Starting phenix.real_space_refine on Tue Mar 3 18:03:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6t7d_10394/03_2026/6t7d_10394.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t7d_10394/03_2026/6t7d_10394.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6t7d_10394/03_2026/6t7d_10394.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t7d_10394/03_2026/6t7d_10394.map" model { file = "/net/cci-nas-00/data/ceres_data/6t7d_10394/03_2026/6t7d_10394.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t7d_10394/03_2026/6t7d_10394.cif" } resolution = 4.4 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= 0.004 sd= 0.020 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: 4 Type Number sf(0) Gaussians P 234 5.49 5 C 4002 2.51 5 N 1716 2.21 5 O 2257 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-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8209 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 392 Classifications: {'peptide': 98} Incomplete info: {'backbone_only': 95} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 430 Unresolved non-hydrogen angles: 610 Unresolved non-hydrogen dihedrals: 275 Unresolved non-hydrogen chiralities: 123 Planarities with less than four sites: {'HIS:plan': 2, 'ARG:plan': 14, 'TYR:plan': 3, 'GLU:plan': 7, 'GLN:plan1': 6, 'PHE:plan': 4, 'ASP:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 206 Chain: "B" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 336 Classifications: {'peptide': 84} Incomplete info: {'backbone_only': 76} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 351 Unresolved non-hydrogen angles: 500 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 105 Planarities with less than four sites: {'HIS:plan': 2, 'ARG:plan': 12, 'ASP:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 2, 'TYR:plan': 4, 'GLU:plan': 4, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 162 Chain: "C" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 440 Classifications: {'peptide': 110} Incomplete info: {'backbone_only': 101} Link IDs: {'PTRANS': 5, 'TRANS': 104} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 420 Unresolved non-hydrogen angles: 605 Unresolved non-hydrogen dihedrals: 255 Unresolved non-hydrogen chiralities: 135 Planarities with less than four sites: {'ARG:plan': 12, 'GLN:plan1': 4, 'PHE:plan': 1, 'HIS:plan': 2, 'ASN:plan1': 6, 'TYR:plan': 3, 'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 175 Chain: "D" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 380 Classifications: {'peptide': 95} Incomplete info: {'backbone_only': 90} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 376 Unresolved non-hydrogen angles: 540 Unresolved non-hydrogen dihedrals: 239 Unresolved non-hydrogen chiralities: 117 Planarities with less than four sites: {'ARG:plan': 7, 'GLU:plan': 6, 'TYR:plan': 5, 'GLN:plan1': 2, 'HIS:plan': 3, 'ASP:plan': 2, 'ASN:plan1': 3, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 159 Chain: "E" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 388 Classifications: {'peptide': 97} Incomplete info: {'backbone_only': 94} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 425 Unresolved non-hydrogen angles: 604 Unresolved non-hydrogen dihedrals: 271 Unresolved non-hydrogen chiralities: 122 Planarities with less than four sites: {'HIS:plan': 2, 'ARG:plan': 14, 'TYR:plan': 3, 'GLU:plan': 7, 'GLN:plan1': 6, 'PHE:plan': 4, 'ASP:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 206 Chain: "F" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 349 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 78} Link IDs: {'PTRANS': 1, 'TRANS': 85} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 363 Unresolved non-hydrogen angles: 515 Unresolved non-hydrogen dihedrals: 232 Unresolved non-hydrogen chiralities: 107 Planarities with less than four sites: {'ARG:plan': 13, 'HIS:plan': 2, 'ASP:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 2, 'TYR:plan': 4, 'GLU:plan': 4, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 167 Chain: "G" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 440 Classifications: {'peptide': 110} Incomplete info: {'backbone_only': 101} Link IDs: {'PTRANS': 5, 'TRANS': 104} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 420 Unresolved non-hydrogen angles: 605 Unresolved non-hydrogen dihedrals: 255 Unresolved non-hydrogen chiralities: 135 Planarities with less than four sites: {'ARG:plan': 12, 'GLN:plan1': 4, 'PHE:plan': 1, 'HIS:plan': 2, 'ASN:plan1': 6, 'TYR:plan': 3, 'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 175 Chain: "H" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 380 Classifications: {'peptide': 95} Incomplete info: {'backbone_only': 90} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 376 Unresolved non-hydrogen angles: 540 Unresolved non-hydrogen dihedrals: 239 Unresolved non-hydrogen chiralities: 117 Planarities with less than four sites: {'ARG:plan': 7, 'GLU:plan': 6, 'TYR:plan': 5, 'GLN:plan1': 2, 'HIS:plan': 3, 'ASP:plan': 2, 'ASN:plan1': 3, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 159 Chain: "I" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2376 Classifications: {'DNA': 117} Link IDs: {'rna3p': 116} Chain: "J" Number of atoms: 2421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2421 Classifications: {'DNA': 117} Link IDs: {'rna3p': 116} Chain: "K" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 307 Classifications: {'peptide': 77} Incomplete info: {'backbone_only': 74, 'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 5, 'TRANS': 71} Chain breaks: 1 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 374 Unresolved non-hydrogen angles: 517 Unresolved non-hydrogen dihedrals: 268 Unresolved non-hydrogen chiralities: 86 Planarities with less than four sites: {'HIS:plan': 3, 'ARG:plan': 10, 'ASN:plan1': 2, 'PHE:plan': 2, 'TRP:plan': 2, 'GLU:plan': 6, 'GLN:plan1': 1, 'ASP:plan': 4, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 178 Time building chain proxies: 2.18, per 1000 atoms: 0.27 Number of scatterers: 8209 At special positions: 0 Unit cell: (74.55, 124.95, 115.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) P 234 15.00 O 2257 8.00 N 1716 7.00 C 4002 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=0, symmetry=0 Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 237.2 milliseconds 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 0 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 8 sheets defined 67.6% alpha, 1.9% beta 117 base pairs and 202 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.829A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N HIS A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.901A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.925A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.811A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.677A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 95 removed outlier: 3.670A pdb=" N ASN C 94 " --> pdb=" O ASP C 90 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 90 through 95' Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 121 removed outlier: 3.603A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.745A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN E 76 " --> pdb=" O ARG E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 50 through 76 removed outlier: 3.769A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.677A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 95 removed outlier: 3.668A pdb=" N ASN G 94 " --> pdb=" O ASP G 90 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 90 through 95' Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.604A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 71 removed outlier: 4.078A pdb=" N ILE K 62 " --> pdb=" O VAL K 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 90 Processing helix chain 'K' and resid 92 through 94 No H-bonds generated for 'chain 'K' and resid 92 through 94' Processing helix chain 'K' and resid 95 through 113 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.154A 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 'C' and resid 42 through 43 removed outlier: 6.888A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.124A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.562A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.195A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 419 hydrogen bonds defined for protein. 1245 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 278 hydrogen bonds 552 hydrogen bond angles 0 basepair planarities 117 basepair parallelities 202 stacking parallelities Total time for adding SS restraints: 1.63 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.29: 1087 1.29 - 1.37: 2209 1.37 - 1.46: 2150 1.46 - 1.54: 2868 1.54 - 1.62: 468 Bond restraints: 8782 Sorted by residual: bond pdb=" C ILE K 96 " pdb=" N PRO K 97 " ideal model delta sigma weight residual 1.335 1.369 -0.034 1.36e-02 5.41e+03 6.22e+00 bond pdb=" C3' DC I 13 " pdb=" O3' DC I 13 " ideal model delta sigma weight residual 1.422 1.492 -0.070 3.00e-02 1.11e+03 5.48e+00 bond pdb=" C3' DG I 110 " pdb=" O3' DG I 110 " ideal model delta sigma weight residual 1.422 1.477 -0.055 3.00e-02 1.11e+03 3.42e+00 bond pdb=" C3' DT I 38 " pdb=" O3' DT I 38 " ideal model delta sigma weight residual 1.422 1.468 -0.046 3.00e-02 1.11e+03 2.38e+00 bond pdb=" C LEU E 65 " pdb=" N PRO E 66 " ideal model delta sigma weight residual 1.335 1.356 -0.021 1.36e-02 5.41e+03 2.30e+00 ... (remaining 8777 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 11129 1.31 - 2.62: 1212 2.62 - 3.93: 162 3.93 - 5.24: 27 5.24 - 6.55: 4 Bond angle restraints: 12534 Sorted by residual: angle pdb=" CA LYS F 20 " pdb=" C LYS F 20 " pdb=" N VAL F 21 " ideal model delta sigma weight residual 119.63 115.92 3.71 8.10e-01 1.52e+00 2.10e+01 angle pdb=" CA LEU F 22 " pdb=" C LEU F 22 " pdb=" N ARG F 23 " ideal model delta sigma weight residual 119.63 115.95 3.68 8.10e-01 1.52e+00 2.06e+01 angle pdb=" C2' DA J 53 " pdb=" C1' DA J 53 " pdb=" N9 DA J 53 " ideal model delta sigma weight residual 113.50 119.97 -6.47 1.50e+00 4.44e-01 1.86e+01 angle pdb=" C PRO K 72 " pdb=" N ASP K 73 " pdb=" CA ASP K 73 " ideal model delta sigma weight residual 122.07 127.37 -5.30 1.43e+00 4.89e-01 1.38e+01 angle pdb=" C3' DC I 13 " pdb=" O3' DC I 13 " pdb=" P DT I 14 " ideal model delta sigma weight residual 120.20 125.32 -5.12 1.50e+00 4.44e-01 1.17e+01 ... (remaining 12529 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.40: 2011 30.40 - 60.80: 1387 60.80 - 91.20: 69 91.20 - 121.60: 0 121.60 - 152.00: 3 Dihedral angle restraints: 3470 sinusoidal: 2627 harmonic: 843 Sorted by residual: dihedral pdb=" CA TYR H 34 " pdb=" C TYR H 34 " pdb=" N SER H 35 " pdb=" CA SER H 35 " ideal model delta harmonic sigma weight residual 180.00 -159.04 -20.96 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA TYR D 34 " pdb=" C TYR D 34 " pdb=" N SER D 35 " pdb=" CA SER D 35 " ideal model delta harmonic sigma weight residual -180.00 -159.06 -20.94 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA LYS D 43 " pdb=" C LYS D 43 " pdb=" N GLN D 44 " pdb=" CA GLN D 44 " ideal model delta harmonic sigma weight residual 180.00 160.29 19.71 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 3467 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 863 0.080 - 0.159: 68 0.159 - 0.239: 4 0.239 - 0.318: 0 0.318 - 0.398: 1 Chirality restraints: 936 Sorted by residual: chirality pdb=" C1' DA J 53 " pdb=" O4' DA J 53 " pdb=" C2' DA J 53 " pdb=" N9 DA J 53 " both_signs ideal model delta sigma weight residual False 2.42 2.02 0.40 2.00e-01 2.50e+01 3.95e+00 chirality pdb=" P DC I 111 " pdb=" OP1 DC I 111 " pdb=" OP2 DC I 111 " pdb=" O5' DC I 111 " both_signs ideal model delta sigma weight residual True 2.35 -2.55 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" P DT I 14 " pdb=" OP1 DT I 14 " pdb=" OP2 DT I 14 " pdb=" O5' DT I 14 " both_signs ideal model delta sigma weight residual True 2.35 -2.54 -0.19 2.00e-01 2.50e+01 9.28e-01 ... (remaining 933 not shown) Planarity restraints: 1077 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA J 53 " -0.013 2.00e-02 2.50e+03 3.54e-02 3.44e+01 pdb=" N9 DA J 53 " 0.086 2.00e-02 2.50e+03 pdb=" C8 DA J 53 " -0.072 2.00e-02 2.50e+03 pdb=" N7 DA J 53 " 0.016 2.00e-02 2.50e+03 pdb=" C5 DA J 53 " 0.006 2.00e-02 2.50e+03 pdb=" C6 DA J 53 " 0.002 2.00e-02 2.50e+03 pdb=" N6 DA J 53 " 0.009 2.00e-02 2.50e+03 pdb=" N1 DA J 53 " -0.015 2.00e-02 2.50e+03 pdb=" C2 DA J 53 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DA J 53 " -0.019 2.00e-02 2.50e+03 pdb=" C4 DA J 53 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 95 " -0.029 2.00e-02 2.50e+03 1.61e-02 6.45e+00 pdb=" N1 DT I 95 " 0.041 2.00e-02 2.50e+03 pdb=" C2 DT I 95 " -0.004 2.00e-02 2.50e+03 pdb=" O2 DT I 95 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DT I 95 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DT I 95 " -0.003 2.00e-02 2.50e+03 pdb=" O4 DT I 95 " -0.006 2.00e-02 2.50e+03 pdb=" C5 DT I 95 " -0.001 2.00e-02 2.50e+03 pdb=" C7 DT I 95 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DT I 95 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 60 " 0.012 2.00e-02 2.50e+03 2.33e-02 5.42e+00 pdb=" C VAL F 60 " -0.040 2.00e-02 2.50e+03 pdb=" O VAL F 60 " 0.015 2.00e-02 2.50e+03 pdb=" N PHE F 61 " 0.014 2.00e-02 2.50e+03 ... (remaining 1074 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 344 2.67 - 3.22: 6460 3.22 - 3.78: 15338 3.78 - 4.34: 17796 4.34 - 4.90: 23191 Nonbonded interactions: 63129 Sorted by model distance: nonbonded pdb=" N3 DC I 2 " pdb=" N1 DG J 145 " model vdw 2.107 3.200 nonbonded pdb=" O2 DC I 2 " pdb=" C2 DG J 145 " model vdw 2.130 3.260 nonbonded pdb=" C2 DC I 2 " pdb=" N1 DG J 145 " model vdw 2.198 3.340 nonbonded pdb=" O2 DC I 2 " pdb=" N2 DG J 145 " model vdw 2.292 3.120 nonbonded pdb=" N4 DC I 2 " pdb=" O6 DG J 145 " model vdw 2.340 3.120 ... (remaining 63124 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' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 18 through 101) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.180 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.600 Find NCS groups from input model: 0.120 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 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 : 0.005 0.070 8782 Z= 0.275 Angle : 0.858 6.553 12534 Z= 0.554 Chirality : 0.047 0.398 936 Planarity : 0.005 0.035 1077 Dihedral : 32.584 152.004 3470 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.34 (0.24), residues: 833 helix: -1.43 (0.18), residues: 571 sheet: None (None), residues: 0 loop : -1.42 (0.35), residues: 262 Details of bonding type rmsd covalent geometry : bond 0.00529 ( 8782) covalent geometry : angle 0.85838 (12534) hydrogen bonds : bond 0.12693 ( 697) hydrogen bonds : angle 5.32746 ( 1797) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.181 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0371 time to fit residues: 1.3429 Evaluate side-chains 16 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 20.0000 chunk 97 optimal weight: 50.0000 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 30.0000 chunk 65 optimal weight: 50.0000 chunk 62 optimal weight: 40.0000 chunk 51 optimal weight: 40.0000 chunk 100 optimal weight: 50.0000 chunk 38 optimal weight: 40.0000 chunk 61 optimal weight: 0.9990 overall best weight: 14.3594 ------------------------------------------------------------------------------- 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 = 0.3582 r_free = 0.3582 target = 0.074302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.052605 restraints weight = 57253.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.052205 restraints weight = 60650.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.052651 restraints weight = 51773.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.052614 restraints weight = 37979.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.052711 restraints weight = 37085.846| |-----------------------------------------------------------------------------| r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.050 8782 Z= 0.376 Angle : 0.741 5.958 12534 Z= 0.475 Chirality : 0.042 0.150 936 Planarity : 0.004 0.018 1077 Dihedral : 31.975 146.274 3470 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.84 (0.27), residues: 833 helix: 1.13 (0.20), residues: 588 sheet: None (None), residues: 0 loop : -0.73 (0.37), residues: 245 Details of bonding type rmsd covalent geometry : bond 0.00765 ( 8782) covalent geometry : angle 0.74099 (12534) hydrogen bonds : bond 0.09555 ( 697) hydrogen bonds : angle 4.14321 ( 1797) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.189 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0371 time to fit residues: 1.3656 Evaluate side-chains 16 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 30 optimal weight: 30.0000 chunk 86 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 87 optimal weight: 20.0000 chunk 45 optimal weight: 30.0000 chunk 15 optimal weight: 30.0000 chunk 102 optimal weight: 50.0000 chunk 26 optimal weight: 30.0000 chunk 28 optimal weight: 50.0000 chunk 19 optimal weight: 20.0000 chunk 35 optimal weight: 50.0000 overall best weight: 18.0000 ------------------------------------------------------------------------------- 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 = 0.3523 r_free = 0.3523 target = 0.071704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.049508 restraints weight = 57625.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.049713 restraints weight = 46303.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.049618 restraints weight = 37494.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.049796 restraints weight = 34765.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.049791 restraints weight = 32838.955| |-----------------------------------------------------------------------------| r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.5406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.058 8782 Z= 0.433 Angle : 0.817 6.179 12534 Z= 0.518 Chirality : 0.047 0.172 936 Planarity : 0.005 0.021 1077 Dihedral : 32.675 158.428 3470 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 21.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.50 (0.27), residues: 833 helix: 1.10 (0.20), residues: 584 sheet: None (None), residues: 0 loop : -1.49 (0.35), residues: 249 Details of bonding type rmsd covalent geometry : bond 0.00877 ( 8782) covalent geometry : angle 0.81650 (12534) hydrogen bonds : bond 0.10520 ( 697) hydrogen bonds : angle 4.71871 ( 1797) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.174 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0382 time to fit residues: 1.4184 Evaluate side-chains 16 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 24 optimal weight: 20.0000 chunk 47 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 chunk 46 optimal weight: 30.0000 chunk 49 optimal weight: 30.0000 chunk 56 optimal weight: 20.0000 chunk 30 optimal weight: 50.0000 chunk 66 optimal weight: 50.0000 chunk 96 optimal weight: 0.0040 chunk 19 optimal weight: 30.0000 chunk 65 optimal weight: 50.0000 overall best weight: 14.0008 ------------------------------------------------------------------------------- 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 = 0.3549 r_free = 0.3549 target = 0.072943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.050874 restraints weight = 57580.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.050873 restraints weight = 51357.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.050889 restraints weight = 48346.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.050976 restraints weight = 43036.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.051038 restraints weight = 39037.130| |-----------------------------------------------------------------------------| r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.5568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 8782 Z= 0.352 Angle : 0.722 5.630 12534 Z= 0.460 Chirality : 0.041 0.150 936 Planarity : 0.004 0.019 1077 Dihedral : 32.470 154.998 3470 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.18 (0.28), residues: 833 helix: 1.70 (0.21), residues: 589 sheet: None (None), residues: 0 loop : -1.56 (0.36), residues: 244 Details of bonding type rmsd covalent geometry : bond 0.00706 ( 8782) covalent geometry : angle 0.72201 (12534) hydrogen bonds : bond 0.08766 ( 697) hydrogen bonds : angle 4.06905 ( 1797) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.193 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0374 time to fit residues: 1.3754 Evaluate side-chains 16 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 4 optimal weight: 20.0000 chunk 60 optimal weight: 40.0000 chunk 87 optimal weight: 20.0000 chunk 8 optimal weight: 30.0000 chunk 48 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 chunk 51 optimal weight: 30.0000 chunk 10 optimal weight: 1.9990 chunk 62 optimal weight: 20.0000 chunk 64 optimal weight: 20.0000 chunk 70 optimal weight: 40.0000 overall best weight: 14.3998 ------------------------------------------------------------------------------- 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 = 0.3535 r_free = 0.3535 target = 0.072365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.050403 restraints weight = 57788.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.050391 restraints weight = 51339.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.050347 restraints weight = 47279.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.050422 restraints weight = 45110.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.050523 restraints weight = 40036.199| |-----------------------------------------------------------------------------| r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.5882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 8782 Z= 0.364 Angle : 0.728 5.869 12534 Z= 0.463 Chirality : 0.041 0.147 936 Planarity : 0.004 0.021 1077 Dihedral : 32.509 153.832 3470 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.17 (0.28), residues: 833 helix: 1.83 (0.21), residues: 575 sheet: None (None), residues: 0 loop : -1.74 (0.34), residues: 258 Details of bonding type rmsd covalent geometry : bond 0.00738 ( 8782) covalent geometry : angle 0.72836 (12534) hydrogen bonds : bond 0.09026 ( 697) hydrogen bonds : angle 4.20440 ( 1797) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.231 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0364 time to fit residues: 1.3986 Evaluate side-chains 16 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 8 optimal weight: 30.0000 chunk 22 optimal weight: 50.0000 chunk 52 optimal weight: 50.0000 chunk 66 optimal weight: 50.0000 chunk 15 optimal weight: 40.0000 chunk 80 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 98 optimal weight: 0.0270 chunk 60 optimal weight: 40.0000 chunk 30 optimal weight: 30.0000 chunk 70 optimal weight: 40.0000 overall best weight: 16.0054 ------------------------------------------------------------------------------- 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 = 0.3511 r_free = 0.3511 target = 0.071359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.048514 restraints weight = 58125.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.048805 restraints weight = 43855.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.048768 restraints weight = 35391.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.048907 restraints weight = 32821.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.048924 restraints weight = 32625.795| |-----------------------------------------------------------------------------| r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.6512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 8782 Z= 0.396 Angle : 0.766 6.604 12534 Z= 0.485 Chirality : 0.043 0.149 936 Planarity : 0.004 0.021 1077 Dihedral : 32.620 155.286 3470 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 22.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.62 (0.28), residues: 833 helix: 1.58 (0.21), residues: 565 sheet: None (None), residues: 0 loop : -2.27 (0.33), residues: 268 Details of bonding type rmsd covalent geometry : bond 0.00803 ( 8782) covalent geometry : angle 0.76588 (12534) hydrogen bonds : bond 0.09967 ( 697) hydrogen bonds : angle 4.51404 ( 1797) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.182 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0365 time to fit residues: 1.3435 Evaluate side-chains 16 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 70 optimal weight: 50.0000 chunk 22 optimal weight: 50.0000 chunk 51 optimal weight: 30.0000 chunk 93 optimal weight: 10.0000 chunk 17 optimal weight: 50.0000 chunk 75 optimal weight: 20.0000 chunk 0 optimal weight: 80.0000 chunk 15 optimal weight: 40.0000 chunk 29 optimal weight: 10.0000 chunk 60 optimal weight: 50.0000 chunk 69 optimal weight: 5.9990 overall best weight: 15.1998 ------------------------------------------------------------------------------- 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 = 0.3520 r_free = 0.3520 target = 0.071678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.048847 restraints weight = 58152.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.049388 restraints weight = 44998.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.049224 restraints weight = 32444.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.049344 restraints weight = 34419.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.049369 restraints weight = 31764.197| |-----------------------------------------------------------------------------| r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.6689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 8782 Z= 0.372 Angle : 0.738 6.800 12534 Z= 0.468 Chirality : 0.041 0.155 936 Planarity : 0.004 0.022 1077 Dihedral : 32.569 155.092 3470 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 20.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.77 (0.28), residues: 833 helix: 1.77 (0.21), residues: 561 sheet: None (None), residues: 0 loop : -2.34 (0.33), residues: 272 Details of bonding type rmsd covalent geometry : bond 0.00751 ( 8782) covalent geometry : angle 0.73813 (12534) hydrogen bonds : bond 0.09254 ( 697) hydrogen bonds : angle 4.26580 ( 1797) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.175 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0363 time to fit residues: 1.3398 Evaluate side-chains 16 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 87 optimal weight: 20.0000 chunk 28 optimal weight: 50.0000 chunk 101 optimal weight: 50.0000 chunk 80 optimal weight: 10.0000 chunk 32 optimal weight: 20.0000 chunk 0 optimal weight: 80.0000 chunk 90 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 42 optimal weight: 40.0000 chunk 49 optimal weight: 30.0000 chunk 23 optimal weight: 30.0000 overall best weight: 14.0000 ------------------------------------------------------------------------------- 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 = 0.3527 r_free = 0.3527 target = 0.071981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.048798 restraints weight = 57536.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.049113 restraints weight = 44445.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.049143 restraints weight = 33512.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.049314 restraints weight = 31533.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.049366 restraints weight = 29386.285| |-----------------------------------------------------------------------------| r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.6873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 8782 Z= 0.353 Angle : 0.725 5.882 12534 Z= 0.459 Chirality : 0.041 0.157 936 Planarity : 0.004 0.021 1077 Dihedral : 32.501 152.946 3470 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 19.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.85 (0.29), residues: 833 helix: 1.91 (0.21), residues: 560 sheet: None (None), residues: 0 loop : -2.49 (0.34), residues: 273 Details of bonding type rmsd covalent geometry : bond 0.00715 ( 8782) covalent geometry : angle 0.72522 (12534) hydrogen bonds : bond 0.09000 ( 697) hydrogen bonds : angle 4.17977 ( 1797) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.184 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0352 time to fit residues: 1.2877 Evaluate side-chains 16 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 32 optimal weight: 20.0000 chunk 82 optimal weight: 10.0000 chunk 74 optimal weight: 30.0000 chunk 86 optimal weight: 10.0000 chunk 68 optimal weight: 40.0000 chunk 5 optimal weight: 30.0000 chunk 8 optimal weight: 30.0000 chunk 84 optimal weight: 10.0000 chunk 96 optimal weight: 50.0000 chunk 11 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 overall best weight: 12.0000 ------------------------------------------------------------------------------- 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 = 0.3542 r_free = 0.3542 target = 0.072629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.049542 restraints weight = 57337.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.049880 restraints weight = 41897.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.049867 restraints weight = 31656.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.049878 restraints weight = 31776.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.050091 restraints weight = 29777.897| |-----------------------------------------------------------------------------| r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.6908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 8782 Z= 0.310 Angle : 0.690 5.336 12534 Z= 0.437 Chirality : 0.039 0.158 936 Planarity : 0.003 0.021 1077 Dihedral : 32.400 151.906 3470 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.29 (0.30), residues: 833 helix: 2.25 (0.21), residues: 572 sheet: None (None), residues: 0 loop : -2.55 (0.35), residues: 261 Details of bonding type rmsd covalent geometry : bond 0.00626 ( 8782) covalent geometry : angle 0.68985 (12534) hydrogen bonds : bond 0.08136 ( 697) hydrogen bonds : angle 3.86442 ( 1797) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.183 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0365 time to fit residues: 1.3489 Evaluate side-chains 16 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 30 optimal weight: 40.0000 chunk 20 optimal weight: 20.0000 chunk 76 optimal weight: 10.0000 chunk 13 optimal weight: 40.0000 chunk 17 optimal weight: 50.0000 chunk 88 optimal weight: 20.0000 chunk 90 optimal weight: 10.0000 chunk 10 optimal weight: 0.0370 chunk 32 optimal weight: 30.0000 chunk 38 optimal weight: 7.9990 chunk 0 optimal weight: 80.0000 overall best weight: 9.6072 ------------------------------------------------------------------------------- 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 = 0.3535 r_free = 0.3535 target = 0.072583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.051979 restraints weight = 58398.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.052187 restraints weight = 45906.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.052193 restraints weight = 36879.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.052399 restraints weight = 34326.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.052430 restraints weight = 31409.065| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.6896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8782 Z= 0.267 Angle : 0.653 4.895 12534 Z= 0.414 Chirality : 0.036 0.161 936 Planarity : 0.003 0.021 1077 Dihedral : 32.206 149.099 3470 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.84 (0.30), residues: 833 helix: 2.77 (0.21), residues: 566 sheet: None (None), residues: 0 loop : -2.47 (0.35), residues: 267 Details of bonding type rmsd covalent geometry : bond 0.00539 ( 8782) covalent geometry : angle 0.65300 (12534) hydrogen bonds : bond 0.07189 ( 697) hydrogen bonds : angle 3.47376 ( 1797) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.159 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0366 time to fit residues: 1.2989 Evaluate side-chains 16 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 36 optimal weight: 20.0000 chunk 26 optimal weight: 40.0000 chunk 46 optimal weight: 50.0000 chunk 4 optimal weight: 0.0470 chunk 5 optimal weight: 30.0000 chunk 74 optimal weight: 30.0000 chunk 9 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 chunk 95 optimal weight: 20.0000 chunk 2 optimal weight: 0.0980 chunk 81 optimal weight: 10.0000 overall best weight: 8.0290 ------------------------------------------------------------------------------- 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 = 0.3558 r_free = 0.3558 target = 0.073649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.052682 restraints weight = 58199.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.052688 restraints weight = 46137.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.052893 restraints weight = 35902.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.053052 restraints weight = 33816.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.053110 restraints weight = 31431.161| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.6888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 8782 Z= 0.234 Angle : 0.618 4.708 12534 Z= 0.392 Chirality : 0.035 0.159 936 Planarity : 0.003 0.020 1077 Dihedral : 32.003 146.458 3470 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.45 (0.31), residues: 833 helix: 3.29 (0.21), residues: 565 sheet: None (None), residues: 0 loop : -2.38 (0.36), residues: 268 Details of bonding type rmsd covalent geometry : bond 0.00471 ( 8782) covalent geometry : angle 0.61806 (12534) hydrogen bonds : bond 0.06276 ( 697) hydrogen bonds : angle 3.09156 ( 1797) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1070.13 seconds wall clock time: 19 minutes 6.41 seconds (1146.41 seconds total)