Starting phenix.real_space_refine on Thu Aug 6 01:31:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ots_17183/08_2026/8ots_17183_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ots_17183/08_2026/8ots_17183.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ots_17183/08_2026/8ots_17183_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ots_17183/08_2026/8ots_17183_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ots_17183/08_2026/8ots_17183.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ots_17183/08_2026/8ots_17183.map" } resolution = 3.3 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= 0.004 sd= 0.025 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: 5 Type Number sf(0) Gaussians P 252 5.49 5 S 14 5.16 5 C 7442 2.51 5 N 2489 2.21 5 O 2963 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 86 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: 13160 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 773 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 837 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "D" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 783 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 2592 Classifications: {'DNA': 127} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 126} Chain: "J" Number of atoms: 2609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 2609 Classifications: {'DNA': 127} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 126} Chain: "K" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 363 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved non-hydrogen bonds: 238 Unresolved non-hydrogen angles: 299 Unresolved non-hydrogen dihedrals: 197 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 7, 'GLU:plan': 5, 'PHE:plan': 5, 'ARG:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 118 Chain: "M" Number of atoms: 798 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 79, 399 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 2, 'TRANS': 76} Unresolved non-hydrogen bonds: 278 Unresolved non-hydrogen angles: 343 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'ARG:plan': 10, 'HIS:plan': 2, 'ASN:plan1': 4, 'GLU:plan': 11, 'GLN:plan1': 5, 'PHE:plan': 2, 'ASP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 161 Conformer: "B" Number of residues, atoms: 79, 399 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 2, 'TRANS': 76} Unresolved non-hydrogen bonds: 278 Unresolved non-hydrogen angles: 343 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'ARG:plan': 10, 'HIS:plan': 2, 'ASN:plan1': 4, 'GLU:plan': 11, 'GLN:plan1': 5, 'PHE:plan': 2, 'ASP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 161 Chain: "N" Number of atoms: 782 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 78, 391 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 1, 'TRANS': 76} Unresolved non-hydrogen bonds: 277 Unresolved non-hydrogen angles: 345 Unresolved non-hydrogen dihedrals: 229 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASP:plan': 8, 'ARG:plan': 10, 'HIS:plan': 6, 'ASN:plan1': 3, 'GLU:plan': 4, 'PHE:plan': 1, 'GLN:plan1': 8, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 181 Conformer: "B" Number of residues, atoms: 78, 391 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 1, 'TRANS': 76} Unresolved non-hydrogen bonds: 277 Unresolved non-hydrogen angles: 345 Unresolved non-hydrogen dihedrals: 229 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASP:plan': 8, 'ARG:plan': 10, 'HIS:plan': 6, 'ASN:plan1': 3, 'GLU:plan': 4, 'PHE:plan': 1, 'GLN:plan1': 8, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 181 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-1': 1, 'PTD:plan-2': 1} Unresolved non-hydrogen planarities: 2 Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-1': 1, 'PTD:plan-2': 1} Unresolved non-hydrogen planarities: 2 Chain: "E" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 15 Unusual residues: {'PTD': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'PTD:plan-1': 3, 'PTD:plan-2': 3} Unresolved non-hydrogen planarities: 6 Chain: "G" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-1': 1, 'PTD:plan-2': 1} Unresolved non-hydrogen planarities: 2 Chain: "H" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PTD': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'PTD:plan-1': 2, 'PTD:plan-2': 2} Unresolved non-hydrogen planarities: 4 Residues with excluded nonbonded symmetry interactions: 157 residue: pdb=" N AVAL M 354 " occ=0.50 ... (8 atoms not shown) pdb=" CB BVAL M 354 " occ=0.50 residue: pdb=" N ALYS M 355 " occ=0.50 ... (8 atoms not shown) pdb=" CB BLYS M 355 " occ=0.50 residue: pdb=" N AARG M 356 " occ=0.50 ... (8 atoms not shown) pdb=" CB BARG M 356 " occ=0.50 residue: pdb=" N AARG M 357 " occ=0.50 ... (8 atoms not shown) pdb=" CB BARG M 357 " occ=0.50 residue: pdb=" N ATHR M 358 " occ=0.50 ... (8 atoms not shown) pdb=" CB BTHR M 358 " occ=0.50 residue: pdb=" N AHIS M 359 " occ=0.50 ... (8 atoms not shown) pdb=" CB BHIS M 359 " occ=0.50 residue: pdb=" N AASN M 360 " occ=0.50 ... (8 atoms not shown) pdb=" CB BASN M 360 " occ=0.50 residue: pdb=" N AVAL M 361 " occ=0.50 ... (8 atoms not shown) pdb=" CB BVAL M 361 " occ=0.50 residue: pdb=" N ALEU M 362 " occ=0.50 ... (8 atoms not shown) pdb=" CB BLEU M 362 " occ=0.50 residue: pdb=" N AGLU M 363 " occ=0.50 ... (8 atoms not shown) pdb=" CB BGLU M 363 " occ=0.50 residue: pdb=" N AARG M 364 " occ=0.50 ... (8 atoms not shown) pdb=" CB BARG M 364 " occ=0.50 residue: pdb=" N AGLN M 365 " occ=0.50 ... (8 atoms not shown) pdb=" CB BGLN M 365 " occ=0.50 ... (remaining 145 not shown) Time building chain proxies: 3.01, per 1000 atoms: 0.23 Number of scatterers: 13160 At special positions: 0 Unit cell: (120.4, 116.1, 144.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 252 15.00 O 2963 8.00 N 2489 7.00 C 7442 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=16, symmetry=0 Number of additional bonds: simple=16, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 482.1 milliseconds 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2166 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 10 sheets defined 76.9% alpha, 2.0% beta 127 base pairs and 226 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.809A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.741A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.945A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.519A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 124 removed outlier: 3.513A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 139 through 160 Processing helix chain 'K' and resid 163 through 176 Processing helix chain 'K' and resid 180 through 189 Processing helix chain 'K' and resid 193 through 210 Proline residue: K 202 - end of helix Processing helix chain 'M' and resid 355 through 379 Processing helix chain 'M' and resid 380 through 385 removed outlier: 6.555A pdb=" N AGLU M 383 " --> pdb=" O AGLN M 380 " (cutoff:3.500A) Processing helix chain 'M' and resid 391 through 432 Processing helix chain 'N' and resid 24 through 48 Processing helix chain 'N' and resid 59 through 100 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.724A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.172A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.821A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.930A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.214A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 697 hydrogen bonds defined for protein. 2055 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 326 hydrogen bonds 652 hydrogen bond angles 0 basepair planarities 127 basepair parallelities 226 stacking parallelities Total time for adding SS restraints: 2.61 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2089 1.33 - 1.45: 4448 1.45 - 1.57: 6796 1.57 - 1.69: 506 1.69 - 1.81: 24 Bond restraints: 13863 Sorted by residual: bond pdb=" NE ARG A 40 " pdb=" CZ ARG A 40 " ideal model delta sigma weight residual 1.326 1.369 -0.043 1.10e-02 8.26e+03 1.52e+01 bond pdb=" N1 DC I 8 " pdb=" C6 DC I 8 " ideal model delta sigma weight residual 1.367 1.389 -0.022 6.00e-03 2.78e+04 1.34e+01 bond pdb=" N3 DA J 14 " pdb=" C4 DA J 14 " ideal model delta sigma weight residual 1.344 1.365 -0.021 6.00e-03 2.78e+04 1.20e+01 bond pdb=" N1 DT I 134 " pdb=" C2 DT I 134 " ideal model delta sigma weight residual 1.376 1.403 -0.027 8.00e-03 1.56e+04 1.16e+01 bond pdb=" N1 DC I 8 " pdb=" C2 DC I 8 " ideal model delta sigma weight residual 1.397 1.428 -0.031 1.00e-02 1.00e+04 9.35e+00 ... (remaining 13858 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 18516 1.85 - 3.71: 1233 3.71 - 5.56: 89 5.56 - 7.41: 33 7.41 - 9.26: 3 Bond angle restraints: 19874 Sorted by residual: angle pdb=" C HIS H 49 " pdb=" N PRO H 50 " pdb=" CA PRO H 50 " ideal model delta sigma weight residual 119.56 127.44 -7.88 1.02e+00 9.61e-01 5.97e+01 angle pdb=" C3' DT I 14 " pdb=" O3' DT I 14 " pdb=" P DA I 15 " ideal model delta sigma weight residual 119.70 128.96 -9.26 1.20e+00 6.94e-01 5.96e+01 angle pdb=" C HIS D 49 " pdb=" N PRO D 50 " pdb=" CA PRO D 50 " ideal model delta sigma weight residual 119.56 127.01 -7.45 1.02e+00 9.61e-01 5.33e+01 angle pdb=" C AALA M 390 " pdb=" N APRO M 391 " pdb=" CA APRO M 391 " ideal model delta sigma weight residual 120.03 127.02 -6.99 9.90e-01 1.02e+00 4.98e+01 angle pdb=" C AVAL N 50 " pdb=" N APRO N 51 " pdb=" CA APRO N 51 " ideal model delta sigma weight residual 119.56 126.33 -6.77 1.02e+00 9.61e-01 4.40e+01 ... (remaining 19869 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.59: 6517 35.59 - 71.17: 1156 71.17 - 106.76: 6 106.76 - 142.35: 0 142.35 - 177.93: 2 Dihedral angle restraints: 7681 sinusoidal: 4356 harmonic: 3325 Sorted by residual: dihedral pdb=" CA PRO H 103 " pdb=" C PRO H 103 " pdb=" N GLY H 104 " pdb=" CA GLY H 104 " ideal model delta harmonic sigma weight residual 180.00 159.20 20.80 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA PRO D 103 " pdb=" C PRO D 103 " pdb=" N GLY D 104 " pdb=" CA GLY D 104 " ideal model delta harmonic sigma weight residual 180.00 159.40 20.60 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" C4' DT I 89 " pdb=" C3' DT I 89 " pdb=" O3' DT I 89 " pdb=" P DA I 90 " ideal model delta sinusoidal sigma weight residual -140.00 37.93 -177.93 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 7678 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1487 0.049 - 0.099: 644 0.099 - 0.148: 165 0.148 - 0.198: 29 0.198 - 0.247: 7 Chirality restraints: 2332 Sorted by residual: chirality pdb=" CG LEU F 22 " pdb=" CB LEU F 22 " pdb=" CD1 LEU F 22 " pdb=" CD2 LEU F 22 " both_signs ideal model delta sigma weight residual False -2.59 -2.84 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CG LEU C 116 " pdb=" CB LEU C 116 " pdb=" CD1 LEU C 116 " pdb=" CD2 LEU C 116 " both_signs ideal model delta sigma weight residual False -2.59 -2.84 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA ARG K 201 " pdb=" N ARG K 201 " pdb=" C ARG K 201 " pdb=" CB ARG K 201 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 2329 not shown) Planarity restraints: 1680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG J 78 " 0.087 2.00e-02 2.50e+03 5.29e-02 8.40e+01 pdb=" N9 DG J 78 " -0.014 2.00e-02 2.50e+03 pdb=" C8 DG J 78 " -0.091 2.00e-02 2.50e+03 pdb=" N7 DG J 78 " -0.061 2.00e-02 2.50e+03 pdb=" C5 DG J 78 " 0.015 2.00e-02 2.50e+03 pdb=" C6 DG J 78 " 0.023 2.00e-02 2.50e+03 pdb=" O6 DG J 78 " 0.066 2.00e-02 2.50e+03 pdb=" N1 DG J 78 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DG J 78 " -0.005 2.00e-02 2.50e+03 pdb=" N2 DG J 78 " -0.083 2.00e-02 2.50e+03 pdb=" N3 DG J 78 " 0.034 2.00e-02 2.50e+03 pdb=" C4 DG J 78 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 27 " 0.102 2.00e-02 2.50e+03 4.94e-02 7.31e+01 pdb=" N9 DG I 27 " 0.003 2.00e-02 2.50e+03 pdb=" C8 DG I 27 " -0.032 2.00e-02 2.50e+03 pdb=" N7 DG I 27 " -0.060 2.00e-02 2.50e+03 pdb=" C5 DG I 27 " -0.047 2.00e-02 2.50e+03 pdb=" C6 DG I 27 " 0.003 2.00e-02 2.50e+03 pdb=" O6 DG I 27 " 0.100 2.00e-02 2.50e+03 pdb=" N1 DG I 27 " 0.009 2.00e-02 2.50e+03 pdb=" C2 DG I 27 " -0.007 2.00e-02 2.50e+03 pdb=" N2 DG I 27 " -0.026 2.00e-02 2.50e+03 pdb=" N3 DG I 27 " -0.012 2.00e-02 2.50e+03 pdb=" C4 DG I 27 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 121 " -0.010 2.00e-02 2.50e+03 4.76e-02 6.79e+01 pdb=" N9 DG I 121 " 0.005 2.00e-02 2.50e+03 pdb=" C8 DG I 121 " -0.072 2.00e-02 2.50e+03 pdb=" N7 DG I 121 " -0.037 2.00e-02 2.50e+03 pdb=" C5 DG I 121 " 0.042 2.00e-02 2.50e+03 pdb=" C6 DG I 121 " 0.005 2.00e-02 2.50e+03 pdb=" O6 DG I 121 " 0.017 2.00e-02 2.50e+03 pdb=" N1 DG I 121 " -0.018 2.00e-02 2.50e+03 pdb=" C2 DG I 121 " 0.005 2.00e-02 2.50e+03 pdb=" N2 DG I 121 " -0.084 2.00e-02 2.50e+03 pdb=" N3 DG I 121 " 0.074 2.00e-02 2.50e+03 pdb=" C4 DG I 121 " 0.074 2.00e-02 2.50e+03 ... (remaining 1677 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 5814 2.99 - 3.46: 12609 3.46 - 3.94: 25698 3.94 - 4.42: 28166 4.42 - 4.90: 37174 Nonbonded interactions: 109461 Sorted by model distance: nonbonded pdb=" N GLU C 41 " pdb=" OE1 GLU C 41 " model vdw 2.508 3.120 nonbonded pdb=" OD1 ASP A 123 " pdb=" NE2 HIS E 113 " model vdw 2.515 3.120 nonbonded pdb=" O5' DA J 137 " pdb=" O4' DA J 137 " model vdw 2.531 2.432 nonbonded pdb=" OE1 GLN E 85 " pdb=" OG1 THR F 82 " model vdw 2.543 3.040 nonbonded pdb=" O ILE E 62 " pdb=" NE2 GLN E 93 " model vdw 2.556 3.120 ... (remaining 109456 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' selection = (chain 'E' and resid 40 through 201) } ncs_group { reference = (chain 'B' and resid 22 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 9 through 116) selection = (chain 'G' and resid 9 through 116) } ncs_group { reference = (chain 'D' and resid 33 through 200) selection = (chain 'H' and resid 33 through 201) } 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=0.00 max=1.00 mean=0.93 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: 1.090 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: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.390 Find NCS groups from input model: 0.180 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 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 : 0.010 0.173 13879 Z= 0.787 Angle : 1.016 9.265 19874 Z= 0.788 Chirality : 0.057 0.247 2332 Planarity : 0.011 0.053 1680 Dihedral : 25.595 177.935 5515 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 0.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 0.63 % Allowed : 0.32 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.70 (0.21), residues: 1116 helix: 1.26 (0.15), residues: 871 sheet: None (None), residues: 0 loop : 1.01 (0.35), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 40 TYR 0.016 0.003 TYR C 57 PHE 0.008 0.002 PHE H 70 TRP 0.000 0.000 TRP K 207 HIS 0.004 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00867 / 0.54 (13863) covalent geometry : angle 1.01552 / 0.79 (19874) hydrogen bonds : bond 0.15382 / 10.01 ( 1023) hydrogen bonds : angle 5.04788 / 3.63 ( 2707) Misc. bond : bond 0.16922 / 11.04 ( 16) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 155 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ILE cc_start: 0.8736 (mt) cc_final: 0.8529 (mt) REVERT: C 76 THR cc_start: 0.9160 (p) cc_final: 0.8932 (t) REVERT: E 56 LYS cc_start: 0.9154 (tttt) cc_final: 0.8836 (ttmt) REVERT: G 38 ASN cc_start: 0.7744 (m-40) cc_final: 0.7291 (m110) REVERT: G 90 ASP cc_start: 0.7777 (t70) cc_final: 0.7537 (t0) REVERT: G 99 ARG cc_start: 0.8188 (mmm160) cc_final: 0.7918 (tpt90) outliers start: 4 outliers final: 2 residues processed: 157 average time/residue: 0.1756 time to fit residues: 35.5907 Evaluate side-chains 83 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 81 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain D residue 85 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 20.0000 chunk 113 optimal weight: 20.0000 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 10.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 95 GLN D 109 HIS G 38 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.100355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.068636 restraints weight = 78280.756| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 3.39 r_work: 0.3177 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3131 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 93 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 93 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3131 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13879 Z= 0.166 Angle : 0.653 8.074 19874 Z= 0.386 Chirality : 0.045 0.273 2332 Planarity : 0.005 0.042 1680 Dihedral : 28.507 172.693 4019 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.22 % Allowed : 6.81 % Favored : 90.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.14 (0.23), residues: 1116 helix: 3.17 (0.16), residues: 881 sheet: None (None), residues: 0 loop : 0.99 (0.38), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 99 TYR 0.031 0.002 TYR F 88 PHE 0.008 0.001 PHE A 67 TRP 0.000 0.000 TRP K 207 HIS 0.007 0.002 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.17 (13863) covalent geometry : angle 0.65340 / 0.39 (19874) hydrogen bonds : bond 0.05653 / 3.79 ( 1023) hydrogen bonds : angle 3.17183 / 2.28 ( 2707) Misc. bond : bond 0.00463 / 0.27 ( 16) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ILE cc_start: 0.8836 (mt) cc_final: 0.8454 (mp) REVERT: C 76 THR cc_start: 0.9172 (p) cc_final: 0.8915 (t) REVERT: E 56 LYS cc_start: 0.9112 (tttt) cc_final: 0.8738 (ttmt) REVERT: F 74 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8272 (tm-30) REVERT: G 73 ASN cc_start: 0.8994 (m-40) cc_final: 0.8760 (t0) REVERT: G 90 ASP cc_start: 0.7996 (t70) cc_final: 0.7737 (t0) REVERT: H 105 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8306 (mm-30) outliers start: 14 outliers final: 7 residues processed: 103 average time/residue: 0.1368 time to fit residues: 19.2770 Evaluate side-chains 90 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 31 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 90 optimal weight: 20.0000 chunk 110 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN C 104 GLN G 31 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.103259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.069246 restraints weight = 91260.982| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 3.79 r_work: 0.3138 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 93 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 93 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13879 Z= 0.156 Angle : 0.580 7.682 19874 Z= 0.352 Chirality : 0.041 0.353 2332 Planarity : 0.004 0.063 1680 Dihedral : 28.404 172.334 4019 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Rotamer: Outliers : 1.90 % Allowed : 9.03 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.65 (0.24), residues: 1116 helix: 3.64 (0.16), residues: 882 sheet: None (None), residues: 0 loop : 0.64 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 99 TYR 0.018 0.001 TYR H 121 PHE 0.006 0.001 PHE A 67 TRP 0.000 0.000 TRP K 207 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.16 (13863) covalent geometry : angle 0.57980 / 0.35 (19874) hydrogen bonds : bond 0.04744 / 3.17 ( 1023) hydrogen bonds : angle 2.88048 / 2.06 ( 2707) Misc. bond : bond 0.00106 / 0.04 ( 16) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ILE cc_start: 0.8812 (mt) cc_final: 0.8403 (mp) REVERT: A 58 THR cc_start: 0.9252 (p) cc_final: 0.8669 (t) REVERT: C 76 THR cc_start: 0.9229 (p) cc_final: 0.8947 (t) REVERT: C 92 GLU cc_start: 0.9127 (OUTLIER) cc_final: 0.8129 (mm-30) REVERT: E 56 LYS cc_start: 0.9107 (tttt) cc_final: 0.8743 (ttmt) REVERT: E 73 GLU cc_start: 0.8413 (tt0) cc_final: 0.8035 (tt0) REVERT: E 120 MET cc_start: 0.8525 (mtp) cc_final: 0.8319 (mtt) REVERT: F 25 ASN cc_start: 0.8466 (m-40) cc_final: 0.8101 (m-40) REVERT: F 74 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8416 (tm-30) REVERT: F 84 MET cc_start: 0.8791 (mmm) cc_final: 0.8526 (mmp) REVERT: G 73 ASN cc_start: 0.8852 (m-40) cc_final: 0.8620 (t0) outliers start: 12 outliers final: 8 residues processed: 97 average time/residue: 0.1213 time to fit residues: 16.5496 Evaluate side-chains 92 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 31 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 34 optimal weight: 0.0050 chunk 76 optimal weight: 20.0000 chunk 52 optimal weight: 6.9990 chunk 109 optimal weight: 7.9990 chunk 114 optimal weight: 40.0000 chunk 53 optimal weight: 20.0000 chunk 88 optimal weight: 20.0000 chunk 91 optimal weight: 20.0000 chunk 58 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 95 optimal weight: 30.0000 overall best weight: 4.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 75 HIS D 47 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.097769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.066454 restraints weight = 86038.093| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.31 r_work: 0.3068 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 93 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 93 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 13879 Z= 0.258 Angle : 0.688 7.330 19874 Z= 0.391 Chirality : 0.044 0.333 2332 Planarity : 0.005 0.038 1680 Dihedral : 28.630 171.823 4019 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 3.33 % Allowed : 9.35 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.14 (0.23), residues: 1116 helix: 3.33 (0.16), residues: 882 sheet: None (None), residues: 0 loop : 0.24 (0.36), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 99 TYR 0.022 0.002 TYR D 121 PHE 0.014 0.002 PHE E 78 TRP 0.000 0.000 TRP K 207 HIS 0.010 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.26 (13863) covalent geometry : angle 0.68802 / 0.39 (19874) hydrogen bonds : bond 0.05161 / 3.44 ( 1023) hydrogen bonds : angle 3.10719 / 2.22 ( 2707) Misc. bond : bond 0.00091 / 0.06 ( 16) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ILE cc_start: 0.8930 (mt) cc_final: 0.8654 (mt) REVERT: C 76 THR cc_start: 0.9282 (p) cc_final: 0.9039 (t) REVERT: E 56 LYS cc_start: 0.9150 (tttt) cc_final: 0.8738 (ttmt) REVERT: E 73 GLU cc_start: 0.8371 (tt0) cc_final: 0.7890 (tt0) REVERT: F 25 ASN cc_start: 0.8534 (m-40) cc_final: 0.8146 (m-40) REVERT: F 74 GLU cc_start: 0.8868 (tm-30) cc_final: 0.8525 (tm-30) outliers start: 21 outliers final: 15 residues processed: 101 average time/residue: 0.1286 time to fit residues: 18.2309 Evaluate side-chains 89 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 101 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 19 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 80 optimal weight: 20.0000 chunk 73 optimal weight: 30.0000 chunk 14 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 49 HIS F 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.099752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.068382 restraints weight = 90565.839| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 3.50 r_work: 0.3110 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3110 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 93 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 93 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13879 Z= 0.144 Angle : 0.570 6.766 19874 Z= 0.344 Chirality : 0.040 0.351 2332 Planarity : 0.004 0.050 1680 Dihedral : 28.457 169.617 4019 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 2.06 % Allowed : 10.78 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.71 (0.24), residues: 1116 helix: 3.77 (0.16), residues: 882 sheet: None (None), residues: 0 loop : 0.24 (0.37), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 99 TYR 0.023 0.002 TYR D 121 PHE 0.009 0.001 PHE E 67 TRP 0.000 0.000 TRP K 207 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.14 (13863) covalent geometry : angle 0.56976 / 0.34 (19874) hydrogen bonds : bond 0.04231 / 2.82 ( 1023) hydrogen bonds : angle 2.71166 / 1.94 ( 2707) Misc. bond : bond 0.00054 / 0.02 ( 16) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.9254 (p) cc_final: 0.8785 (t) REVERT: B 52 GLU cc_start: 0.8430 (mm-30) cc_final: 0.8153 (mm-30) REVERT: B 84 MET cc_start: 0.9088 (mmm) cc_final: 0.8384 (tmm) REVERT: C 76 THR cc_start: 0.9259 (p) cc_final: 0.8999 (t) REVERT: E 56 LYS cc_start: 0.9123 (tttt) cc_final: 0.8710 (ttmt) REVERT: F 74 GLU cc_start: 0.8935 (tm-30) cc_final: 0.8543 (tm-30) REVERT: H 59 MET cc_start: 0.9196 (tpp) cc_final: 0.8993 (tpp) outliers start: 13 outliers final: 8 residues processed: 91 average time/residue: 0.1377 time to fit residues: 17.7124 Evaluate side-chains 85 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain H residue 101 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 81 optimal weight: 20.0000 chunk 49 optimal weight: 2.9990 chunk 116 optimal weight: 50.0000 chunk 80 optimal weight: 20.0000 chunk 68 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 88 optimal weight: 20.0000 chunk 103 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.097273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.064309 restraints weight = 111587.607| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 3.86 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3203 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 93 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 93 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3203 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 13879 Z= 0.238 Angle : 0.641 6.537 19874 Z= 0.371 Chirality : 0.042 0.328 2332 Planarity : 0.004 0.045 1680 Dihedral : 28.593 173.226 4019 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.69 % Allowed : 10.30 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.32 (0.24), residues: 1116 helix: 3.54 (0.16), residues: 881 sheet: None (None), residues: 0 loop : -0.05 (0.36), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 99 TYR 0.023 0.002 TYR D 121 PHE 0.009 0.001 PHE E 78 TRP 0.000 0.000 TRP K 207 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.24 (13863) covalent geometry : angle 0.64057 / 0.37 (19874) hydrogen bonds : bond 0.04807 / 3.20 ( 1023) hydrogen bonds : angle 2.94390 / 2.10 ( 2707) Misc. bond : bond 0.00045 / 0.02 ( 16) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ILE cc_start: 0.8697 (mt) cc_final: 0.8442 (mt) REVERT: A 52 ARG cc_start: 0.8210 (mtp180) cc_final: 0.7812 (ttt180) REVERT: A 58 THR cc_start: 0.9265 (p) cc_final: 0.8772 (t) REVERT: B 52 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7665 (mm-30) REVERT: C 76 THR cc_start: 0.9249 (p) cc_final: 0.8964 (t) REVERT: C 104 GLN cc_start: 0.8603 (mp10) cc_final: 0.8302 (pm20) REVERT: E 56 LYS cc_start: 0.9042 (tttt) cc_final: 0.8649 (ttmt) REVERT: F 25 ASN cc_start: 0.8241 (m-40) cc_final: 0.7844 (m-40) REVERT: F 74 GLU cc_start: 0.8295 (tm-30) cc_final: 0.7873 (tm-30) REVERT: G 92 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7937 (pm20) outliers start: 17 outliers final: 15 residues processed: 90 average time/residue: 0.1338 time to fit residues: 17.1050 Evaluate side-chains 92 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 101 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 49 optimal weight: 0.8980 chunk 93 optimal weight: 20.0000 chunk 106 optimal weight: 0.0030 chunk 60 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 73 optimal weight: 30.0000 chunk 114 optimal weight: 7.9990 chunk 88 optimal weight: 30.0000 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 20.0000 chunk 41 optimal weight: 0.7980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 73 ASN ** 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 = 0.3982 r_free = 0.3982 target = 0.098613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.065782 restraints weight = 111145.110| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 4.05 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3293 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 93 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 93 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3293 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13879 Z= 0.130 Angle : 0.553 5.939 19874 Z= 0.337 Chirality : 0.039 0.343 2332 Planarity : 0.004 0.041 1680 Dihedral : 28.405 172.438 4019 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.06 % Allowed : 11.09 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.83 (0.24), residues: 1116 helix: 3.90 (0.16), residues: 885 sheet: None (None), residues: 0 loop : 0.03 (0.37), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 99 TYR 0.023 0.001 TYR D 121 PHE 0.010 0.001 PHE E 67 TRP 0.000 0.000 TRP K 207 HIS 0.002 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.13 (13863) covalent geometry : angle 0.55332 / 0.34 (19874) hydrogen bonds : bond 0.03957 / 2.64 ( 1023) hydrogen bonds : angle 2.56875 / 1.83 ( 2707) Misc. bond : bond 0.00021 / 0.01 ( 16) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8202 (mtp180) cc_final: 0.7833 (ttt180) REVERT: A 58 THR cc_start: 0.9285 (p) cc_final: 0.8824 (t) REVERT: B 27 GLN cc_start: 0.9012 (mm-40) cc_final: 0.8723 (mm110) REVERT: C 76 THR cc_start: 0.9210 (p) cc_final: 0.8909 (t) REVERT: C 104 GLN cc_start: 0.8581 (mp10) cc_final: 0.8255 (pm20) REVERT: E 45 THR cc_start: 0.9112 (p) cc_final: 0.8877 (t) REVERT: E 56 LYS cc_start: 0.8989 (tttt) cc_final: 0.8587 (ttmt) REVERT: F 25 ASN cc_start: 0.8153 (m-40) cc_final: 0.7730 (m-40) REVERT: F 74 GLU cc_start: 0.8347 (tm-30) cc_final: 0.7874 (tm-30) REVERT: F 84 MET cc_start: 0.8782 (mmm) cc_final: 0.8432 (tpt) REVERT: H 59 MET cc_start: 0.8856 (tpp) cc_final: 0.8346 (tpp) outliers start: 13 outliers final: 10 residues processed: 84 average time/residue: 0.1455 time to fit residues: 17.1966 Evaluate side-chains 86 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 101 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 3 optimal weight: 5.9990 chunk 115 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 72 optimal weight: 50.0000 chunk 77 optimal weight: 20.0000 chunk 27 optimal weight: 0.0170 chunk 102 optimal weight: 7.9990 chunk 96 optimal weight: 50.0000 chunk 74 optimal weight: 20.0000 overall best weight: 4.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.095837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.062165 restraints weight = 113956.199| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 4.02 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3187 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 93 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 93 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3187 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 13879 Z= 0.269 Angle : 0.668 6.526 19874 Z= 0.380 Chirality : 0.043 0.313 2332 Planarity : 0.005 0.056 1680 Dihedral : 28.616 175.953 4019 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.54 % Allowed : 11.41 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.35 (0.24), residues: 1116 helix: 3.60 (0.16), residues: 881 sheet: None (None), residues: 0 loop : -0.20 (0.37), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 99 TYR 0.022 0.002 TYR D 121 PHE 0.012 0.002 PHE G 25 TRP 0.000 0.000 TRP K 207 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.27 (13863) covalent geometry : angle 0.66754 / 0.38 (19874) hydrogen bonds : bond 0.04915 / 3.28 ( 1023) hydrogen bonds : angle 2.99626 / 2.14 ( 2707) Misc. bond : bond 0.00025 / 0.01 ( 16) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ILE cc_start: 0.8739 (mt) cc_final: 0.8483 (mt) REVERT: A 52 ARG cc_start: 0.8235 (mtp180) cc_final: 0.7844 (ttt180) REVERT: A 58 THR cc_start: 0.9288 (p) cc_final: 0.8886 (t) REVERT: B 52 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7699 (mm-30) REVERT: E 56 LYS cc_start: 0.9041 (tttt) cc_final: 0.8636 (ttmt) REVERT: E 59 GLU cc_start: 0.8167 (pm20) cc_final: 0.7851 (pm20) REVERT: E 105 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7852 (mm-30) REVERT: F 25 ASN cc_start: 0.8419 (m-40) cc_final: 0.7903 (m-40) REVERT: F 84 MET cc_start: 0.8836 (mmm) cc_final: 0.8493 (tpt) REVERT: G 41 GLU cc_start: 0.8680 (mp0) cc_final: 0.8414 (mp0) REVERT: G 92 GLU cc_start: 0.8109 (mp0) cc_final: 0.7896 (pm20) REVERT: H 59 MET cc_start: 0.8960 (tpp) cc_final: 0.8524 (tpp) outliers start: 16 outliers final: 14 residues processed: 91 average time/residue: 0.1361 time to fit residues: 17.4871 Evaluate side-chains 93 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 101 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 17 optimal weight: 8.9990 chunk 93 optimal weight: 20.0000 chunk 30 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 = 0.3972 r_free = 0.3972 target = 0.098083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.065047 restraints weight = 121594.808| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 4.20 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3267 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 93 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 93 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3267 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13879 Z= 0.136 Angle : 0.564 6.217 19874 Z= 0.341 Chirality : 0.039 0.332 2332 Planarity : 0.004 0.045 1680 Dihedral : 28.431 174.872 4019 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.58 % Allowed : 13.15 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.80 (0.24), residues: 1116 helix: 3.91 (0.16), residues: 885 sheet: None (None), residues: 0 loop : -0.13 (0.37), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 33 TYR 0.025 0.001 TYR D 121 PHE 0.008 0.001 PHE E 67 TRP 0.000 0.000 TRP K 207 HIS 0.001 0.000 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.14 (13863) covalent geometry : angle 0.56436 / 0.34 (19874) hydrogen bonds : bond 0.03997 / 2.66 ( 1023) hydrogen bonds : angle 2.57743 / 1.84 ( 2707) Misc. bond : bond 0.00027 / 0.02 ( 16) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ILE cc_start: 0.8658 (mt) cc_final: 0.8403 (mt) REVERT: A 52 ARG cc_start: 0.8220 (mtp180) cc_final: 0.7851 (ttt180) REVERT: A 58 THR cc_start: 0.9295 (p) cc_final: 0.8899 (t) REVERT: C 104 GLN cc_start: 0.8556 (mp10) cc_final: 0.8263 (pm20) REVERT: E 45 THR cc_start: 0.9124 (p) cc_final: 0.8916 (t) REVERT: E 56 LYS cc_start: 0.8981 (tttt) cc_final: 0.8575 (ttmt) REVERT: E 59 GLU cc_start: 0.8050 (pm20) cc_final: 0.7715 (pm20) REVERT: F 25 ASN cc_start: 0.8294 (m-40) cc_final: 0.7793 (m-40) REVERT: F 84 MET cc_start: 0.8773 (mmm) cc_final: 0.8349 (tpt) REVERT: F 88 TYR cc_start: 0.8570 (m-10) cc_final: 0.8174 (m-10) REVERT: G 41 GLU cc_start: 0.8716 (mp0) cc_final: 0.8419 (mp0) outliers start: 10 outliers final: 10 residues processed: 86 average time/residue: 0.1308 time to fit residues: 16.0502 Evaluate side-chains 87 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 101 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 23 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 84 optimal weight: 40.0000 chunk 78 optimal weight: 20.0000 chunk 33 optimal weight: 6.9990 chunk 38 optimal weight: 0.2980 chunk 104 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.100847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.066467 restraints weight = 145332.069| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 4.51 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3257 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 93 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 93 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3257 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13879 Z= 0.166 Angle : 0.581 6.939 19874 Z= 0.345 Chirality : 0.039 0.314 2332 Planarity : 0.004 0.042 1680 Dihedral : 28.455 176.169 4019 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.90 % Allowed : 13.00 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.79 (0.24), residues: 1116 helix: 3.93 (0.16), residues: 882 sheet: None (None), residues: 0 loop : -0.17 (0.37), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 99 TYR 0.023 0.001 TYR D 121 PHE 0.009 0.001 PHE A 67 TRP 0.000 0.000 TRP K 207 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.17 (13863) covalent geometry : angle 0.58128 / 0.34 (19874) hydrogen bonds : bond 0.04103 / 2.74 ( 1023) hydrogen bonds : angle 2.63179 / 1.88 ( 2707) Misc. bond : bond 0.00017 / 0.01 ( 16) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ILE cc_start: 0.8658 (mt) cc_final: 0.8405 (mt) REVERT: A 52 ARG cc_start: 0.8239 (mtp180) cc_final: 0.7871 (ttt180) REVERT: A 58 THR cc_start: 0.9253 (p) cc_final: 0.8882 (t) REVERT: C 9 LYS cc_start: 0.5692 (tttp) cc_final: 0.5355 (tttp) REVERT: C 104 GLN cc_start: 0.8565 (mp10) cc_final: 0.8233 (pm20) REVERT: E 45 THR cc_start: 0.9124 (p) cc_final: 0.8887 (t) REVERT: E 56 LYS cc_start: 0.8988 (tttt) cc_final: 0.8566 (ttmt) REVERT: E 59 GLU cc_start: 0.8014 (pm20) cc_final: 0.7675 (pm20) REVERT: F 25 ASN cc_start: 0.8314 (m-40) cc_final: 0.7747 (m-40) REVERT: F 84 MET cc_start: 0.8850 (mmm) cc_final: 0.8420 (tpt) REVERT: F 88 TYR cc_start: 0.8604 (m-10) cc_final: 0.8132 (m-10) outliers start: 12 outliers final: 12 residues processed: 87 average time/residue: 0.1171 time to fit residues: 14.4356 Evaluate side-chains 90 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 101 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 65 optimal weight: 0.8980 chunk 109 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 92 optimal weight: 20.0000 chunk 87 optimal weight: 20.0000 chunk 53 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 82 optimal weight: 20.0000 chunk 91 optimal weight: 20.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.100937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.066733 restraints weight = 132096.622| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 4.33 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 93 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 93 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13879 Z= 0.162 Angle : 0.579 6.356 19874 Z= 0.345 Chirality : 0.039 0.316 2332 Planarity : 0.004 0.048 1680 Dihedral : 28.444 176.428 4019 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.74 % Allowed : 13.63 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.79 (0.24), residues: 1116 helix: 3.93 (0.16), residues: 882 sheet: None (None), residues: 0 loop : -0.19 (0.37), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 99 TYR 0.023 0.001 TYR D 121 PHE 0.008 0.001 PHE E 67 TRP 0.000 0.000 TRP K 207 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.16 (13863) covalent geometry : angle 0.57917 / 0.34 (19874) hydrogen bonds : bond 0.04059 / 2.71 ( 1023) hydrogen bonds : angle 2.61350 / 1.86 ( 2707) Misc. bond : bond 0.00017 / 0.01 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3386.58 seconds wall clock time: 58 minutes 19.53 seconds (3499.53 seconds total)