Starting phenix.real_space_refine on Sat Aug 23 14:31:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ott_17184/08_2025/8ott_17184.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ott_17184/08_2025/8ott_17184.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/8ott_17184/08_2025/8ott_17184.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ott_17184/08_2025/8ott_17184.map" model { file = "/net/cci-nas-00/data/ceres_data/8ott_17184/08_2025/8ott_17184.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ott_17184/08_2025/8ott_17184.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.018 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 288 5.49 5 S 14 5.16 5 C 7231 2.51 5 N 2441 2.21 5 O 2999 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12973 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 774 Classifications: {'peptide': 94} Modifications used: {'COO': 1} 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: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 838 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "D" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Modifications used: {'COO': 1} 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: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 832 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2935 Classifications: {'DNA': 144} Link IDs: {'rna3p': 143} Chain: "J" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2969 Classifications: {'DNA': 144} Link IDs: {'rna3p': 143} Chain: "M" Number of atoms: 538 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 53, 269 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 2, 'TRANS': 50} Unresolved non-hydrogen bonds: 181 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASN:plan1': 5, 'ARG:plan': 7, 'HIS:plan': 1, 'GLU:plan': 5, 'GLN:plan1': 2, 'PHE:plan': 2, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 105 Conformer: "B" Number of residues, atoms: 53, 269 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 2, 'TRANS': 50} Unresolved non-hydrogen bonds: 181 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASN:plan1': 5, 'ARG:plan': 7, 'HIS:plan': 1, 'GLU:plan': 5, 'GLN:plan1': 2, 'PHE:plan': 2, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 105 Chain: "N" Number of atoms: 512 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 51, 256 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 1, 'TRANS': 49} Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 5, 'ARG:plan': 6, 'HIS:plan': 4, 'ASN:plan1': 1, 'GLU:plan': 3, 'PHE:plan': 1, 'GLN:plan1': 3, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 112 Conformer: "B" Number of residues, atoms: 51, 256 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 1, 'TRANS': 49} Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 5, 'ARG:plan': 6, 'HIS:plan': 4, 'ASN:plan1': 1, 'GLU:plan': 3, 'PHE:plan': 1, 'GLN:plan1': 3, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 112 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PTD': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'PTD:plan-1': 2, 'PTD:plan-2': 2} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-1': 1, 'PTD:plan-2': 1} Unresolved non-hydrogen planarities: 2 Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PTD': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'PTD:plan-1': 2, 'PTD:plan-2': 2} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PTD': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'PTD:plan-1': 2, 'PTD:plan-2': 2} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-1': 1, 'PTD:plan-2': 1} Unresolved non-hydrogen planarities: 2 Residues with excluded nonbonded symmetry interactions: 104 residue: pdb=" N AASN M 353 " occ=0.50 ... (8 atoms not shown) pdb=" CB BASN M 353 " occ=0.50 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 ... (remaining 92 not shown) Time building chain proxies: 2.77, per 1000 atoms: 0.21 Number of scatterers: 12973 At special positions: 0 Unit cell: (138.58, 114.92, 109.005, 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 288 15.00 O 2999 8.00 N 2441 7.00 C 7231 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: 0.84 Conformation dependent library (CDL) restraints added in 400.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1816 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 10 sheets defined 76.1% alpha, 2.3% beta 143 base pairs and 274 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.751A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.742A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.526A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.507A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.419A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) 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 removed outlier: 3.538A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 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 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.517A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG F 92 " --> pdb=" O TYR F 88 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 37 through 39 No H-bonds generated for 'chain 'G' and resid 37 through 39' 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 123 removed outlier: 3.560A pdb=" N ALA H 107 " --> pdb=" O PRO H 103 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 354 through 381 removed outlier: 3.657A pdb=" N BILE M 381 " --> pdb=" O BLEU M 377 " (cutoff:3.500A) Processing helix chain 'M' and resid 382 through 385 Processing helix chain 'M' and resid 391 through 405 Processing helix chain 'N' and resid 24 through 50 Processing helix chain 'N' and resid 51 through 54 Processing helix chain 'N' and resid 59 through 73 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.989A 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: 6.987A 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: 6.678A 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: 6.832A 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: 6.872A 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 78 550 hydrogen bonds defined for protein. 1608 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 370 hydrogen bonds 740 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 274 stacking parallelities Total time for adding SS restraints: 2.23 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2293 1.33 - 1.45: 4570 1.45 - 1.57: 6300 1.57 - 1.69: 574 1.69 - 1.81: 24 Bond restraints: 13761 Sorted by residual: bond pdb=" C3' DG J 101 " pdb=" C2' DG J 101 " ideal model delta sigma weight residual 1.525 1.560 -0.035 2.00e-02 2.50e+03 3.03e+00 bond pdb=" C3' DG I 99 " pdb=" C2' DG I 99 " ideal model delta sigma weight residual 1.525 1.558 -0.033 2.00e-02 2.50e+03 2.72e+00 bond pdb=" C3' DG I 40 " pdb=" C2' DG I 40 " ideal model delta sigma weight residual 1.525 1.558 -0.033 2.00e-02 2.50e+03 2.65e+00 bond pdb=" C1 PTD D 201 " pdb=" C2 PTD D 201 " ideal model delta sigma weight residual 1.499 1.531 -0.032 2.00e-02 2.50e+03 2.53e+00 bond pdb=" C1 PTD D 202 " pdb=" C2 PTD D 202 " ideal model delta sigma weight residual 1.499 1.531 -0.032 2.00e-02 2.50e+03 2.50e+00 ... (remaining 13756 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 17486 1.16 - 2.32: 1969 2.32 - 3.49: 364 3.49 - 4.65: 30 4.65 - 5.81: 2 Bond angle restraints: 19851 Sorted by residual: angle pdb=" C2' DG I 99 " pdb=" C1' DG I 99 " pdb=" N9 DG I 99 " ideal model delta sigma weight residual 113.50 118.08 -4.58 1.50e+00 4.44e-01 9.31e+00 angle pdb=" O4' DG I 67 " pdb=" C1' DG I 67 " pdb=" N9 DG I 67 " ideal model delta sigma weight residual 108.40 104.32 4.08 1.50e+00 4.44e-01 7.40e+00 angle pdb=" C ARG G 32 " pdb=" CA ARG G 32 " pdb=" CB ARG G 32 " ideal model delta sigma weight residual 110.81 106.48 4.33 1.60e+00 3.91e-01 7.32e+00 angle pdb=" CG ARG B 92 " pdb=" CD ARG B 92 " pdb=" NE ARG B 92 " ideal model delta sigma weight residual 112.00 106.19 5.81 2.20e+00 2.07e-01 6.98e+00 angle pdb=" C2' DC I 70 " pdb=" C1' DC I 70 " pdb=" N1 DC I 70 " ideal model delta sigma weight residual 113.50 117.42 -3.92 1.50e+00 4.44e-01 6.82e+00 ... (remaining 19846 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.68: 6255 31.68 - 63.37: 1249 63.37 - 95.05: 8 95.05 - 126.73: 0 126.73 - 158.41: 1 Dihedral angle restraints: 7513 sinusoidal: 4716 harmonic: 2797 Sorted by residual: dihedral pdb=" CA ALA G 14 " pdb=" C ALA G 14 " pdb=" N LYS G 15 " pdb=" CA LYS G 15 " ideal model delta harmonic sigma weight residual -180.00 -150.75 -29.25 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" C4' DT I 77 " pdb=" C3' DT I 77 " pdb=" O3' DT I 77 " pdb=" P DC I 78 " ideal model delta sinusoidal sigma weight residual 220.00 61.59 158.41 1 3.50e+01 8.16e-04 1.51e+01 dihedral pdb=" CA TYR D 83 " pdb=" C TYR D 83 " pdb=" N ASN D 84 " pdb=" CA ASN D 84 " ideal model delta harmonic sigma weight residual 180.00 160.95 19.05 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 7510 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1728 0.045 - 0.089: 414 0.089 - 0.134: 108 0.134 - 0.179: 41 0.179 - 0.223: 4 Chirality restraints: 2295 Sorted by residual: chirality pdb=" CA LYS G 15 " pdb=" N LYS G 15 " pdb=" C LYS G 15 " pdb=" CB LYS G 15 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA LYS F 77 " pdb=" N LYS F 77 " pdb=" C LYS F 77 " pdb=" CB LYS F 77 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" C4' DG I 67 " pdb=" C5' DG I 67 " pdb=" O4' DG I 67 " pdb=" C3' DG I 67 " both_signs ideal model delta sigma weight residual False -2.53 -2.34 -0.19 2.00e-01 2.50e+01 8.98e-01 ... (remaining 2292 not shown) Planarity restraints: 1541 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 67 " 0.064 2.00e-02 2.50e+03 2.56e-02 1.96e+01 pdb=" N9 DG I 67 " -0.052 2.00e-02 2.50e+03 pdb=" C8 DG I 67 " -0.010 2.00e-02 2.50e+03 pdb=" N7 DG I 67 " -0.007 2.00e-02 2.50e+03 pdb=" C5 DG I 67 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DG I 67 " 0.013 2.00e-02 2.50e+03 pdb=" O6 DG I 67 " 0.021 2.00e-02 2.50e+03 pdb=" N1 DG I 67 " 0.005 2.00e-02 2.50e+03 pdb=" C2 DG I 67 " -0.003 2.00e-02 2.50e+03 pdb=" N2 DG I 67 " -0.006 2.00e-02 2.50e+03 pdb=" N3 DG I 67 " -0.010 2.00e-02 2.50e+03 pdb=" C4 DG I 67 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 92 " 0.378 9.50e-02 1.11e+02 1.69e-01 1.77e+01 pdb=" NE ARG B 92 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG B 92 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 92 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 92 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 69 " 0.052 2.00e-02 2.50e+03 2.19e-02 1.31e+01 pdb=" N9 DA I 69 " -0.043 2.00e-02 2.50e+03 pdb=" C8 DA I 69 " -0.006 2.00e-02 2.50e+03 pdb=" N7 DA I 69 " -0.004 2.00e-02 2.50e+03 pdb=" C5 DA I 69 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DA I 69 " 0.004 2.00e-02 2.50e+03 pdb=" N6 DA I 69 " 0.022 2.00e-02 2.50e+03 pdb=" N1 DA I 69 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 69 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DA I 69 " -0.009 2.00e-02 2.50e+03 pdb=" C4 DA I 69 " -0.009 2.00e-02 2.50e+03 ... (remaining 1538 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 5905 2.99 - 3.47: 12237 3.47 - 3.95: 25579 3.95 - 4.42: 28008 4.42 - 4.90: 37126 Nonbonded interactions: 108855 Sorted by model distance: nonbonded pdb=" OG1 THR H 90 " pdb=" OE1 GLU H 93 " model vdw 2.513 3.040 nonbonded pdb=" OG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 2.520 3.040 nonbonded pdb=" N6 DA I 69 " pdb=" O6 DG J 78 " model vdw 2.528 3.120 nonbonded pdb=" O LEU A 103 " pdb=" OG1 THR A 107 " model vdw 2.556 3.040 nonbonded pdb=" N GLN G 24 " pdb=" OE1 GLU G 56 " model vdw 2.559 3.120 ... (remaining 108850 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 202) } ncs_group { reference = (chain 'B' and resid 22 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 10 through 115 or (resid 116 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2)))) selection = (chain 'G' and resid 10 through 116) } ncs_group { reference = (chain 'D' and resid 32 through 201) selection = chain 'H' } 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=0.95 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: 2.060 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 12.370 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 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:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.169 13777 Z= 0.626 Angle : 0.774 5.811 19851 Z= 0.478 Chirality : 0.046 0.223 2295 Planarity : 0.010 0.169 1541 Dihedral : 24.297 158.413 5697 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 1.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.16 % Allowed : 0.79 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.24), residues: 939 helix: 0.97 (0.17), residues: 703 sheet: None (None), residues: 0 loop : 0.12 (0.37), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 92 TYR 0.020 0.003 TYR C 57 PHE 0.023 0.003 PHE H 70 HIS 0.007 0.002 HIS D 49 Details of bonding type rmsd covalent geometry : bond 0.00484 (13761) covalent geometry : angle 0.77368 (19851) hydrogen bonds : bond 0.10810 ( 920) hydrogen bonds : angle 4.22319 ( 2348) Misc. bond : bond 0.16776 ( 16) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 34 LYS cc_start: 0.8808 (tptm) cc_final: 0.8485 (tppt) outliers start: 1 outliers final: 1 residues processed: 190 average time/residue: 0.1615 time to fit residues: 39.0783 Evaluate side-chains 116 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 115 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 40.0000 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.0670 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 9.9990 chunk 106 optimal weight: 10.0000 overall best weight: 1.5524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN D 49 HIS F 75 HIS H 95 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.093063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.068684 restraints weight = 54609.494| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.91 r_work: 0.3247 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3235 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 125 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 125 | |-----------------------------------------------------------------------------| r_final: 0.3234 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 13777 Z= 0.214 Angle : 0.615 7.730 19851 Z= 0.360 Chirality : 0.037 0.167 2295 Planarity : 0.005 0.036 1541 Dihedral : 29.082 157.409 4203 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.95 % Allowed : 10.48 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.28 (0.27), residues: 939 helix: 2.83 (0.19), residues: 711 sheet: None (None), residues: 0 loop : -0.03 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 99 TYR 0.012 0.002 TYR H 42 PHE 0.014 0.001 PHE A 67 HIS 0.005 0.001 HIS H 109 Details of bonding type rmsd covalent geometry : bond 0.00475 (13761) covalent geometry : angle 0.61456 (19851) hydrogen bonds : bond 0.04746 ( 920) hydrogen bonds : angle 2.90589 ( 2348) Misc. bond : bond 0.00143 ( 16) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 133 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: B 53 GLU cc_start: 0.8867 (tp30) cc_final: 0.8582 (tp30) REVERT: D 34 LYS cc_start: 0.8927 (tptm) cc_final: 0.8574 (tppt) REVERT: G 38 ASN cc_start: 0.8841 (m-40) cc_final: 0.8588 (m110) REVERT: G 73 ASN cc_start: 0.9090 (m-40) cc_final: 0.8569 (t0) REVERT: H 59 MET cc_start: 0.9154 (tpt) cc_final: 0.8668 (tpt) outliers start: 6 outliers final: 3 residues processed: 135 average time/residue: 0.1118 time to fit residues: 21.0063 Evaluate side-chains 110 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 107 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 36 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 12 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 99 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 = 0.3879 r_free = 0.3879 target = 0.091141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.066106 restraints weight = 56506.000| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.93 r_work: 0.3189 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3177 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 125 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 125 | |-----------------------------------------------------------------------------| r_final: 0.3177 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13777 Z= 0.202 Angle : 0.558 5.763 19851 Z= 0.331 Chirality : 0.034 0.154 2295 Planarity : 0.004 0.034 1541 Dihedral : 28.960 159.773 4203 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.59 % Allowed : 10.32 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.79 (0.27), residues: 939 helix: 3.23 (0.18), residues: 711 sheet: None (None), residues: 0 loop : 0.01 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 99 TYR 0.020 0.002 TYR H 40 PHE 0.010 0.001 PHE A 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00448 (13761) covalent geometry : angle 0.55833 (19851) hydrogen bonds : bond 0.04155 ( 920) hydrogen bonds : angle 2.68518 ( 2348) Misc. bond : bond 0.00178 ( 16) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 53 GLU cc_start: 0.8840 (tp30) cc_final: 0.8536 (tp30) REVERT: B 84 MET cc_start: 0.9217 (mmm) cc_final: 0.8951 (mmm) REVERT: C 38 ASN cc_start: 0.8486 (m-40) cc_final: 0.8259 (t0) REVERT: C 110 ASN cc_start: 0.8545 (m-40) cc_final: 0.8027 (m110) REVERT: D 34 LYS cc_start: 0.8987 (tptm) cc_final: 0.8691 (tppt) REVERT: G 13 LYS cc_start: 0.7541 (tptt) cc_final: 0.7067 (tppt) REVERT: G 38 ASN cc_start: 0.8744 (m-40) cc_final: 0.8219 (m110) REVERT: G 73 ASN cc_start: 0.9144 (m-40) cc_final: 0.8842 (t0) REVERT: H 59 MET cc_start: 0.9161 (tpt) cc_final: 0.8887 (mmm) outliers start: 10 outliers final: 6 residues processed: 131 average time/residue: 0.1291 time to fit residues: 22.8337 Evaluate side-chains 113 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 107 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 4 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 53 optimal weight: 20.0000 chunk 100 optimal weight: 9.9990 chunk 17 optimal weight: 20.0000 chunk 107 optimal weight: 50.0000 chunk 94 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN D 49 HIS D 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.083670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.059774 restraints weight = 53022.710| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.85 r_work: 0.2970 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2965 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 125 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 125 | |-----------------------------------------------------------------------------| r_final: 0.2965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.5032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 13777 Z= 0.297 Angle : 0.623 7.176 19851 Z= 0.364 Chirality : 0.039 0.155 2295 Planarity : 0.004 0.034 1541 Dihedral : 29.716 160.671 4203 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.43 % Allowed : 12.70 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.84 (0.27), residues: 939 helix: 3.32 (0.18), residues: 711 sheet: None (None), residues: 0 loop : -0.16 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 33 TYR 0.018 0.002 TYR H 40 PHE 0.011 0.002 PHE E 67 HIS 0.005 0.002 HIS C 82 Details of bonding type rmsd covalent geometry : bond 0.00669 (13761) covalent geometry : angle 0.62329 (19851) hydrogen bonds : bond 0.04687 ( 920) hydrogen bonds : angle 2.76194 ( 2348) Misc. bond : bond 0.00156 ( 16) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 110 ASN cc_start: 0.8594 (m-40) cc_final: 0.8234 (m110) REVERT: D 34 LYS cc_start: 0.9052 (tptm) cc_final: 0.8841 (tppt) REVERT: E 59 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7310 (pm20) REVERT: F 25 ASN cc_start: 0.8204 (m-40) cc_final: 0.7968 (m-40) REVERT: G 13 LYS cc_start: 0.7664 (tptt) cc_final: 0.7268 (tppt) REVERT: H 59 MET cc_start: 0.9186 (tpt) cc_final: 0.8935 (mmm) outliers start: 9 outliers final: 6 residues processed: 121 average time/residue: 0.1059 time to fit residues: 18.3012 Evaluate side-chains 110 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 14 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 35 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 HIS H 109 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.085451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.061923 restraints weight = 56952.165| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.89 r_work: 0.3012 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3014 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 125 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 125 | |-----------------------------------------------------------------------------| r_final: 0.3014 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.5210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13777 Z= 0.193 Angle : 0.566 8.206 19851 Z= 0.334 Chirality : 0.034 0.157 2295 Planarity : 0.004 0.035 1541 Dihedral : 29.210 159.395 4203 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.11 % Allowed : 13.81 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.95 (0.27), residues: 939 helix: 3.42 (0.18), residues: 711 sheet: None (None), residues: 0 loop : -0.21 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 33 TYR 0.017 0.001 TYR H 40 PHE 0.010 0.001 PHE E 67 HIS 0.005 0.001 HIS H 109 Details of bonding type rmsd covalent geometry : bond 0.00428 (13761) covalent geometry : angle 0.56630 (19851) hydrogen bonds : bond 0.03785 ( 920) hydrogen bonds : angle 2.55173 ( 2348) Misc. bond : bond 0.00198 ( 16) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 114 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8683 (tm-30) cc_final: 0.8346 (pp30) REVERT: C 110 ASN cc_start: 0.8590 (m-40) cc_final: 0.8248 (m110) REVERT: E 59 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7341 (pm20) REVERT: F 25 ASN cc_start: 0.8245 (m-40) cc_final: 0.8041 (m-40) REVERT: G 13 LYS cc_start: 0.7709 (tptt) cc_final: 0.7370 (tppt) REVERT: H 59 MET cc_start: 0.9174 (tpt) cc_final: 0.8729 (tpt) outliers start: 7 outliers final: 3 residues processed: 117 average time/residue: 0.1359 time to fit residues: 22.4009 Evaluate side-chains 107 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 103 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 59 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 76 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 101 optimal weight: 20.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.085454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.061940 restraints weight = 54182.822| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.80 r_work: 0.3023 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3018 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 125 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 125 | |-----------------------------------------------------------------------------| r_final: 0.3018 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.5362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13777 Z= 0.191 Angle : 0.590 14.719 19851 Z= 0.343 Chirality : 0.034 0.239 2295 Planarity : 0.004 0.036 1541 Dihedral : 29.079 158.017 4203 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.95 % Allowed : 13.65 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.98 (0.27), residues: 939 helix: 3.51 (0.18), residues: 705 sheet: None (None), residues: 0 loop : -0.31 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 33 TYR 0.014 0.001 TYR H 40 PHE 0.010 0.001 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00424 (13761) covalent geometry : angle 0.58989 (19851) hydrogen bonds : bond 0.03731 ( 920) hydrogen bonds : angle 2.53621 ( 2348) Misc. bond : bond 0.00186 ( 16) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 111 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 110 ASN cc_start: 0.8642 (m-40) cc_final: 0.8337 (m110) REVERT: E 59 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7239 (pm20) REVERT: H 59 MET cc_start: 0.9175 (tpt) cc_final: 0.8806 (tpt) outliers start: 6 outliers final: 3 residues processed: 114 average time/residue: 0.1264 time to fit residues: 20.6730 Evaluate side-chains 104 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 100 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 59 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 38 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.3754 r_free = 0.3754 target = 0.086300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.062835 restraints weight = 55752.937| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.84 r_work: 0.3044 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3044 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 125 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 125 | |-----------------------------------------------------------------------------| r_final: 0.3044 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.5520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13777 Z= 0.168 Angle : 0.576 13.373 19851 Z= 0.337 Chirality : 0.034 0.303 2295 Planarity : 0.004 0.036 1541 Dihedral : 28.844 156.611 4203 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.11 % Allowed : 15.56 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.03 (0.27), residues: 939 helix: 3.55 (0.18), residues: 705 sheet: None (None), residues: 0 loop : -0.32 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 33 TYR 0.011 0.001 TYR C 57 PHE 0.009 0.001 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00368 (13761) covalent geometry : angle 0.57648 (19851) hydrogen bonds : bond 0.03503 ( 920) hydrogen bonds : angle 2.48970 ( 2348) Misc. bond : bond 0.00270 ( 16) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 117 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8689 (tm-30) cc_final: 0.8396 (pp30) REVERT: C 110 ASN cc_start: 0.8671 (m-40) cc_final: 0.8433 (m110) REVERT: E 59 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7251 (pm20) REVERT: H 59 MET cc_start: 0.9144 (tpt) cc_final: 0.8758 (tpt) outliers start: 7 outliers final: 3 residues processed: 121 average time/residue: 0.1226 time to fit residues: 21.3707 Evaluate side-chains 112 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 108 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 95 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 51 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 88 optimal weight: 5.9990 chunk 2 optimal weight: 0.2980 chunk 42 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 73 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 107 optimal weight: 30.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3758 r_free = 0.3758 target = 0.086524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.063195 restraints weight = 55904.660| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.82 r_work: 0.3052 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 125 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 125 | |-----------------------------------------------------------------------------| r_final: 0.3050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.5641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13777 Z= 0.170 Angle : 0.596 12.862 19851 Z= 0.346 Chirality : 0.034 0.282 2295 Planarity : 0.004 0.037 1541 Dihedral : 28.827 155.949 4199 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.79 % Allowed : 16.83 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.08 (0.27), residues: 939 helix: 3.58 (0.18), residues: 705 sheet: None (None), residues: 0 loop : -0.30 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 33 TYR 0.011 0.001 TYR C 57 PHE 0.008 0.001 PHE E 67 HIS 0.003 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00372 (13761) covalent geometry : angle 0.59551 (19851) hydrogen bonds : bond 0.03492 ( 920) hydrogen bonds : angle 2.48246 ( 2348) Misc. bond : bond 0.00250 ( 16) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 114 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8730 (tm-30) cc_final: 0.8424 (pp30) REVERT: E 59 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7262 (pm20) REVERT: H 59 MET cc_start: 0.9132 (tpt) cc_final: 0.8891 (mmm) outliers start: 5 outliers final: 3 residues processed: 118 average time/residue: 0.1246 time to fit residues: 21.3197 Evaluate side-chains 109 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 105 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 32 optimal weight: 0.0170 chunk 38 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 108 optimal weight: 50.0000 chunk 105 optimal weight: 6.9990 overall best weight: 1.0024 ------------------------------------------------------------------------------- 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 = 0.3761 r_free = 0.3761 target = 0.086359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.062481 restraints weight = 58842.707| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.90 r_work: 0.3054 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3052 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 125 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 125 | |-----------------------------------------------------------------------------| r_final: 0.3052 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.5747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13777 Z= 0.170 Angle : 0.640 18.875 19851 Z= 0.364 Chirality : 0.035 0.433 2295 Planarity : 0.004 0.037 1541 Dihedral : 28.828 155.392 4199 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.95 % Allowed : 17.14 % Favored : 81.90 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.01 (0.27), residues: 939 helix: 3.56 (0.18), residues: 705 sheet: None (None), residues: 0 loop : -0.40 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 23 TYR 0.012 0.001 TYR C 57 PHE 0.009 0.001 PHE E 67 HIS 0.005 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00373 (13761) covalent geometry : angle 0.63973 (19851) hydrogen bonds : bond 0.03497 ( 920) hydrogen bonds : angle 2.52066 ( 2348) Misc. bond : bond 0.00381 ( 16) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 111 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8738 (tm-30) cc_final: 0.8431 (pp30) REVERT: C 38 ASN cc_start: 0.8014 (t0) cc_final: 0.7553 (t0) REVERT: E 59 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7281 (pm20) REVERT: G 104 GLN cc_start: 0.8599 (mp10) cc_final: 0.8390 (mp10) REVERT: H 42 TYR cc_start: 0.8556 (t80) cc_final: 0.8295 (t80) REVERT: H 59 MET cc_start: 0.9143 (tpt) cc_final: 0.8924 (mmm) outliers start: 6 outliers final: 3 residues processed: 115 average time/residue: 0.1159 time to fit residues: 19.6059 Evaluate side-chains 112 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 108 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 105 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 0.3980 chunk 49 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- 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 = 0.3719 r_free = 0.3719 target = 0.084234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.060152 restraints weight = 58248.582| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.91 r_work: 0.2985 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 125 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 125 | |-----------------------------------------------------------------------------| r_final: 0.2990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.5823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 13777 Z= 0.260 Angle : 0.702 27.268 19851 Z= 0.392 Chirality : 0.039 0.426 2295 Planarity : 0.004 0.036 1541 Dihedral : 29.346 157.000 4199 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.48 % Allowed : 17.94 % Favored : 81.59 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.88 (0.27), residues: 939 helix: 3.50 (0.18), residues: 702 sheet: None (None), residues: 0 loop : -0.54 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 86 TYR 0.013 0.002 TYR H 42 PHE 0.010 0.001 PHE A 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00582 (13761) covalent geometry : angle 0.70169 (19851) hydrogen bonds : bond 0.04198 ( 920) hydrogen bonds : angle 2.70176 ( 2348) Misc. bond : bond 0.00479 ( 16) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 108 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8806 (tm-30) cc_final: 0.8499 (pp30) REVERT: C 38 ASN cc_start: 0.8132 (t0) cc_final: 0.7690 (t0) REVERT: E 59 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7333 (pm20) REVERT: F 53 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8387 (mm-30) REVERT: H 59 MET cc_start: 0.9160 (tpt) cc_final: 0.8947 (mmm) outliers start: 3 outliers final: 2 residues processed: 110 average time/residue: 0.1078 time to fit residues: 17.6637 Evaluate side-chains 109 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 106 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 59 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 34 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 47 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.085644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.061674 restraints weight = 57175.883| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.87 r_work: 0.3037 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 125 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 125 | |-----------------------------------------------------------------------------| r_final: 0.3042 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.5926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13777 Z= 0.175 Angle : 0.626 14.519 19851 Z= 0.360 Chirality : 0.036 0.414 2295 Planarity : 0.004 0.039 1541 Dihedral : 28.993 155.152 4199 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.63 % Allowed : 17.94 % Favored : 81.43 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.96 (0.27), residues: 939 helix: 3.55 (0.18), residues: 705 sheet: None (None), residues: 0 loop : -0.52 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 86 TYR 0.012 0.001 TYR C 57 PHE 0.010 0.001 PHE E 67 HIS 0.004 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00383 (13761) covalent geometry : angle 0.62628 (19851) hydrogen bonds : bond 0.03513 ( 920) hydrogen bonds : angle 2.56586 ( 2348) Misc. bond : bond 0.00361 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3215.86 seconds wall clock time: 55 minutes 32.73 seconds (3332.73 seconds total)