Starting phenix.real_space_refine on Thu May 15 06:08:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ots_17183/05_2025/8ots_17183_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ots_17183/05_2025/8ots_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ots_17183/05_2025/8ots_17183.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ots_17183/05_2025/8ots_17183.map" model { file = "/net/cci-nas-00/data/ceres_data/8ots_17183/05_2025/8ots_17183_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ots_17183/05_2025/8ots_17183_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 7, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 5, 'GLU:plan': 5, 'ARG:plan': 3} 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: {'GLN:plan1': 5, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 10} 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: {'GLN:plan1': 5, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 10} 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: {'GLN:plan1': 8, 'ASP:plan': 8, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 6, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 10} 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: {'GLN:plan1': 8, 'ASP:plan': 8, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 6, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 10} 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-2': 1, 'PTD:plan-1': 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-2': 1, 'PTD:plan-1': 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-2': 3, 'PTD:plan-1': 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-2': 1, 'PTD:plan-1': 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-2': 2, 'PTD:plan-1': 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: 7.63, per 1000 atoms: 0.58 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: 3.30 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 5.55 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: 5.12 Time building geometry restraints manager: 3.80 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=" N BARG M 356 " pdb=" CA BARG M 356 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.19e-02 7.06e+03 8.47e+00 bond pdb=" N BARG M 378 " pdb=" CA BARG M 378 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.19e-02 7.06e+03 6.73e+00 bond pdb=" N BARG M 367 " pdb=" CA BARG M 367 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.20e-02 6.94e+03 6.48e+00 bond pdb=" NE ARG E 69 " pdb=" CZ ARG E 69 " ideal model delta sigma weight residual 1.326 1.354 -0.028 1.10e-02 8.26e+03 6.47e+00 ... (remaining 13858 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 18235 1.75 - 3.51: 1433 3.51 - 5.26: 170 5.26 - 7.01: 30 7.01 - 8.76: 6 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=" 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 angle pdb=" C LEU D 102 " pdb=" N PRO D 103 " pdb=" CA PRO D 103 " ideal model delta sigma weight residual 120.14 126.86 -6.72 1.06e+00 8.90e-01 4.01e+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: 1482 0.049 - 0.099: 633 0.099 - 0.148: 191 0.148 - 0.198: 21 0.198 - 0.247: 5 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 133 or resid 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 124 or resid 200)) selection = (chain 'H' and (resid 33 through 124 or resid 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 34.540 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 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 : 0.011 0.173 13879 Z= 0.760 Angle : 1.028 8.765 19874 Z= 0.705 Chirality : 0.058 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.000 0.000 TRP K 207 HIS 0.004 0.001 HIS H 49 PHE 0.008 0.002 PHE H 70 TYR 0.016 0.003 TYR C 57 ARG 0.005 0.000 ARG F 40 Details of bonding type rmsd hydrogen bonds : bond 0.15382 ( 1023) hydrogen bonds : angle 5.04788 ( 2707) covalent geometry : bond 0.00896 (13863) covalent geometry : angle 1.02833 (19874) Misc. bond : bond 0.16922 ( 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 : 0.999 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: 0.8528 (mt) REVERT: C 76 THR cc_start: 0.9160 (p) cc_final: 0.8931 (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: 0.7289 (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: 0.3960 time to fit residues: 79.4387 Evaluate side-chains 81 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 79 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 98 optimal weight: 9.9990 chunk 88 optimal weight: 8.9990 chunk 49 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 106 optimal weight: 20.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN D 47 GLN D 95 GLN D 109 HIS G 31 HIS G 38 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.100124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.068064 restraints weight = 89205.500| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 3.61 r_work: 0.3156 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3110 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 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 = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 93 | |-----------------------------------------------------------------------------| r_final: 0.3110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13879 Z= 0.163 Angle : 0.547 5.154 19874 Z= 0.330 Chirality : 0.034 0.128 2332 Planarity : 0.004 0.034 1680 Dihedral : 28.063 172.289 4019 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.69 % Allowed : 7.13 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.43 (0.23), residues: 1116 helix: 3.39 (0.16), residues: 882 sheet: None (None), residues: 0 loop : 1.00 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP K 207 HIS 0.005 0.001 HIS G 31 PHE 0.013 0.001 PHE A 67 TYR 0.024 0.002 TYR F 88 ARG 0.008 0.000 ARG D 99 Details of bonding type rmsd hydrogen bonds : bond 0.04204 ( 1023) hydrogen bonds : angle 2.87613 ( 2707) covalent geometry : bond 0.00354 (13863) covalent geometry : angle 0.54705 (19874) Misc. bond : bond 0.00124 ( 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 114 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ILE cc_start: 0.8855 (mt) cc_final: 0.8500 (mt) REVERT: C 76 THR cc_start: 0.9189 (p) cc_final: 0.8910 (t) REVERT: E 56 LYS cc_start: 0.9125 (tttt) cc_final: 0.8748 (ttmt) REVERT: F 74 GLU cc_start: 0.8663 (tm-30) cc_final: 0.8398 (tm-30) REVERT: F 84 MET cc_start: 0.8825 (mmm) cc_final: 0.8512 (mmp) REVERT: G 56 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8512 (tm-30) REVERT: G 90 ASP cc_start: 0.8102 (t70) cc_final: 0.7830 (t0) REVERT: G 99 ARG cc_start: 0.8452 (mmm160) cc_final: 0.8250 (mmt180) outliers start: 17 outliers final: 9 residues processed: 109 average time/residue: 0.3548 time to fit residues: 51.4888 Evaluate side-chains 88 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 1.015 ------------------------------------------------------------------------------- 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 24 optimal weight: 0.6980 chunk 109 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 41 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 54 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 111 optimal weight: 20.0000 chunk 114 optimal weight: 30.0000 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS D 49 HIS E 68 GLN F 75 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.097604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.065269 restraints weight = 87171.189| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 3.46 r_work: 0.3099 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3097 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 93 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 93 | |-----------------------------------------------------------------------------| r_final: 0.3097 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13879 Z= 0.210 Angle : 0.553 6.880 19874 Z= 0.330 Chirality : 0.034 0.141 2332 Planarity : 0.004 0.032 1680 Dihedral : 28.112 175.341 4019 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 3.01 % Allowed : 8.40 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.66 (0.23), residues: 1116 helix: 3.67 (0.16), residues: 882 sheet: None (None), residues: 0 loop : 0.59 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP K 207 HIS 0.006 0.001 HIS F 75 PHE 0.008 0.001 PHE E 78 TYR 0.021 0.002 TYR D 121 ARG 0.009 0.001 ARG D 99 Details of bonding type rmsd hydrogen bonds : bond 0.04115 ( 1023) hydrogen bonds : angle 2.78515 ( 2707) covalent geometry : bond 0.00473 (13863) covalent geometry : angle 0.55309 (19874) Misc. bond : bond 0.00134 ( 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 105 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.9194 (tpp) cc_final: 0.8496 (mmm) REVERT: C 76 THR cc_start: 0.9235 (p) cc_final: 0.8975 (t) REVERT: E 56 LYS cc_start: 0.9152 (tttt) cc_final: 0.8765 (ttmt) REVERT: F 25 ASN cc_start: 0.8817 (m-40) cc_final: 0.8285 (m110) REVERT: F 74 GLU cc_start: 0.8919 (tm-30) cc_final: 0.8549 (tm-30) REVERT: G 56 GLU cc_start: 0.8890 (tm-30) cc_final: 0.8597 (tm-30) REVERT: G 90 ASP cc_start: 0.8093 (t70) cc_final: 0.7715 (t0) outliers start: 19 outliers final: 13 residues processed: 100 average time/residue: 0.3209 time to fit residues: 43.9297 Evaluate side-chains 89 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.992 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 13 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 115 optimal weight: 40.0000 chunk 24 optimal weight: 3.9990 chunk 61 optimal weight: 0.0470 overall best weight: 1.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.099022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.066453 restraints weight = 124912.821| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 4.26 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3295 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 93 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 93 | |-----------------------------------------------------------------------------| r_final: 0.3295 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3197 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= 0.151 Angle : 0.510 5.846 19874 Z= 0.308 Chirality : 0.032 0.126 2332 Planarity : 0.004 0.036 1680 Dihedral : 27.896 178.681 4019 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.90 % Allowed : 9.51 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.98 (0.24), residues: 1116 helix: 3.92 (0.16), residues: 884 sheet: None (None), residues: 0 loop : 0.53 (0.39), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP K 207 HIS 0.003 0.001 HIS B 75 PHE 0.010 0.001 PHE E 67 TYR 0.021 0.001 TYR D 121 ARG 0.009 0.000 ARG D 99 Details of bonding type rmsd hydrogen bonds : bond 0.03474 ( 1023) hydrogen bonds : angle 2.49467 ( 2707) covalent geometry : bond 0.00329 (13863) covalent geometry : angle 0.51006 (19874) Misc. bond : bond 0.00022 ( 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 94 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ILE cc_start: 0.8562 (mt) cc_final: 0.8328 (mt) REVERT: A 52 ARG cc_start: 0.8234 (mtp180) cc_final: 0.7861 (ttt180) REVERT: A 58 THR cc_start: 0.9192 (p) cc_final: 0.8823 (t) REVERT: B 84 MET cc_start: 0.8950 (tpp) cc_final: 0.8183 (mmm) REVERT: C 76 THR cc_start: 0.9203 (p) cc_final: 0.8912 (t) REVERT: C 90 ASP cc_start: 0.8160 (t0) cc_final: 0.7950 (t0) REVERT: C 104 GLN cc_start: 0.8595 (mp10) cc_final: 0.8379 (mp10) REVERT: E 45 THR cc_start: 0.9093 (p) cc_final: 0.8859 (t) REVERT: E 56 LYS cc_start: 0.9010 (tttt) cc_final: 0.8558 (ttmt) REVERT: F 25 ASN cc_start: 0.8261 (m-40) cc_final: 0.7540 (m-40) REVERT: F 74 GLU cc_start: 0.8275 (tm-30) cc_final: 0.7811 (tm-30) REVERT: F 84 MET cc_start: 0.8839 (mmm) cc_final: 0.8440 (tpt) REVERT: F 88 TYR cc_start: 0.8630 (m-80) cc_final: 0.8079 (m-10) REVERT: G 56 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8090 (tm-30) REVERT: G 90 ASP cc_start: 0.7756 (t70) cc_final: 0.7119 (t0) REVERT: G 92 GLU cc_start: 0.8332 (mp0) cc_final: 0.7935 (pm20) outliers start: 12 outliers final: 9 residues processed: 89 average time/residue: 0.2942 time to fit residues: 36.4772 Evaluate side-chains 88 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.957 ------------------------------------------------------------------------------- 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 100 VAL 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 H residue 101 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 78 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.096208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.062754 restraints weight = 136343.697| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 4.33 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 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 = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 93 | |-----------------------------------------------------------------------------| r_final: 0.3197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13879 Z= 0.238 Angle : 0.571 8.090 19874 Z= 0.336 Chirality : 0.035 0.126 2332 Planarity : 0.004 0.037 1680 Dihedral : 28.173 177.356 4019 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.54 % Allowed : 9.03 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.65 (0.24), residues: 1116 helix: 3.72 (0.16), residues: 885 sheet: None (None), residues: 0 loop : 0.23 (0.37), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP K 207 HIS 0.005 0.001 HIS B 75 PHE 0.008 0.001 PHE G 25 TYR 0.026 0.002 TYR D 121 ARG 0.011 0.001 ARG D 99 Details of bonding type rmsd hydrogen bonds : bond 0.04386 ( 1023) hydrogen bonds : angle 2.85246 ( 2707) covalent geometry : bond 0.00547 (13863) covalent geometry : angle 0.57113 (19874) Misc. bond : bond 0.00025 ( 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 98 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ILE cc_start: 0.8761 (mt) cc_final: 0.8479 (mt) REVERT: B 84 MET cc_start: 0.8930 (tpp) cc_final: 0.8385 (mmm) REVERT: E 56 LYS cc_start: 0.9051 (tttt) cc_final: 0.8636 (ttmt) REVERT: F 25 ASN cc_start: 0.8490 (m-40) cc_final: 0.7868 (m-40) REVERT: F 88 TYR cc_start: 0.8592 (m-10) cc_final: 0.8140 (m-80) REVERT: G 15 LYS cc_start: 0.8833 (mptt) cc_final: 0.7844 (mtpp) REVERT: G 56 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8227 (tm-30) REVERT: G 90 ASP cc_start: 0.7830 (t70) cc_final: 0.6989 (t70) REVERT: G 92 GLU cc_start: 0.8454 (mp0) cc_final: 0.7893 (pm20) outliers start: 16 outliers final: 13 residues processed: 92 average time/residue: 0.2679 time to fit residues: 35.2591 Evaluate side-chains 90 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 D residue 85 LYS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 46 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 55 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 36 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.097322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.063876 restraints weight = 135339.572| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 4.31 r_work (final): 0.3255 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| r_final: 0.3257 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13879 Z= 0.187 Angle : 0.533 6.933 19874 Z= 0.318 Chirality : 0.033 0.130 2332 Planarity : 0.004 0.035 1680 Dihedral : 28.037 178.138 4019 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.90 % Allowed : 10.62 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.83 (0.24), residues: 1116 helix: 3.88 (0.16), residues: 885 sheet: None (None), residues: 0 loop : 0.16 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP K 207 HIS 0.004 0.001 HIS B 75 PHE 0.010 0.001 PHE A 67 TYR 0.023 0.001 TYR D 121 ARG 0.008 0.000 ARG D 99 Details of bonding type rmsd hydrogen bonds : bond 0.03727 ( 1023) hydrogen bonds : angle 2.61382 ( 2707) covalent geometry : bond 0.00421 (13863) covalent geometry : angle 0.53325 (19874) Misc. bond : bond 0.00018 ( 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 92 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ILE cc_start: 0.8684 (mt) cc_final: 0.8414 (mt) REVERT: A 52 ARG cc_start: 0.8255 (mtp180) cc_final: 0.7974 (ttt-90) REVERT: B 84 MET cc_start: 0.8918 (tpp) cc_final: 0.7984 (mmm) REVERT: E 45 THR cc_start: 0.9108 (p) cc_final: 0.8888 (t) REVERT: E 56 LYS cc_start: 0.9019 (tttt) cc_final: 0.8508 (ttmt) REVERT: E 90 MET cc_start: 0.8132 (tpp) cc_final: 0.7892 (mmm) REVERT: F 25 ASN cc_start: 0.8428 (m-40) cc_final: 0.7758 (m-40) REVERT: F 84 MET cc_start: 0.8834 (mmm) cc_final: 0.8393 (tpt) REVERT: F 88 TYR cc_start: 0.8621 (m-10) cc_final: 0.8147 (m-10) REVERT: G 56 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8170 (tm-30) REVERT: G 90 ASP cc_start: 0.7792 (t70) cc_final: 0.7192 (t0) REVERT: G 92 GLU cc_start: 0.8395 (mp0) cc_final: 0.7871 (pm20) REVERT: H 71 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8437 (tm-30) REVERT: H 105 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8090 (mm-30) outliers start: 12 outliers final: 12 residues processed: 87 average time/residue: 0.2781 time to fit residues: 34.8576 Evaluate side-chains 91 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU 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 100 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain F residue 30 THR 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 63 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 12 optimal weight: 0.7980 chunk 76 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 107 optimal weight: 30.0000 chunk 27 optimal weight: 4.9990 chunk 45 optimal weight: 0.3980 chunk 85 optimal weight: 10.0000 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.098557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.065400 restraints weight = 173503.594| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 4.66 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3236 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 93 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 93 | |-----------------------------------------------------------------------------| r_final: 0.3236 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13879 Z= 0.192 Angle : 0.539 7.040 19874 Z= 0.320 Chirality : 0.034 0.171 2332 Planarity : 0.004 0.035 1680 Dihedral : 28.042 177.061 4019 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.90 % Allowed : 11.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.83 (0.24), residues: 1116 helix: 3.92 (0.16), residues: 882 sheet: None (None), residues: 0 loop : 0.02 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP K 207 HIS 0.004 0.001 HIS B 75 PHE 0.009 0.001 PHE A 67 TYR 0.026 0.001 TYR D 121 ARG 0.010 0.000 ARG D 99 Details of bonding type rmsd hydrogen bonds : bond 0.03783 ( 1023) hydrogen bonds : angle 2.62754 ( 2707) covalent geometry : bond 0.00434 (13863) covalent geometry : angle 0.53915 (19874) Misc. bond : bond 0.00018 ( 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 92 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8268 (mtp180) cc_final: 0.7970 (ttt-90) REVERT: B 84 MET cc_start: 0.8971 (tpp) cc_final: 0.8434 (mmm) REVERT: C 104 GLN cc_start: 0.8730 (mp10) cc_final: 0.8432 (pm20) REVERT: E 45 THR cc_start: 0.9153 (p) cc_final: 0.8925 (t) REVERT: E 56 LYS cc_start: 0.9038 (tttt) cc_final: 0.8602 (ttpt) REVERT: E 90 MET cc_start: 0.8126 (tpp) cc_final: 0.7897 (mmm) REVERT: F 25 ASN cc_start: 0.8423 (m-40) cc_final: 0.7762 (m-40) REVERT: F 84 MET cc_start: 0.8840 (mmm) cc_final: 0.8414 (tpt) REVERT: F 88 TYR cc_start: 0.8536 (m-10) cc_final: 0.8140 (m-10) REVERT: G 56 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8191 (tm-30) REVERT: G 90 ASP cc_start: 0.7857 (t70) cc_final: 0.7257 (t0) REVERT: G 92 GLU cc_start: 0.8369 (mp0) cc_final: 0.7863 (pm20) REVERT: H 71 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8490 (tm-30) REVERT: H 105 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8072 (mm-30) outliers start: 12 outliers final: 12 residues processed: 87 average time/residue: 0.2589 time to fit residues: 32.9831 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 : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU 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 100 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain F residue 30 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 89 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 19 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.097726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.064485 restraints weight = 182202.175| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 4.80 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3256 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 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 = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 93 | |-----------------------------------------------------------------------------| r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13879 Z= 0.171 Angle : 0.522 6.507 19874 Z= 0.312 Chirality : 0.033 0.139 2332 Planarity : 0.004 0.038 1680 Dihedral : 27.949 177.388 4019 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.74 % Allowed : 12.04 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.92 (0.24), residues: 1116 helix: 4.00 (0.16), residues: 882 sheet: None (None), residues: 0 loop : -0.01 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP K 207 HIS 0.004 0.001 HIS B 75 PHE 0.009 0.001 PHE A 67 TYR 0.024 0.001 TYR D 121 ARG 0.009 0.000 ARG D 99 Details of bonding type rmsd hydrogen bonds : bond 0.03553 ( 1023) hydrogen bonds : angle 2.53266 ( 2707) covalent geometry : bond 0.00382 (13863) covalent geometry : angle 0.52228 (19874) Misc. bond : bond 0.00016 ( 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 91 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8240 (mtp180) cc_final: 0.7953 (ttt-90) REVERT: B 84 MET cc_start: 0.8949 (tpp) cc_final: 0.8360 (mmm) REVERT: C 104 GLN cc_start: 0.8815 (mp10) cc_final: 0.8571 (pm20) REVERT: E 45 THR cc_start: 0.9108 (p) cc_final: 0.8867 (t) REVERT: E 56 LYS cc_start: 0.9012 (tttt) cc_final: 0.8575 (ttpt) REVERT: E 90 MET cc_start: 0.8073 (tpp) cc_final: 0.7818 (mmm) REVERT: F 25 ASN cc_start: 0.8400 (m-40) cc_final: 0.7729 (m-40) REVERT: F 84 MET cc_start: 0.8798 (mmm) cc_final: 0.8350 (tpt) REVERT: F 88 TYR cc_start: 0.8536 (m-10) cc_final: 0.8140 (m-10) REVERT: G 56 GLU cc_start: 0.8541 (tm-30) cc_final: 0.8152 (tm-30) REVERT: G 90 ASP cc_start: 0.7826 (t70) cc_final: 0.7246 (t0) REVERT: G 92 GLU cc_start: 0.8381 (mp0) cc_final: 0.7859 (pm20) REVERT: H 59 MET cc_start: 0.8678 (tpp) cc_final: 0.8471 (tpp) REVERT: H 71 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8429 (tm-30) outliers start: 11 outliers final: 10 residues processed: 88 average time/residue: 0.2606 time to fit residues: 33.3130 Evaluate side-chains 85 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain F residue 30 THR 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 41 optimal weight: 2.9990 chunk 101 optimal weight: 50.0000 chunk 63 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 77 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 106 optimal weight: 8.9990 chunk 38 optimal weight: 0.0870 overall best weight: 1.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.100465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.068437 restraints weight = 190865.132| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 4.80 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3288 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 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 = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 93 | |-----------------------------------------------------------------------------| r_final: 0.3288 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13879 Z= 0.152 Angle : 0.515 5.948 19874 Z= 0.309 Chirality : 0.032 0.149 2332 Planarity : 0.003 0.039 1680 Dihedral : 27.873 177.102 4019 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.58 % Allowed : 12.52 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.04 (0.24), residues: 1116 helix: 4.09 (0.16), residues: 882 sheet: None (None), residues: 0 loop : -0.01 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP K 207 HIS 0.003 0.001 HIS B 75 PHE 0.011 0.001 PHE E 104 TYR 0.024 0.001 TYR D 121 ARG 0.010 0.000 ARG D 99 Details of bonding type rmsd hydrogen bonds : bond 0.03346 ( 1023) hydrogen bonds : angle 2.45202 ( 2707) covalent geometry : bond 0.00333 (13863) covalent geometry : angle 0.51520 (19874) Misc. bond : bond 0.00012 ( 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 91 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8258 (mtp180) cc_final: 0.7974 (ttt-90) REVERT: B 44 LYS cc_start: 0.8528 (mtpt) cc_final: 0.8113 (mttm) REVERT: B 84 MET cc_start: 0.8968 (tpp) cc_final: 0.8424 (mmm) REVERT: C 104 GLN cc_start: 0.8818 (mp10) cc_final: 0.8600 (pm20) REVERT: E 45 THR cc_start: 0.9099 (p) cc_final: 0.8851 (t) REVERT: E 56 LYS cc_start: 0.9022 (tttt) cc_final: 0.8588 (ttpt) REVERT: F 25 ASN cc_start: 0.8367 (m-40) cc_final: 0.7737 (m-40) REVERT: F 84 MET cc_start: 0.8804 (mmm) cc_final: 0.8315 (tpt) REVERT: F 88 TYR cc_start: 0.8450 (m-10) cc_final: 0.8127 (m-10) REVERT: G 56 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8114 (tm-30) REVERT: G 90 ASP cc_start: 0.7851 (t70) cc_final: 0.7241 (t0) REVERT: G 92 GLU cc_start: 0.8283 (mp0) cc_final: 0.7827 (pm20) REVERT: H 71 GLU cc_start: 0.8713 (tm-30) cc_final: 0.8437 (tm-30) outliers start: 10 outliers final: 9 residues processed: 87 average time/residue: 0.2605 time to fit residues: 33.1593 Evaluate side-chains 85 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 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 100 VAL Chi-restraints excluded: chain D residue 85 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 8 optimal weight: 0.2980 chunk 6 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 75 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.098203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.064763 restraints weight = 212959.997| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 5.14 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3270 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 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 = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 93 | |-----------------------------------------------------------------------------| r_final: 0.3270 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13879 Z= 0.169 Angle : 0.529 7.516 19874 Z= 0.314 Chirality : 0.033 0.144 2332 Planarity : 0.004 0.039 1680 Dihedral : 27.892 176.693 4019 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.43 % Allowed : 13.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.02 (0.24), residues: 1116 helix: 4.07 (0.16), residues: 882 sheet: None (None), residues: 0 loop : -0.01 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP K 207 HIS 0.004 0.001 HIS B 75 PHE 0.008 0.001 PHE A 67 TYR 0.026 0.001 TYR D 121 ARG 0.010 0.000 ARG D 99 Details of bonding type rmsd hydrogen bonds : bond 0.03529 ( 1023) hydrogen bonds : angle 2.51662 ( 2707) covalent geometry : bond 0.00376 (13863) covalent geometry : angle 0.52905 (19874) Misc. bond : bond 0.00014 ( 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 88 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8189 (mtp180) cc_final: 0.7878 (ttt-90) REVERT: B 84 MET cc_start: 0.8958 (tpp) cc_final: 0.8388 (mmm) REVERT: C 104 GLN cc_start: 0.8825 (mp10) cc_final: 0.8500 (pm20) REVERT: E 45 THR cc_start: 0.9062 (p) cc_final: 0.8839 (t) REVERT: E 56 LYS cc_start: 0.9024 (tttt) cc_final: 0.8562 (ttmt) REVERT: F 25 ASN cc_start: 0.8258 (m-40) cc_final: 0.7589 (m-40) REVERT: F 84 MET cc_start: 0.8814 (mmm) cc_final: 0.8382 (tpt) REVERT: F 88 TYR cc_start: 0.8485 (m-10) cc_final: 0.8160 (m-10) REVERT: G 56 GLU cc_start: 0.8528 (tm-30) cc_final: 0.8133 (tm-30) REVERT: G 90 ASP cc_start: 0.7857 (t70) cc_final: 0.7303 (t0) REVERT: G 92 GLU cc_start: 0.8307 (mp0) cc_final: 0.7790 (pm20) REVERT: H 71 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8414 (tm-30) outliers start: 9 outliers final: 9 residues processed: 85 average time/residue: 0.2572 time to fit residues: 31.8098 Evaluate side-chains 85 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 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 100 VAL Chi-restraints excluded: chain D residue 85 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 104 optimal weight: 10.0000 chunk 63 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 102 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 116 optimal weight: 20.0000 chunk 4 optimal weight: 0.8980 chunk 114 optimal weight: 40.0000 chunk 71 optimal weight: 0.8980 chunk 8 optimal weight: 0.0970 chunk 34 optimal weight: 0.8980 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.100016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.066633 restraints weight = 222167.799| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 5.27 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3307 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 93 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 93 | |-----------------------------------------------------------------------------| r_final: 0.3307 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13879 Z= 0.140 Angle : 0.513 7.477 19874 Z= 0.307 Chirality : 0.032 0.142 2332 Planarity : 0.003 0.041 1680 Dihedral : 27.764 177.020 4019 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.27 % Allowed : 13.95 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.19 (0.24), residues: 1116 helix: 4.19 (0.15), residues: 882 sheet: None (None), residues: 0 loop : 0.07 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP K 207 HIS 0.002 0.001 HIS F 75 PHE 0.010 0.001 PHE E 67 TYR 0.023 0.001 TYR D 121 ARG 0.010 0.000 ARG D 99 Details of bonding type rmsd hydrogen bonds : bond 0.03151 ( 1023) hydrogen bonds : angle 2.35420 ( 2707) covalent geometry : bond 0.00297 (13863) covalent geometry : angle 0.51325 (19874) Misc. bond : bond 0.00011 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6761.89 seconds wall clock time: 116 minutes 54.78 seconds (7014.78 seconds total)