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 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 0.038 17202 Z= 0.162 Angle : 0.655 9.154 24495 Z= 0.359 Chirality : 0.046 0.320 2779 Planarity : 0.004 0.061 2092 Dihedral : 30.099 179.810 4625 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.83 % Allowed : 22.24 % 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: 1.68 (0.24), residues: 1262 helix: 2.17 (0.18), residues: 793 sheet: -0.19 (0.64), residues: 71 loop : -0.83 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG K 645 TYR 0.010 0.001 TYR C 57 PHE 0.007 0.001 PHE F 61 TRP 0.013 0.001 TRP K 364 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.16 (17202) covalent geometry : angle 0.65499 / 0.36 (24495) hydrogen bonds : bond 0.04818 / 3.04 ( 960) hydrogen bonds : angle 3.29409 / 2.41 ( 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 197 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8682 (mtp85) REVERT: B 93 GLN cc_start: 0.8723 (mm-40) cc_final: 0.8360 (mp10) REVERT: C 73 ASN cc_start: 0.8331 (m110) cc_final: 0.8094 (t0) REVERT: D 30 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7499 (mtp-110) REVERT: D 68 GLU cc_start: 0.8311 (tp30) cc_final: 0.8024 (tp30) REVERT: D 83 ARG cc_start: 0.8671 (mmt90) cc_final: 0.8433 (mmt90) REVERT: D 90 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8069 (mp0) REVERT: E 79 LYS cc_start: 0.9174 (tttt) cc_final: 0.8965 (tttp) REVERT: E 129 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.8140 (tpt90) REVERT: G 73 ASN cc_start: 0.8444 (m-40) cc_final: 0.7690 (t0) REVERT: H 31 LYS cc_start: 0.8284 (mppt) cc_final: 0.7954 (mppt) REVERT: H 82 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8867 (mttm) REVERT: H 90 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8085 (mp0) REVERT: K 320 TYR cc_start: 0.8276 (OUTLIER) cc_final: 0.7390 (m-10) REVERT: K 645 ARG cc_start: 0.8318 (ttp80) cc_final: 0.8115 (tmm-80) outliers start: 31 outliers final: 23 residues processed: 181 average time/residue: 0.8034 time to fit residues: 156.1478 Evaluate side-chains 192 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 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 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 3.9990 chunk 127 optimal weight: 20.0000 chunk 21 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 48 optimal weight: 0.0970 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.097144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.069057 restraints weight = 33719.762| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.19 r_work: 0.2932 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17202 Z= 0.139 Angle : 0.653 9.141 24495 Z= 0.359 Chirality : 0.046 0.321 2779 Planarity : 0.004 0.066 2092 Dihedral : 30.086 179.934 4625 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.01 % Allowed : 22.24 % 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: 1.73 (0.24), residues: 1262 helix: 2.21 (0.18), residues: 793 sheet: -0.19 (0.64), residues: 71 loop : -0.82 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG K 645 TYR 0.010 0.001 TYR C 57 PHE 0.008 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 0.00259 / 0.14 (17202) covalent geometry : angle 0.65334 / 0.36 (24495) hydrogen bonds : bond 0.04657 / 2.92 ( 960) hydrogen bonds : angle 3.27804 / 2.40 ( 2463) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5968.30 seconds wall clock time: 101 minutes 58.52 seconds (6118.52 seconds total)