Starting phenix.real_space_refine on Wed Jul 30 21:53:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ots_17183/07_2025/8ots_17183_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ots_17183/07_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_17183/07_2025/8ots_17183.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ots_17183/07_2025/8ots_17183.map" model { file = "/net/cci-nas-00/data/ceres_data/8ots_17183/07_2025/8ots_17183_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ots_17183/07_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 10.36, per 1000 atoms: 0.79 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: 4.51 Conformation dependent library (CDL) restraints added in 2.3 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: 11.40 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: 9.09 Time building geometry restraints manager: 4.66 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: 152.660 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: 40.310 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 43.780 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:3.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 241.090 ------------------------------------------------------------------------------- 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 : 1.600 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: 0.6410 time to fit residues: 129.8923 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 : 1.026 ------------------------------------------------------------------------------- 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 = 56)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.068060 restraints weight = 89205.437| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 3.61 r_work: 0.3159 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3103 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 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 = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 93 | |-----------------------------------------------------------------------------| r_final: 0.3103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 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 : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ILE cc_start: 0.8857 (mt) cc_final: 0.8499 (mt) REVERT: C 76 THR cc_start: 0.9195 (p) cc_final: 0.8920 (t) REVERT: E 56 LYS cc_start: 0.9138 (tttt) cc_final: 0.8766 (ttmt) REVERT: F 74 GLU cc_start: 0.8654 (tm-30) cc_final: 0.8398 (tm-30) REVERT: F 84 MET cc_start: 0.8821 (mmm) cc_final: 0.8512 (mmp) REVERT: G 56 GLU cc_start: 0.8797 (tm-30) cc_final: 0.8539 (tm-30) REVERT: G 73 ASN cc_start: 0.8807 (m-40) cc_final: 0.8606 (t0) REVERT: G 90 ASP cc_start: 0.8089 (t70) cc_final: 0.7830 (t0) outliers start: 17 outliers final: 9 residues processed: 109 average time/residue: 0.3575 time to fit residues: 51.5714 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 : 1.080 ------------------------------------------------------------------------------- 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: 1.9990 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: 2.9990 chunk 2 optimal weight: 0.4980 chunk 54 optimal weight: 7.9990 chunk 74 optimal weight: 9.9990 chunk 111 optimal weight: 20.0000 chunk 114 optimal weight: 30.0000 overall best weight: 2.6988 ------------------------------------------------------------------------------- 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 = 0.3971 r_free = 0.3971 target = 0.097435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.065226 restraints weight = 87238.422| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 3.48 r_work: 0.3095 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3088 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 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 = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 93 | |-----------------------------------------------------------------------------| r_final: 0.3087 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.3006 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= 0.206 Angle : 0.555 7.027 19874 Z= 0.329 Chirality : 0.035 0.151 2332 Planarity : 0.004 0.032 1680 Dihedral : 28.130 176.205 4019 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 2.85 % Allowed : 8.87 % Favored : 88.27 % 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: 4.62 (0.23), residues: 1116 helix: 3.64 (0.16), residues: 882 sheet: None (None), residues: 0 loop : 0.54 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP K 207 HIS 0.007 0.001 HIS F 75 PHE 0.009 0.001 PHE E 78 TYR 0.022 0.002 TYR D 121 ARG 0.009 0.001 ARG D 99 Details of bonding type rmsd hydrogen bonds : bond 0.04150 ( 1023) hydrogen bonds : angle 2.80414 ( 2707) covalent geometry : bond 0.00468 (13863) covalent geometry : angle 0.55499 (19874) Misc. bond : bond 0.00077 ( 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 104 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.9198 (tpp) cc_final: 0.8505 (mmm) REVERT: C 76 THR cc_start: 0.9239 (p) cc_final: 0.8980 (t) REVERT: E 56 LYS cc_start: 0.9157 (tttt) cc_final: 0.8771 (ttmt) REVERT: F 25 ASN cc_start: 0.8818 (m-40) cc_final: 0.8310 (m110) REVERT: G 56 GLU cc_start: 0.8916 (tm-30) cc_final: 0.8617 (tm-30) REVERT: G 90 ASP cc_start: 0.8094 (t70) cc_final: 0.7654 (t0) REVERT: H 71 GLU cc_start: 0.9010 (tm-30) cc_final: 0.8808 (tm-30) outliers start: 18 outliers final: 13 residues processed: 99 average time/residue: 0.3106 time to fit residues: 42.4945 Evaluate side-chains 85 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.984 ------------------------------------------------------------------------------- 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: 0.8980 chunk 44 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 chunk 86 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 115 optimal weight: 40.0000 chunk 24 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 = 0.4014 r_free = 0.4014 target = 0.099604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.068032 restraints weight = 118290.108| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 3.93 r_work: 0.3110 rms_B_bonded: 4.90 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 | |-----------------------------------------------------------------------------| r_final: 0.3110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3225 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= 0.162 Angle : 0.516 5.843 19874 Z= 0.311 Chirality : 0.033 0.124 2332 Planarity : 0.004 0.042 1680 Dihedral : 27.947 178.706 4019 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.22 % Allowed : 9.35 % 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: 4.96 (0.24), residues: 1116 helix: 3.90 (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 0.004 0.001 HIS B 75 PHE 0.010 0.001 PHE E 67 TYR 0.023 0.001 TYR D 121 ARG 0.009 0.000 ARG D 99 Details of bonding type rmsd hydrogen bonds : bond 0.03566 ( 1023) hydrogen bonds : angle 2.54149 ( 2707) covalent geometry : bond 0.00356 (13863) covalent geometry : angle 0.51624 (19874) Misc. bond : bond 0.00026 ( 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: 14 poor density : 80 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ILE cc_start: 0.8936 (mt) cc_final: 0.8600 (mt) REVERT: A 52 ARG cc_start: 0.8436 (mtp180) cc_final: 0.8035 (ttt180) REVERT: A 58 THR cc_start: 0.9231 (p) cc_final: 0.8953 (t) REVERT: B 84 MET cc_start: 0.9187 (tpp) cc_final: 0.8534 (mmm) REVERT: C 76 THR cc_start: 0.9262 (p) cc_final: 0.8997 (t) REVERT: E 45 THR cc_start: 0.9083 (p) cc_final: 0.8812 (t) REVERT: E 56 LYS cc_start: 0.9163 (tttt) cc_final: 0.8773 (ttmt) REVERT: F 25 ASN cc_start: 0.8668 (m-40) cc_final: 0.8114 (m-40) REVERT: F 84 MET cc_start: 0.9004 (mmm) cc_final: 0.8675 (tpt) REVERT: F 88 TYR cc_start: 0.9016 (m-80) cc_final: 0.8517 (m-10) REVERT: G 56 GLU cc_start: 0.8926 (tm-30) cc_final: 0.8604 (tm-30) REVERT: G 90 ASP cc_start: 0.7979 (t70) cc_final: 0.7531 (t0) REVERT: G 92 GLU cc_start: 0.8548 (mp0) cc_final: 0.8158 (pm20) REVERT: H 71 GLU cc_start: 0.9040 (tm-30) cc_final: 0.8804 (tm-30) outliers start: 14 outliers final: 12 residues processed: 89 average time/residue: 0.2824 time to fit residues: 35.7413 Evaluate side-chains 88 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 1.023 ------------------------------------------------------------------------------- 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 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 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 12 optimal weight: 0.9980 chunk 104 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 82 optimal weight: 10.0000 chunk 113 optimal weight: 50.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 = 0.3945 r_free = 0.3945 target = 0.096496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.063055 restraints weight = 134917.487| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 4.31 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 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 = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 93 | |-----------------------------------------------------------------------------| r_final: 0.3206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13879 Z= 0.236 Angle : 0.561 7.369 19874 Z= 0.331 Chirality : 0.035 0.133 2332 Planarity : 0.004 0.035 1680 Dihedral : 28.120 178.185 4019 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.54 % Allowed : 9.35 % Favored : 88.11 % 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: 4.74 (0.24), residues: 1116 helix: 3.78 (0.16), residues: 885 sheet: None (None), residues: 0 loop : 0.28 (0.38), 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 0.025 0.002 TYR D 121 ARG 0.009 0.000 ARG D 99 Details of bonding type rmsd hydrogen bonds : bond 0.04164 ( 1023) hydrogen bonds : angle 2.77821 ( 2707) covalent geometry : bond 0.00539 (13863) covalent geometry : angle 0.56087 (19874) Misc. bond : bond 0.00022 ( 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 : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ILE cc_start: 0.8749 (mt) cc_final: 0.8469 (mt) REVERT: B 84 MET cc_start: 0.8949 (tpp) cc_final: 0.8418 (mmm) REVERT: E 56 LYS cc_start: 0.9054 (tttt) cc_final: 0.8580 (ttmt) REVERT: F 25 ASN cc_start: 0.8475 (m-40) cc_final: 0.7899 (m-40) REVERT: F 88 TYR cc_start: 0.8591 (m-10) cc_final: 0.8134 (m-80) REVERT: G 15 LYS cc_start: 0.8825 (mptt) cc_final: 0.7839 (mtpp) REVERT: G 56 GLU cc_start: 0.8579 (tm-30) cc_final: 0.8226 (tm-30) REVERT: G 90 ASP cc_start: 0.7835 (t70) cc_final: 0.7046 (t0) REVERT: G 92 GLU cc_start: 0.8444 (mp0) cc_final: 0.7835 (pm20) REVERT: H 71 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8378 (tm-30) outliers start: 16 outliers final: 15 residues processed: 92 average time/residue: 0.2981 time to fit residues: 38.8503 Evaluate side-chains 90 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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 100 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 122 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 55 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 29 optimal weight: 9.9990 chunk 24 optimal weight: 0.8980 chunk 93 optimal weight: 6.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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 = 0.099686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.068148 restraints weight = 123521.113| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 4.03 r_work: 0.3109 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3103 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 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 = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 93 | |-----------------------------------------------------------------------------| r_final: 0.3103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.3659 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= 0.150 Angle : 0.512 5.680 19874 Z= 0.308 Chirality : 0.032 0.131 2332 Planarity : 0.004 0.045 1680 Dihedral : 27.918 178.709 4019 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.06 % Allowed : 10.14 % Favored : 87.80 % 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: 5.05 (0.24), residues: 1116 helix: 4.03 (0.16), residues: 885 sheet: None (None), residues: 0 loop : 0.23 (0.38), residues: 231 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 A 67 TYR 0.022 0.001 TYR D 121 ARG 0.009 0.000 ARG D 99 Details of bonding type rmsd hydrogen bonds : bond 0.03384 ( 1023) hydrogen bonds : angle 2.42920 ( 2707) covalent geometry : bond 0.00325 (13863) covalent geometry : angle 0.51177 (19874) Misc. bond : bond 0.00015 ( 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: 13 poor density : 82 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ILE cc_start: 0.8965 (mt) cc_final: 0.8593 (mt) REVERT: A 52 ARG cc_start: 0.8444 (mtp180) cc_final: 0.8143 (ttt-90) REVERT: B 84 MET cc_start: 0.9175 (tpp) cc_final: 0.8515 (mmm) REVERT: C 56 GLU cc_start: 0.8337 (tt0) cc_final: 0.8116 (tm-30) REVERT: C 104 GLN cc_start: 0.8924 (mp10) cc_final: 0.8629 (pm20) REVERT: E 45 THR cc_start: 0.9106 (p) cc_final: 0.8824 (t) REVERT: E 56 LYS cc_start: 0.9153 (tttt) cc_final: 0.8800 (ttpt) REVERT: F 25 ASN cc_start: 0.8662 (m-40) cc_final: 0.8116 (m-40) REVERT: F 84 MET cc_start: 0.8984 (mmm) cc_final: 0.8595 (tpt) REVERT: F 88 TYR cc_start: 0.8930 (m-10) cc_final: 0.8591 (m-10) REVERT: G 56 GLU cc_start: 0.8937 (tm-30) cc_final: 0.8614 (tm-30) REVERT: G 90 ASP cc_start: 0.7987 (t70) cc_final: 0.7538 (t0) REVERT: G 92 GLU cc_start: 0.8582 (mp0) cc_final: 0.8099 (pm20) REVERT: H 71 GLU cc_start: 0.9094 (tm-30) cc_final: 0.8821 (tm-30) outliers start: 13 outliers final: 10 residues processed: 90 average time/residue: 0.2974 time to fit residues: 38.0666 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 : 1.183 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 63 optimal weight: 5.9990 chunk 36 optimal weight: 20.0000 chunk 12 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 107 optimal weight: 30.0000 chunk 27 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 = 0.3971 r_free = 0.3971 target = 0.097341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.064263 restraints weight = 175276.734| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 4.67 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3208 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 93 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 93 | |-----------------------------------------------------------------------------| r_final: 0.3208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 13879 Z= 0.258 Angle : 0.587 6.754 19874 Z= 0.343 Chirality : 0.036 0.142 2332 Planarity : 0.004 0.040 1680 Dihedral : 28.215 176.611 4019 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.22 % Allowed : 10.62 % 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 (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: 4.64 (0.24), residues: 1116 helix: 3.78 (0.16), residues: 882 sheet: None (None), residues: 0 loop : -0.04 (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 B 75 PHE 0.008 0.001 PHE G 25 TYR 0.027 0.002 TYR D 121 ARG 0.009 0.000 ARG D 99 Details of bonding type rmsd hydrogen bonds : bond 0.04433 ( 1023) hydrogen bonds : angle 2.88024 ( 2707) covalent geometry : bond 0.00594 (13863) covalent geometry : angle 0.58689 (19874) Misc. bond : bond 0.00023 ( 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 89 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8312 (mtp180) cc_final: 0.8009 (ttt-90) REVERT: E 56 LYS cc_start: 0.9056 (tttt) cc_final: 0.8616 (ttpt) REVERT: F 25 ASN cc_start: 0.8448 (m-40) cc_final: 0.7765 (m-40) REVERT: F 88 TYR cc_start: 0.8579 (m-10) cc_final: 0.8198 (m-80) REVERT: G 56 GLU cc_start: 0.8613 (tm-30) cc_final: 0.8221 (tm-30) REVERT: G 90 ASP cc_start: 0.7940 (t70) cc_final: 0.7380 (t0) REVERT: G 92 GLU cc_start: 0.8358 (mp0) cc_final: 0.7980 (pm20) REVERT: H 71 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8405 (tm-30) outliers start: 14 outliers final: 12 residues processed: 84 average time/residue: 0.2850 time to fit residues: 34.2981 Evaluate side-chains 84 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 1.083 ------------------------------------------------------------------------------- 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 100 VAL 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: 0.0470 chunk 90 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 88 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 overall best weight: 1.7884 ------------------------------------------------------------------------------- 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 = 0.3982 r_free = 0.3982 target = 0.097940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.064560 restraints weight = 177945.548| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 4.74 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3233 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 93 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 93 | |-----------------------------------------------------------------------------| r_final: 0.3233 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13879 Z= 0.166 Angle : 0.529 6.411 19874 Z= 0.316 Chirality : 0.033 0.141 2332 Planarity : 0.004 0.045 1680 Dihedral : 28.034 177.931 4019 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.74 % Allowed : 11.41 % 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 (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: 4.88 (0.24), residues: 1116 helix: 3.99 (0.16), residues: 882 sheet: None (None), residues: 0 loop : -0.13 (0.37), 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 E 67 TYR 0.024 0.001 TYR D 121 ARG 0.010 0.000 ARG D 99 Details of bonding type rmsd hydrogen bonds : bond 0.03551 ( 1023) hydrogen bonds : angle 2.53470 ( 2707) covalent geometry : bond 0.00368 (13863) covalent geometry : angle 0.52864 (19874) Misc. bond : bond 0.00019 ( 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 87 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8250 (mtp180) cc_final: 0.7958 (ttt-90) REVERT: B 84 MET cc_start: 0.8977 (tpp) cc_final: 0.8247 (mmm) REVERT: E 45 THR cc_start: 0.9162 (p) cc_final: 0.8933 (t) REVERT: E 56 LYS cc_start: 0.9032 (tttt) cc_final: 0.8602 (ttpt) REVERT: F 25 ASN cc_start: 0.8414 (m-40) cc_final: 0.7764 (m-40) REVERT: F 84 MET cc_start: 0.8784 (mmm) cc_final: 0.8329 (tpt) REVERT: F 88 TYR cc_start: 0.8528 (m-10) cc_final: 0.8152 (m-10) REVERT: G 56 GLU cc_start: 0.8565 (tm-30) cc_final: 0.8169 (tm-30) REVERT: G 90 ASP cc_start: 0.7841 (t70) cc_final: 0.7269 (t0) REVERT: G 92 GLU cc_start: 0.8258 (mp0) cc_final: 0.7798 (pm20) REVERT: H 71 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8370 (tm-30) outliers start: 11 outliers final: 10 residues processed: 83 average time/residue: 0.2725 time to fit residues: 32.8721 Evaluate side-chains 83 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 1.100 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 41 optimal weight: 2.9990 chunk 101 optimal weight: 40.0000 chunk 63 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 77 optimal weight: 7.9990 chunk 48 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 106 optimal weight: 20.0000 chunk 38 optimal weight: 0.0870 overall best weight: 1.7762 ------------------------------------------------------------------------------- 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 = 0.3984 r_free = 0.3984 target = 0.098149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.064641 restraints weight = 196829.628| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 4.97 r_work (final): 0.3262 ------------------------------------------------------------------------------- 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: 0.8358 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13879 Z= 0.167 Angle : 0.529 5.724 19874 Z= 0.316 Chirality : 0.033 0.156 2332 Planarity : 0.004 0.042 1680 Dihedral : 27.977 177.222 4019 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.43 % Allowed : 12.04 % Favored : 86.53 % 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: 4.93 (0.24), residues: 1116 helix: 4.03 (0.16), residues: 882 sheet: None (None), residues: 0 loop : -0.15 (0.37), 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 0.009 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 0.03511 ( 1023) hydrogen bonds : angle 2.51297 ( 2707) covalent geometry : bond 0.00371 (13863) covalent geometry : angle 0.52854 (19874) Misc. bond : bond 0.00016 ( 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 87 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8253 (mtp180) cc_final: 0.7970 (ttt-90) REVERT: B 84 MET cc_start: 0.8983 (tpp) cc_final: 0.8238 (mmm) REVERT: C 104 GLN cc_start: 0.8768 (mp10) cc_final: 0.8448 (pm20) REVERT: E 45 THR cc_start: 0.9135 (p) cc_final: 0.8900 (t) REVERT: E 56 LYS cc_start: 0.9023 (tttt) cc_final: 0.8570 (ttpt) REVERT: F 25 ASN cc_start: 0.8418 (m-40) cc_final: 0.7752 (m-40) REVERT: F 84 MET cc_start: 0.8784 (mmm) cc_final: 0.8333 (tpt) REVERT: F 88 TYR cc_start: 0.8489 (m-10) cc_final: 0.8120 (m-10) REVERT: G 56 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8146 (tm-30) REVERT: G 90 ASP cc_start: 0.7888 (t70) cc_final: 0.7329 (t0) REVERT: G 92 GLU cc_start: 0.8287 (mp0) cc_final: 0.7764 (pm20) REVERT: H 71 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8378 (tm-30) outliers start: 9 outliers final: 9 residues processed: 85 average time/residue: 0.2745 time to fit residues: 33.7175 Evaluate side-chains 83 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 1.018 ------------------------------------------------------------------------------- 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 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: 0.0570 chunk 6 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 95 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 100 optimal weight: 50.0000 chunk 0 optimal weight: 20.0000 chunk 107 optimal weight: 5.9990 chunk 75 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 overall best weight: 2.6106 ------------------------------------------------------------------------------- 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 = 0.3962 r_free = 0.3962 target = 0.097047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.063345 restraints weight = 222696.209| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 5.19 r_work (final): 0.3204 ------------------------------------------------------------------------------- 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) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 93 | |-----------------------------------------------------------------------------| r_final: 0.3203 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13879 Z= 0.201 Angle : 0.553 6.203 19874 Z= 0.327 Chirality : 0.034 0.143 2332 Planarity : 0.004 0.039 1680 Dihedral : 28.063 176.838 4019 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.58 % Allowed : 12.04 % Favored : 86.37 % 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: 4.80 (0.24), residues: 1116 helix: 3.95 (0.16), residues: 882 sheet: None (None), residues: 0 loop : -0.22 (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 E 104 TYR 0.026 0.001 TYR D 121 ARG 0.010 0.000 ARG D 99 Details of bonding type rmsd hydrogen bonds : bond 0.03874 ( 1023) hydrogen bonds : angle 2.66816 ( 2707) covalent geometry : bond 0.00456 (13863) covalent geometry : angle 0.55256 (19874) Misc. bond : bond 0.00017 ( 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 86 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8325 (mtp180) cc_final: 0.8032 (ttt-90) REVERT: B 84 MET cc_start: 0.8981 (tpp) cc_final: 0.8155 (mmm) REVERT: E 56 LYS cc_start: 0.9048 (tttt) cc_final: 0.8641 (ttpt) REVERT: F 25 ASN cc_start: 0.8306 (m-40) cc_final: 0.7655 (m-40) REVERT: F 84 MET cc_start: 0.8740 (mmm) cc_final: 0.8348 (tpt) REVERT: F 88 TYR cc_start: 0.8494 (m-10) cc_final: 0.8197 (m-10) REVERT: G 56 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8181 (tm-30) REVERT: G 90 ASP cc_start: 0.7944 (t70) cc_final: 0.7452 (t0) REVERT: G 92 GLU cc_start: 0.8293 (mp0) cc_final: 0.7818 (pm20) REVERT: H 71 GLU cc_start: 0.8732 (tm-30) cc_final: 0.8373 (tm-30) outliers start: 10 outliers final: 9 residues processed: 84 average time/residue: 0.2647 time to fit residues: 32.1166 Evaluate side-chains 82 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 1.090 ------------------------------------------------------------------------------- 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 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: 9.9990 chunk 63 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 102 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 116 optimal weight: 20.0000 chunk 4 optimal weight: 0.9990 chunk 114 optimal weight: 40.0000 chunk 71 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.4006 r_free = 0.4006 target = 0.099459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.065877 restraints weight = 229335.258| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 5.31 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 | |-----------------------------------------------------------------------------| r_final: 0.3293 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.4330 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= 0.143 Angle : 0.517 6.268 19874 Z= 0.311 Chirality : 0.032 0.150 2332 Planarity : 0.004 0.045 1680 Dihedral : 27.857 177.582 4019 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.27 % Allowed : 13.15 % Favored : 85.58 % 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: 5.05 (0.24), residues: 1116 helix: 4.14 (0.16), residues: 882 sheet: None (None), residues: 0 loop : -0.19 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP K 207 HIS 0.002 0.001 HIS B 75 PHE 0.009 0.001 PHE E 67 TYR 0.022 0.001 TYR D 121 ARG 0.011 0.000 ARG D 99 Details of bonding type rmsd hydrogen bonds : bond 0.03213 ( 1023) hydrogen bonds : angle 2.38085 ( 2707) covalent geometry : bond 0.00306 (13863) covalent geometry : angle 0.51718 (19874) Misc. bond : bond 0.00012 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8325.26 seconds wall clock time: 146 minutes 14.22 seconds (8774.22 seconds total)