Starting phenix.real_space_refine on Fri Jul 3 06:51:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ott_17184/07_2026/8ott_17184.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ott_17184/07_2026/8ott_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_17184/07_2026/8ott_17184.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ott_17184/07_2026/8ott_17184.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8ott_17184/07_2026/8ott_17184.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ott_17184/07_2026/8ott_17184.cif" model { file = "/net/cci-nas-00/data/ceres_data/8ott_17184/07_2026/8ott_17184.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ott_17184/07_2026/8ott_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-dev-6108/lib/python3.11/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: 2.89, per 1000 atoms: 0.22 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: 1.13 Conformation dependent library (CDL) restraints added in 431.5 milliseconds 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: 1.96 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: 2.63 Time building geometry restraints manager: 1.52 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 1.516 1.560 -0.044 8.00e-03 1.56e+04 3.00e+01 bond pdb=" C3' DG I 99 " pdb=" C2' DG I 99 " ideal model delta sigma weight residual 1.516 1.558 -0.042 8.00e-03 1.56e+04 2.75e+01 bond pdb=" C3' DG I 40 " pdb=" C2' DG I 40 " ideal model delta sigma weight residual 1.516 1.558 -0.042 8.00e-03 1.56e+04 2.70e+01 bond pdb=" C3' DG I 21 " pdb=" C2' DG I 21 " ideal model delta sigma weight residual 1.516 1.556 -0.040 8.00e-03 1.56e+04 2.55e+01 bond pdb=" C3' DT J 99 " pdb=" C2' DT J 99 " ideal model delta sigma weight residual 1.516 1.556 -0.040 8.00e-03 1.56e+04 2.46e+01 ... (remaining 13756 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 16756 1.16 - 2.32: 2446 2.32 - 3.49: 593 3.49 - 4.65: 51 4.65 - 5.81: 5 Bond angle restraints: 19851 Sorted by residual: angle pdb=" O4' DG I 67 " pdb=" C1' DG I 67 " pdb=" N9 DG I 67 " ideal model delta sigma weight residual 108.00 104.32 3.68 7.00e-01 2.04e+00 2.76e+01 angle pdb=" O5' DG I 67 " pdb=" C5' DG I 67 " pdb=" C4' DG I 67 " ideal model delta sigma weight residual 109.40 113.39 -3.99 8.00e-01 1.56e+00 2.49e+01 angle pdb=" N3 DT J 17 " pdb=" C4 DT J 17 " pdb=" O4 DT J 17 " ideal model delta sigma weight residual 119.90 122.71 -2.81 6.00e-01 2.78e+00 2.19e+01 angle pdb=" N3 DT I 108 " pdb=" C4 DT I 108 " pdb=" O4 DT I 108 " ideal model delta sigma weight residual 119.90 122.68 -2.78 6.00e-01 2.78e+00 2.15e+01 angle pdb=" N3 DT I 117 " pdb=" C4 DT I 117 " pdb=" O4 DT I 117 " ideal model delta sigma weight residual 119.90 122.68 -2.78 6.00e-01 2.78e+00 2.15e+01 ... (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: 1393 0.045 - 0.089: 604 0.089 - 0.134: 250 0.134 - 0.179: 43 0.179 - 0.223: 5 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 -0.20 2.00e-01 2.50e+01 9.60e-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: 2.210 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.680 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 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 0.169 13777 Z= 0.867 Angle : 0.879 5.811 19851 Z= 0.718 Chirality : 0.057 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 are 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/Z covalent geometry : bond 0.00688 / 0.65 (13761) covalent geometry : angle 0.87950 / 0.72 (19851) hydrogen bonds : bond 0.10810 / 7.13 ( 920) hydrogen bonds : angle 4.22319 / 3.11 ( 2348) Misc. bond : bond 0.16776 / 10.81 ( 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 : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 34 LYS cc_start: 0.8807 (tptm) cc_final: 0.8485 (tppt) outliers start: 1 outliers final: 1 residues processed: 190 average time/residue: 0.1783 time to fit residues: 43.5219 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 : 0.322 ------------------------------------------------------------------------------- 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: 5.9990 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... C 73 ASN D 49 HIS D 95 GLN H 95 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.093207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.070572 restraints weight = 53004.362| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.79 r_work: 0.3297 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3282 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 125 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 125 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.3282 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 13777 Z= 0.191 Angle : 0.743 14.183 19851 Z= 0.433 Chirality : 0.047 0.258 2295 Planarity : 0.005 0.050 1541 Dihedral : 28.270 162.189 4203 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 1.27 % Allowed : 9.68 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.73 (0.26), residues: 939 helix: 2.39 (0.19), residues: 711 sheet: None (None), residues: 0 loop : -0.06 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 42 TYR 0.020 0.002 TYR G 39 PHE 0.018 0.002 PHE A 67 HIS 0.013 0.002 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.19 (13761) covalent geometry : angle 0.74279 / 0.43 (19851) hydrogen bonds : bond 0.06253 / 4.21 ( 920) hydrogen bonds : angle 3.24823 / 2.38 ( 2348) Misc. bond : bond 0.00469 / 0.25 ( 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 137 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 129 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: D 34 LYS cc_start: 0.8866 (tptm) cc_final: 0.8505 (tppt) REVERT: H 59 MET cc_start: 0.8901 (tpt) cc_final: 0.8456 (tpt) outliers start: 8 outliers final: 3 residues processed: 132 average time/residue: 0.1195 time to fit residues: 22.4689 Evaluate side-chains 112 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 109 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 100 VAL 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: 0.8980 chunk 32 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 100 optimal weight: 20.0000 chunk 52 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 chunk 99 optimal weight: 30.0000 chunk 13 optimal weight: 2.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN F 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.090443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.067219 restraints weight = 54544.528| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.82 r_work: 0.3218 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3204 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 125 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 125 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3204 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.166 13777 Z= 0.222 Angle : 0.723 14.589 19851 Z= 0.405 Chirality : 0.040 0.181 2295 Planarity : 0.004 0.049 1541 Dihedral : 29.160 161.564 4203 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.27 % Allowed : 10.79 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.26 (0.27), residues: 939 helix: 2.84 (0.19), residues: 711 sheet: None (None), residues: 0 loop : -0.10 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 92 TYR 0.012 0.002 TYR C 57 PHE 0.010 0.001 PHE A 67 HIS 0.006 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.22 (13761) covalent geometry : angle 0.72264 / 0.40 (19851) hydrogen bonds : bond 0.05702 / 3.80 ( 920) hydrogen bonds : angle 3.05288 / 2.24 ( 2348) Misc. bond : bond 0.00629 / 0.28 ( 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 123 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: B 53 GLU cc_start: 0.8875 (tp30) cc_final: 0.8596 (tp30) REVERT: D 34 LYS cc_start: 0.8897 (tptm) cc_final: 0.8546 (tppt) REVERT: G 38 ASN cc_start: 0.8879 (m110) cc_final: 0.8661 (m110) REVERT: H 59 MET cc_start: 0.9126 (tpt) cc_final: 0.8598 (tpt) outliers start: 8 outliers final: 5 residues processed: 119 average time/residue: 0.1336 time to fit residues: 22.3124 Evaluate side-chains 114 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 109 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 56 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 100 optimal weight: 6.9990 chunk 17 optimal weight: 20.0000 chunk 107 optimal weight: 20.0000 chunk 94 optimal weight: 9.9990 chunk 41 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 32 optimal weight: 0.0370 overall best weight: 1.3862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.090701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.067388 restraints weight = 53339.203| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.85 r_work: 0.3231 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3216 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3216 r_free = 0.3216 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 125 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3216 r_free = 0.3216 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 125 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3216 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 13777 Z= 0.169 Angle : 0.654 20.647 19851 Z= 0.374 Chirality : 0.039 0.291 2295 Planarity : 0.004 0.037 1541 Dihedral : 29.369 161.174 4203 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.75 % Allowed : 11.75 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.47 (0.27), residues: 939 helix: 3.00 (0.18), residues: 711 sheet: None (None), residues: 0 loop : -0.10 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 86 TYR 0.013 0.002 TYR C 57 PHE 0.011 0.001 PHE E 67 HIS 0.005 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.17 (13761) covalent geometry : angle 0.65435 / 0.37 (19851) hydrogen bonds : bond 0.04725 / 3.13 ( 920) hydrogen bonds : angle 2.82563 / 2.09 ( 2348) Misc. bond : bond 0.00666 / 0.34 ( 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 138 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 53 GLU cc_start: 0.8865 (tp30) cc_final: 0.8633 (tp30) REVERT: D 34 LYS cc_start: 0.8932 (tptm) cc_final: 0.8559 (tppt) REVERT: G 38 ASN cc_start: 0.8809 (m110) cc_final: 0.8604 (m110) REVERT: G 73 ASN cc_start: 0.8894 (m-40) cc_final: 0.8309 (t0) REVERT: H 59 MET cc_start: 0.9164 (tpt) cc_final: 0.8704 (tpt) outliers start: 11 outliers final: 4 residues processed: 133 average time/residue: 0.1370 time to fit residues: 25.2045 Evaluate side-chains 115 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 111 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 93 optimal weight: 10.0000 chunk 88 optimal weight: 20.0000 chunk 9 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 92 optimal weight: 9.9990 chunk 103 optimal weight: 0.9990 chunk 35 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 98 optimal weight: 20.0000 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.091797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.066668 restraints weight = 59475.354| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.99 r_work: 0.3200 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 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 = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 125 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13777 Z= 0.167 Angle : 0.634 16.469 19851 Z= 0.365 Chirality : 0.038 0.239 2295 Planarity : 0.004 0.036 1541 Dihedral : 29.404 161.583 4203 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.75 % Allowed : 11.43 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.66 (0.27), residues: 939 helix: 3.16 (0.18), residues: 711 sheet: None (None), residues: 0 loop : -0.08 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 29 TYR 0.015 0.001 TYR G 57 PHE 0.012 0.001 PHE E 67 HIS 0.008 0.001 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.17 (13761) covalent geometry : angle 0.63362 / 0.37 (19851) hydrogen bonds : bond 0.04720 / 3.14 ( 920) hydrogen bonds : angle 2.77639 / 2.05 ( 2348) Misc. bond : bond 0.00661 / 0.40 ( 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 134 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 53 GLU cc_start: 0.8763 (tp30) cc_final: 0.8545 (tp30) REVERT: B 84 MET cc_start: 0.9313 (tpp) cc_final: 0.9069 (mmm) REVERT: D 34 LYS cc_start: 0.8955 (tptm) cc_final: 0.8580 (tppt) REVERT: G 13 LYS cc_start: 0.7598 (tptt) cc_final: 0.7077 (tppt) REVERT: G 73 ASN cc_start: 0.8988 (m-40) cc_final: 0.8466 (t0) REVERT: H 59 MET cc_start: 0.9122 (tpt) cc_final: 0.8845 (mmm) outliers start: 11 outliers final: 7 residues processed: 129 average time/residue: 0.1133 time to fit residues: 20.7080 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 : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL 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 H residue 47 GLN Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 76 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 41 optimal weight: 0.6980 chunk 38 optimal weight: 0.4980 chunk 39 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 92 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 101 optimal weight: 9.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.090663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.067369 restraints weight = 53346.442| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.81 r_work: 0.3272 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3226 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 125 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 125 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3226 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13777 Z= 0.145 Angle : 0.633 19.067 19851 Z= 0.363 Chirality : 0.038 0.257 2295 Planarity : 0.004 0.048 1541 Dihedral : 29.252 160.813 4203 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.59 % Allowed : 13.02 % 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 are not related in a simple way. whole: 3.78 (0.27), residues: 939 helix: 3.22 (0.18), residues: 714 sheet: None (None), residues: 0 loop : -0.01 (0.41), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 86 TYR 0.013 0.001 TYR C 57 PHE 0.010 0.001 PHE E 67 HIS 0.006 0.001 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.14 (13761) covalent geometry : angle 0.63347 / 0.36 (19851) hydrogen bonds : bond 0.04344 / 2.87 ( 920) hydrogen bonds : angle 2.68281 / 1.99 ( 2348) Misc. bond : bond 0.00462 / 0.19 ( 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 131 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 53 GLU cc_start: 0.8625 (tp30) cc_final: 0.8382 (tp30) REVERT: B 84 MET cc_start: 0.9320 (tpp) cc_final: 0.9102 (mmm) REVERT: D 34 LYS cc_start: 0.8959 (tptm) cc_final: 0.8599 (tppt) REVERT: G 13 LYS cc_start: 0.7549 (tptt) cc_final: 0.7111 (tppt) REVERT: G 73 ASN cc_start: 0.9005 (m-40) cc_final: 0.8628 (t0) REVERT: H 59 MET cc_start: 0.9090 (tpt) cc_final: 0.8830 (mmm) outliers start: 10 outliers final: 6 residues processed: 128 average time/residue: 0.1210 time to fit residues: 22.1496 Evaluate side-chains 118 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 112 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 16 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 38 optimal weight: 0.7980 chunk 90 optimal weight: 9.9990 chunk 36 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.089811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.066416 restraints weight = 54738.680| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.83 r_work: 0.3206 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3193 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 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 = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 125 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3193 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13777 Z= 0.169 Angle : 0.636 14.417 19851 Z= 0.364 Chirality : 0.038 0.313 2295 Planarity : 0.004 0.039 1541 Dihedral : 29.361 161.697 4203 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.75 % Allowed : 13.02 % Favored : 85.24 % Cbeta Deviations : 0.00 % 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 are not related in a simple way. whole: 3.83 (0.27), residues: 939 helix: 3.32 (0.18), residues: 708 sheet: None (None), residues: 0 loop : -0.16 (0.41), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 86 TYR 0.013 0.001 TYR C 57 PHE 0.011 0.001 PHE E 67 HIS 0.004 0.001 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.17 (13761) covalent geometry : angle 0.63565 / 0.36 (19851) hydrogen bonds : bond 0.04562 / 3.03 ( 920) hydrogen bonds : angle 2.74424 / 2.04 ( 2348) Misc. bond : bond 0.00263 / 0.17 ( 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 128 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 53 GLU cc_start: 0.8693 (tp30) cc_final: 0.8436 (tp30) REVERT: B 84 MET cc_start: 0.9341 (tpp) cc_final: 0.9079 (mmm) REVERT: D 34 LYS cc_start: 0.8964 (tptm) cc_final: 0.8608 (tppt) REVERT: G 13 LYS cc_start: 0.7516 (tptt) cc_final: 0.7041 (tppt) REVERT: G 73 ASN cc_start: 0.9028 (m-40) cc_final: 0.8657 (t0) REVERT: H 59 MET cc_start: 0.9174 (tpt) cc_final: 0.8930 (mmm) outliers start: 11 outliers final: 10 residues processed: 126 average time/residue: 0.1137 time to fit residues: 20.2907 Evaluate side-chains 123 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 16 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 39 ILE Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 47 GLN 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: 10.0000 chunk 85 optimal weight: 50.0000 chunk 51 optimal weight: 2.9990 chunk 33 optimal weight: 0.0870 chunk 88 optimal weight: 20.0000 chunk 2 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 73 optimal weight: 20.0000 chunk 94 optimal weight: 9.9990 chunk 107 optimal weight: 50.0000 overall best weight: 1.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.090897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.065462 restraints weight = 55894.958| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.95 r_work: 0.3181 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 125 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 125 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13777 Z= 0.171 Angle : 0.659 15.990 19851 Z= 0.373 Chirality : 0.039 0.288 2295 Planarity : 0.004 0.038 1541 Dihedral : 29.463 161.967 4203 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.43 % Allowed : 13.49 % Favored : 85.08 % Cbeta Deviations : 0.00 % 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 are not related in a simple way. whole: 3.83 (0.27), residues: 939 helix: 3.37 (0.18), residues: 708 sheet: None (None), residues: 0 loop : -0.32 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 86 TYR 0.013 0.001 TYR C 57 PHE 0.011 0.001 PHE E 67 HIS 0.004 0.001 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.17 (13761) covalent geometry : angle 0.65938 / 0.37 (19851) hydrogen bonds : bond 0.04466 / 2.97 ( 920) hydrogen bonds : angle 2.72180 / 2.04 ( 2348) Misc. bond : bond 0.00315 / 0.14 ( 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 127 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 53 GLU cc_start: 0.8719 (tp30) cc_final: 0.8458 (tp30) REVERT: B 84 MET cc_start: 0.9372 (tpp) cc_final: 0.9044 (mmm) REVERT: C 110 ASN cc_start: 0.8541 (m-40) cc_final: 0.8055 (m110) REVERT: D 34 LYS cc_start: 0.8968 (tptm) cc_final: 0.8669 (tppt) REVERT: E 59 GLU cc_start: 0.7331 (pm20) cc_final: 0.7114 (pm20) REVERT: G 13 LYS cc_start: 0.7517 (tptt) cc_final: 0.7040 (tppt) REVERT: G 73 ASN cc_start: 0.9064 (m-40) cc_final: 0.8754 (t0) REVERT: H 59 MET cc_start: 0.9204 (tpt) cc_final: 0.8959 (mmm) outliers start: 9 outliers final: 6 residues processed: 125 average time/residue: 0.0952 time to fit residues: 17.3247 Evaluate side-chains 119 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 113 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 39 ILE 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: 1.9990 chunk 96 optimal weight: 9.9990 chunk 32 optimal weight: 0.0980 chunk 38 optimal weight: 0.3980 chunk 27 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 108 optimal weight: 50.0000 chunk 105 optimal weight: 10.0000 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 47 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.087364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.063584 restraints weight = 57498.120| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.92 r_work: 0.3069 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 125 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 125 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.4505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 13777 Z= 0.151 Angle : 0.655 17.197 19851 Z= 0.372 Chirality : 0.040 0.466 2295 Planarity : 0.004 0.039 1541 Dihedral : 29.301 161.868 4199 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.59 % Allowed : 13.97 % Favored : 84.44 % Cbeta Deviations : 0.22 % 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 are not related in a simple way. whole: 3.86 (0.27), residues: 939 helix: 3.41 (0.18), residues: 708 sheet: None (None), residues: 0 loop : -0.38 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 23 TYR 0.013 0.001 TYR C 57 PHE 0.010 0.001 PHE E 67 HIS 0.005 0.001 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.15 (13761) covalent geometry : angle 0.65470 / 0.37 (19851) hydrogen bonds : bond 0.04205 / 2.77 ( 920) hydrogen bonds : angle 2.64399 / 1.97 ( 2348) Misc. bond : bond 0.00594 / 0.21 ( 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 128 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8852 (mmm) cc_final: 0.8572 (mmm) REVERT: B 53 GLU cc_start: 0.8631 (tp30) cc_final: 0.8389 (tp30) REVERT: B 84 MET cc_start: 0.9346 (tpp) cc_final: 0.9020 (mmm) REVERT: C 110 ASN cc_start: 0.8487 (m-40) cc_final: 0.8030 (m110) REVERT: D 34 LYS cc_start: 0.8976 (tptm) cc_final: 0.8727 (tppt) REVERT: E 59 GLU cc_start: 0.7265 (pm20) cc_final: 0.6995 (pm20) REVERT: G 13 LYS cc_start: 0.7626 (tptt) cc_final: 0.7196 (tppt) REVERT: G 73 ASN cc_start: 0.9031 (m-40) cc_final: 0.8799 (t0) REVERT: H 59 MET cc_start: 0.9137 (tpt) cc_final: 0.8907 (mmm) outliers start: 10 outliers final: 9 residues processed: 126 average time/residue: 0.1010 time to fit residues: 18.5653 Evaluate side-chains 122 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain E residue 124 ILE 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: 8.9990 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 106 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 88 optimal weight: 20.0000 chunk 72 optimal weight: 40.0000 chunk 5 optimal weight: 0.9980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 47 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.085056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.061140 restraints weight = 56226.691| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.90 r_work: 0.3004 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3008 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 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 = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 125 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3008 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.4767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 13777 Z= 0.224 Angle : 0.729 12.254 19851 Z= 0.399 Chirality : 0.042 0.371 2295 Planarity : 0.004 0.040 1541 Dihedral : 29.672 163.002 4199 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.95 % Allowed : 16.35 % Favored : 82.70 % 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 are not related in a simple way. whole: 3.76 (0.27), residues: 939 helix: 3.38 (0.18), residues: 705 sheet: None (None), residues: 0 loop : -0.53 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 92 TYR 0.015 0.001 TYR C 57 PHE 0.014 0.002 PHE A 67 HIS 0.007 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.22 (13761) covalent geometry : angle 0.72910 / 0.40 (19851) hydrogen bonds : bond 0.05098 / 3.38 ( 920) hydrogen bonds : angle 2.79702 / 2.07 ( 2348) Misc. bond : bond 0.00559 / 0.24 ( 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 121 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 115 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8955 (mmm) cc_final: 0.8746 (mmm) REVERT: A 94 GLU cc_start: 0.8761 (tp30) cc_final: 0.8532 (mm-30) REVERT: B 53 GLU cc_start: 0.8736 (tp30) cc_final: 0.8453 (tp30) REVERT: B 84 MET cc_start: 0.9364 (tpp) cc_final: 0.9023 (mmm) REVERT: C 110 ASN cc_start: 0.8556 (m-40) cc_final: 0.8158 (m110) REVERT: D 34 LYS cc_start: 0.8986 (tptm) cc_final: 0.8707 (tppt) REVERT: E 59 GLU cc_start: 0.7382 (pm20) cc_final: 0.7061 (pm20) REVERT: G 13 LYS cc_start: 0.7567 (tptt) cc_final: 0.7138 (tppt) REVERT: G 73 ASN cc_start: 0.9074 (m-40) cc_final: 0.8859 (t0) REVERT: H 59 MET cc_start: 0.9188 (tpt) cc_final: 0.8981 (mmm) outliers start: 6 outliers final: 4 residues processed: 121 average time/residue: 0.1128 time to fit residues: 19.9093 Evaluate side-chains 116 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 112 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain E residue 124 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 34 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 38 optimal weight: 0.0370 chunk 45 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 77 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 overall best weight: 1.3460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 47 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.086072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.062303 restraints weight = 52322.930| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.80 r_work: 0.3042 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3045 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 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 = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 125 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.4856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 13777 Z= 0.165 Angle : 0.688 14.545 19851 Z= 0.384 Chirality : 0.041 0.442 2295 Planarity : 0.004 0.043 1541 Dihedral : 29.508 162.521 4199 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.79 % Allowed : 16.03 % Favored : 83.17 % Cbeta Deviations : 0.22 % 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 are not related in a simple way. whole: 3.81 (0.27), residues: 939 helix: 3.43 (0.18), residues: 705 sheet: None (None), residues: 0 loop : -0.54 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 86 TYR 0.013 0.001 TYR C 57 PHE 0.009 0.001 PHE E 67 HIS 0.007 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.16 (13761) covalent geometry : angle 0.68819 / 0.38 (19851) hydrogen bonds : bond 0.04307 / 2.82 ( 920) hydrogen bonds : angle 2.68574 / 2.00 ( 2348) Misc. bond : bond 0.00481 / 0.20 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3235.86 seconds wall clock time: 55 minutes 51.68 seconds (3351.68 seconds total)