Starting phenix.real_space_refine on Sun Nov 17 04:00:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ots_17183/11_2024/8ots_17183_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ots_17183/11_2024/8ots_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ots_17183/11_2024/8ots_17183.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ots_17183/11_2024/8ots_17183.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ots_17183/11_2024/8ots_17183_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ots_17183/11_2024/8ots_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 8.21, per 1000 atoms: 0.62 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: 3.57 Conformation dependent library (CDL) restraints added in 1.4 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: 6.04 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: 5.40 Time building geometry restraints manager: 4.06 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: 1.020 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: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 36.740 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.060 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.690 ------------------------------------------------------------------------------- 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 : 0.009 0.051 13863 Z= 0.556 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 *********************** 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 : 1.015 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: 0.4221 time to fit residues: 84.4922 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 : 1.013 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 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 13863 Z= 0.199 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 *********************** 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 : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ILE cc_start: 0.8893 (mt) cc_final: 0.8570 (mt) REVERT: C 76 THR cc_start: 0.9242 (p) cc_final: 0.8993 (t) REVERT: E 56 LYS cc_start: 0.9216 (tttt) cc_final: 0.8903 (ttmt) REVERT: F 74 GLU cc_start: 0.8664 (tm-30) cc_final: 0.8393 (tm-30) REVERT: F 84 MET cc_start: 0.8652 (mmm) cc_final: 0.8333 (mmp) REVERT: G 56 GLU cc_start: 0.8807 (tm-30) cc_final: 0.8572 (tm-30) outliers start: 17 outliers final: 9 residues processed: 109 average time/residue: 0.3767 time to fit residues: 55.0705 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 : 1.059 ------------------------------------------------------------------------------- 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 59 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 chunk 106 optimal weight: 40.0000 chunk 114 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 chunk 105 optimal weight: 7.9990 chunk 36 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 overall best weight: 7.1588 ------------------------------------------------------------------------------- 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 G 24 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.075 13863 Z= 0.616 Angle : 0.739 9.329 19874 Z= 0.422 Chirality : 0.044 0.183 2332 Planarity : 0.005 0.040 1680 Dihedral : 28.698 176.909 4019 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 3.17 % Allowed : 8.87 % Favored : 87.96 % 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: 3.51 (0.23), residues: 1116 helix: 2.87 (0.16), residues: 883 sheet: None (None), residues: 0 loop : 0.07 (0.36), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP K 207 HIS 0.009 0.002 HIS F 75 PHE 0.015 0.002 PHE E 78 TYR 0.021 0.002 TYR D 121 ARG 0.009 0.001 ARG D 99 *********************** 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: 20 poor density : 84 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 51 ASP cc_start: 0.8389 (p0) cc_final: 0.8110 (p0) REVERT: E 56 LYS cc_start: 0.9237 (tttt) cc_final: 0.8854 (ttmt) REVERT: G 15 LYS cc_start: 0.8841 (mptt) cc_final: 0.7965 (mtpp) outliers start: 20 outliers final: 14 residues processed: 101 average time/residue: 0.3214 time to fit residues: 44.8439 Evaluate side-chains 85 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 1.037 ------------------------------------------------------------------------------- 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 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 105 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 113 optimal weight: 10.0000 chunk 101 optimal weight: 50.0000 chunk 30 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13863 Z= 0.177 Angle : 0.529 6.422 19874 Z= 0.318 Chirality : 0.033 0.132 2332 Planarity : 0.004 0.036 1680 Dihedral : 28.073 175.849 4019 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.58 % Allowed : 9.35 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.55 (0.24), residues: 1116 helix: 3.65 (0.16), residues: 885 sheet: None (None), residues: 0 loop : 0.22 (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 0.012 0.001 PHE E 67 TYR 0.014 0.001 TYR H 121 ARG 0.009 0.000 ARG D 99 *********************** 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 88 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8526 (mtp180) cc_final: 0.8212 (ttt-90) REVERT: A 58 THR cc_start: 0.9168 (p) cc_final: 0.8880 (t) REVERT: B 84 MET cc_start: 0.8813 (tpp) cc_final: 0.8171 (mmm) REVERT: E 56 LYS cc_start: 0.9207 (tttt) cc_final: 0.8895 (ttmt) REVERT: F 84 MET cc_start: 0.8780 (mmm) cc_final: 0.8545 (tpt) REVERT: F 88 TYR cc_start: 0.8829 (m-80) cc_final: 0.8396 (m-10) REVERT: G 15 LYS cc_start: 0.8816 (mptt) cc_final: 0.7922 (mtpp) REVERT: H 123 SER cc_start: 0.8804 (t) cc_final: 0.8603 (t) outliers start: 10 outliers final: 8 residues processed: 85 average time/residue: 0.2840 time to fit residues: 34.2451 Evaluate side-chains 80 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 1.062 ------------------------------------------------------------------------------- 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 D residue 85 LYS 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 64 optimal weight: 0.9980 chunk 1 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 96 optimal weight: 50.0000 chunk 78 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 101 optimal weight: 50.0000 chunk 28 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13863 Z= 0.291 Angle : 0.556 6.721 19874 Z= 0.330 Chirality : 0.035 0.126 2332 Planarity : 0.004 0.044 1680 Dihedral : 28.120 179.530 4019 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.22 % Allowed : 10.30 % 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: 4.57 (0.24), residues: 1116 helix: 3.69 (0.16), residues: 885 sheet: None (None), residues: 0 loop : 0.09 (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 0.009 0.001 PHE A 67 TYR 0.025 0.002 TYR D 121 ARG 0.008 0.000 ARG D 33 *********************** 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 88 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ILE cc_start: 0.9123 (OUTLIER) cc_final: 0.8743 (mt) REVERT: A 52 ARG cc_start: 0.8571 (mtp180) cc_final: 0.8240 (ttt-90) REVERT: B 84 MET cc_start: 0.8907 (tpp) cc_final: 0.8331 (mmm) REVERT: D 51 ASP cc_start: 0.8213 (p0) cc_final: 0.8008 (p0) REVERT: E 56 LYS cc_start: 0.9222 (tttt) cc_final: 0.8881 (ttpt) REVERT: F 84 MET cc_start: 0.8875 (mmm) cc_final: 0.8536 (tpt) REVERT: F 88 TYR cc_start: 0.8879 (m-10) cc_final: 0.8362 (m-80) outliers start: 14 outliers final: 10 residues processed: 85 average time/residue: 0.2838 time to fit residues: 35.2504 Evaluate side-chains 83 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 51 ILE 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 40.0000 chunk 22 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 113 optimal weight: 50.0000 chunk 93 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 0.4980 chunk 109 optimal weight: 7.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13863 Z= 0.169 Angle : 0.508 5.761 19874 Z= 0.307 Chirality : 0.032 0.131 2332 Planarity : 0.003 0.044 1680 Dihedral : 27.822 179.966 4019 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.58 % Allowed : 11.89 % 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: 3.97 (0.16), residues: 885 sheet: None (None), residues: 0 loop : 0.09 (0.38), residues: 231 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 A 67 TYR 0.022 0.001 TYR D 121 ARG 0.008 0.000 ARG D 99 *********************** 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 88 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8544 (mtp180) cc_final: 0.8232 (ttt-90) REVERT: C 104 GLN cc_start: 0.8905 (mp10) cc_final: 0.8646 (pm20) REVERT: E 45 THR cc_start: 0.9001 (p) cc_final: 0.8670 (t) REVERT: E 56 LYS cc_start: 0.9221 (tttt) cc_final: 0.8880 (ttpt) REVERT: F 84 MET cc_start: 0.8768 (mmm) cc_final: 0.8312 (tpt) REVERT: F 88 TYR cc_start: 0.8766 (m-10) cc_final: 0.8395 (m-10) REVERT: G 56 GLU cc_start: 0.8838 (tm-30) cc_final: 0.8590 (tm-30) outliers start: 10 outliers final: 10 residues processed: 85 average time/residue: 0.2840 time to fit residues: 34.5868 Evaluate side-chains 80 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 51 ILE 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 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 12 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 112 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13863 Z= 0.261 Angle : 0.537 5.616 19874 Z= 0.320 Chirality : 0.034 0.141 2332 Planarity : 0.004 0.040 1680 Dihedral : 27.896 178.121 4019 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % 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: 4.81 (0.24), residues: 1116 helix: 3.91 (0.16), residues: 885 sheet: None (None), residues: 0 loop : -0.07 (0.39), 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 0.008 0.001 PHE A 67 TYR 0.025 0.001 TYR D 121 ARG 0.007 0.000 ARG D 86 *********************** 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 83 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8572 (mtp180) cc_final: 0.8247 (ttt-90) REVERT: E 45 THR cc_start: 0.9052 (p) cc_final: 0.8733 (t) REVERT: E 56 LYS cc_start: 0.9224 (tttt) cc_final: 0.8884 (ttpt) REVERT: F 84 MET cc_start: 0.8828 (mmm) cc_final: 0.8578 (tpt) REVERT: F 88 TYR cc_start: 0.8831 (m-10) cc_final: 0.8389 (m-10) REVERT: G 56 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8652 (tm-30) outliers start: 10 outliers final: 10 residues processed: 80 average time/residue: 0.2871 time to fit residues: 33.1749 Evaluate side-chains 80 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 51 ILE 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 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 67 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 88 optimal weight: 8.9990 chunk 102 optimal weight: 8.9990 chunk 108 optimal weight: 40.0000 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13863 Z= 0.166 Angle : 0.507 6.075 19874 Z= 0.305 Chirality : 0.032 0.139 2332 Planarity : 0.004 0.050 1680 Dihedral : 27.669 178.242 4019 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.43 % Allowed : 13.31 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 5.06 (0.24), residues: 1116 helix: 4.12 (0.16), residues: 882 sheet: None (None), residues: 0 loop : -0.05 (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 A 113 PHE 0.009 0.001 PHE E 67 TYR 0.022 0.001 TYR D 121 ARG 0.005 0.000 ARG D 99 *********************** 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 83 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8536 (mtp180) cc_final: 0.8221 (ttt-90) REVERT: E 45 THR cc_start: 0.8983 (p) cc_final: 0.8664 (t) REVERT: E 56 LYS cc_start: 0.9228 (tttt) cc_final: 0.8894 (ttpt) REVERT: F 84 MET cc_start: 0.8774 (mmm) cc_final: 0.8318 (tpt) REVERT: F 88 TYR cc_start: 0.8695 (m-10) cc_final: 0.8440 (m-10) REVERT: G 56 GLU cc_start: 0.8881 (tm-30) cc_final: 0.8633 (tm-30) outliers start: 9 outliers final: 8 residues processed: 80 average time/residue: 0.2951 time to fit residues: 34.2267 Evaluate side-chains 76 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 36 LYS 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 101 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.9980 chunk 105 optimal weight: 20.0000 chunk 108 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 45 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 chunk 99 optimal weight: 9.9990 chunk 104 optimal weight: 8.9990 chunk 69 optimal weight: 0.9980 overall best weight: 4.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 13863 Z= 0.425 Angle : 0.617 7.251 19874 Z= 0.358 Chirality : 0.037 0.158 2332 Planarity : 0.004 0.037 1680 Dihedral : 28.058 176.607 4019 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.90 % Allowed : 13.00 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.45 (0.24), residues: 1116 helix: 3.70 (0.16), residues: 882 sheet: None (None), residues: 0 loop : -0.35 (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 B 75 PHE 0.009 0.001 PHE A 67 TYR 0.030 0.002 TYR D 121 ARG 0.006 0.001 ARG D 99 *********************** 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 82 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8604 (mtp180) cc_final: 0.8257 (ttt-90) REVERT: A 120 MET cc_start: 0.8286 (mtt) cc_final: 0.8063 (mtt) REVERT: E 56 LYS cc_start: 0.9239 (tttt) cc_final: 0.8919 (ttpt) REVERT: F 88 TYR cc_start: 0.8872 (m-10) cc_final: 0.8433 (m-80) outliers start: 12 outliers final: 11 residues processed: 79 average time/residue: 0.2686 time to fit residues: 30.8412 Evaluate side-chains 78 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 104 GLN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 40.0000 chunk 67 optimal weight: 0.6980 chunk 52 optimal weight: 0.1980 chunk 77 optimal weight: 6.9990 chunk 116 optimal weight: 9.9990 chunk 107 optimal weight: 30.0000 chunk 92 optimal weight: 6.9990 chunk 9 optimal weight: 0.0010 chunk 71 optimal weight: 5.9990 chunk 56 optimal weight: 0.0010 chunk 73 optimal weight: 10.0000 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13863 Z= 0.192 Angle : 0.532 6.040 19874 Z= 0.318 Chirality : 0.033 0.143 2332 Planarity : 0.003 0.045 1680 Dihedral : 27.849 178.173 4019 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.43 % Allowed : 13.31 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.98 (0.16), residues: 882 sheet: None (None), residues: 0 loop : -0.27 (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 0.010 0.001 PHE A 67 TYR 0.023 0.001 TYR D 121 ARG 0.005 0.000 ARG D 86 ********************** 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 81 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8552 (mtp180) cc_final: 0.8230 (ttt-90) REVERT: E 45 THR cc_start: 0.9028 (p) cc_final: 0.8695 (t) REVERT: E 56 LYS cc_start: 0.9248 (tttt) cc_final: 0.8921 (ttpt) REVERT: F 84 MET cc_start: 0.8757 (mmm) cc_final: 0.8365 (tpt) REVERT: F 88 TYR cc_start: 0.8754 (m-10) cc_final: 0.8390 (m-10) outliers start: 9 outliers final: 9 residues processed: 79 average time/residue: 0.2854 time to fit residues: 32.4666 Evaluate side-chains 76 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 1.025 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 85 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 chunk 95 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 81 optimal weight: 7.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.099352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.067032 restraints weight = 210103.573| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 5.00 r_work (final): 0.3231 ------------------------------------------------------------------------------- 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: 0.8376 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13863 Z= 0.195 Angle : 0.530 7.908 19874 Z= 0.316 Chirality : 0.033 0.141 2332 Planarity : 0.003 0.043 1680 Dihedral : 27.820 177.715 4019 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % 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: 4.81 (0.24), residues: 1116 helix: 3.98 (0.16), residues: 882 sheet: None (None), residues: 0 loop : -0.33 (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 A 67 TYR 0.024 0.001 TYR D 121 ARG 0.005 0.000 ARG D 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2311.32 seconds wall clock time: 43 minutes 2.53 seconds (2582.53 seconds total)