Starting phenix.real_space_refine on Fri Sep 11 05:06:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6t7d_10394/09_2026/6t7d_10394.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t7d_10394/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6t7d_10394/09_2026/6t7d_10394.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t7d_10394/09_2026/6t7d_10394.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6t7d_10394/09_2026/6t7d_10394.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t7d_10394/09_2026/6t7d_10394.map" } 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-2.2.1-6174/lib/python3.11/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: 1.94, per 1000 atoms: 0.24 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: 0.78 Conformation dependent library (CDL) restraints added in 481.5 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: 1.21 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: 1.53 Time building geometry restraints manager: 1.02 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=" C3' DC I 13 " pdb=" O3' DC I 13 " ideal model delta sigma weight residual 1.435 1.492 -0.057 1.30e-02 5.92e+03 1.94e+01 bond pdb=" C3' DT I 95 " pdb=" C2' DT I 95 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.52e+01 bond pdb=" C5' DT I 37 " pdb=" C4' DT I 37 " ideal model delta sigma weight residual 1.512 1.537 -0.025 7.00e-03 2.04e+04 1.24e+01 bond pdb=" N7 DA J 53 " pdb=" C5 DA J 53 " ideal model delta sigma weight residual 1.388 1.368 0.020 6.00e-03 2.78e+04 1.16e+01 bond pdb=" C3' DG I 110 " pdb=" O3' DG I 110 " ideal model delta sigma weight residual 1.435 1.477 -0.042 1.30e-02 5.92e+03 1.07e+01 ... (remaining 8777 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 10409 1.31 - 2.62: 1777 2.62 - 3.93: 298 3.93 - 5.24: 43 5.24 - 6.55: 7 Bond angle restraints: 12534 Sorted by residual: angle pdb=" O4' DA J 53 " pdb=" C1' DA J 53 " pdb=" C2' DA J 53 " ideal model delta sigma weight residual 105.90 110.87 -4.97 8.00e-01 1.56e+00 3.85e+01 angle pdb=" O4' DT I 80 " pdb=" C4' DT I 80 " pdb=" C3' DT I 80 " ideal model delta sigma weight residual 106.00 102.57 3.43 6.00e-01 2.78e+00 3.27e+01 angle pdb=" O4' DA J 97 " pdb=" C4' DA J 97 " pdb=" C3' DA J 97 " ideal model delta sigma weight residual 106.00 102.81 3.19 6.00e-01 2.78e+00 2.83e+01 angle pdb=" O4' DA J 51 " pdb=" C1' DA J 51 " pdb=" N9 DA J 51 " ideal model delta sigma weight residual 108.00 104.55 3.45 7.00e-01 2.04e+00 2.43e+01 angle pdb=" O4' DA J 113 " pdb=" C4' DA J 113 " pdb=" C3' DA J 113 " ideal model delta sigma weight residual 106.00 103.05 2.95 6.00e-01 2.78e+00 2.42e+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 - 0.082: 850 0.082 - 0.164: 78 0.164 - 0.246: 7 0.246 - 0.328: 0 0.328 - 0.410: 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 2.43 2.02 0.41 2.00e-01 2.50e+01 4.19e+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 2.34 -2.55 -0.21 2.00e-01 2.50e+01 1.12e+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 2.34 -2.54 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (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: 0.220 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: 0.150 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 10.440 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 8782 Z= 0.637 Angle : 1.023 6.553 12534 Z= 0.949 Chirality : 0.051 0.410 936 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/Z covalent geometry : bond 0.00657 / 0.64 ( 8782) covalent geometry : angle 1.02268 / 0.95 (12534) hydrogen bonds : bond 0.12693 / 9.93 ( 697) hydrogen bonds : angle 5.32746 / 4.23 ( 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 : 0.193 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0370 time to fit residues: 1.3666 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 : 0.192 ------------------------------------------------------------------------------- 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: 10.0000 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: 12.3594 ------------------------------------------------------------------------------- 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 = 0.3636 r_free = 0.3636 target = 0.076861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.053727 restraints weight = 57781.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.054310 restraints weight = 44929.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.054428 restraints weight = 32735.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.054365 restraints weight = 32391.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.054442 restraints weight = 29792.871| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8782 Z= 0.259 Angle : 0.844 7.325 12534 Z= 0.507 Chirality : 0.061 0.292 936 Planarity : 0.005 0.014 1077 Dihedral : 32.179 157.580 3470 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % 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: 0.98 (0.28), residues: 833 helix: 1.19 (0.20), residues: 581 sheet: None (None), residues: 0 loop : -0.50 (0.38), residues: 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.26 ( 8782) covalent geometry : angle 0.84399 / 0.51 (12534) hydrogen bonds : bond 0.08211 / 6.41 ( 697) hydrogen bonds : angle 3.99530 / 3.19 ( 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: 0.0405 time to fit residues: 1.4852 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 : 0.269 ------------------------------------------------------------------------------- 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: 50.0000 chunk 91 optimal weight: 50.0000 chunk 87 optimal weight: 50.0000 chunk 45 optimal weight: 30.0000 chunk 15 optimal weight: 40.0000 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: 30.0000 overall best weight: 28.0000 ------------------------------------------------------------------------------- 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 = 0.3512 r_free = 0.3512 target = 0.071056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.048708 restraints weight = 58140.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.048814 restraints weight = 50948.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.048694 restraints weight = 45572.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.048730 restraints weight = 40913.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.048845 restraints weight = 37055.937| |-----------------------------------------------------------------------------| r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 8782 Z= 0.443 Angle : 1.072 9.244 12534 Z= 0.645 Chirality : 0.076 0.304 936 Planarity : 0.007 0.028 1077 Dihedral : 32.484 150.565 3470 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 32.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % 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: -0.82 (0.26), residues: 833 helix: 0.02 (0.20), residues: 584 sheet: None (None), residues: 0 loop : -1.73 (0.34), residues: 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.44 ( 8782) covalent geometry : angle 1.07234 / 0.65 (12534) hydrogen bonds : bond 0.17474 / 13.54 ( 697) hydrogen bonds : angle 5.88732 / 4.72 ( 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 : 0.128 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0341 time to fit residues: 1.3026 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 : 0.179 ------------------------------------------------------------------------------- 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: 9.9990 chunk 47 optimal weight: 30.0000 chunk 80 optimal weight: 50.0000 chunk 46 optimal weight: 6.9990 chunk 49 optimal weight: 30.0000 chunk 56 optimal weight: 20.0000 chunk 30 optimal weight: 20.0000 chunk 66 optimal weight: 50.0000 chunk 96 optimal weight: 0.0070 chunk 19 optimal weight: 30.0000 chunk 65 optimal weight: 50.0000 overall best weight: 11.4010 ------------------------------------------------------------------------------- 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 = 0.3580 r_free = 0.3580 target = 0.074175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.051415 restraints weight = 57190.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.051494 restraints weight = 46115.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.051515 restraints weight = 38481.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.051725 restraints weight = 34711.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.051718 restraints weight = 32358.290| |-----------------------------------------------------------------------------| r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 8782 Z= 0.222 Angle : 0.770 7.132 12534 Z= 0.470 Chirality : 0.060 0.318 936 Planarity : 0.004 0.018 1077 Dihedral : 32.564 157.675 3470 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % 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: 1.11 (0.28), residues: 833 helix: 1.71 (0.20), residues: 589 sheet: None (None), residues: 0 loop : -1.76 (0.35), residues: 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.22 ( 8782) covalent geometry : angle 0.77035 / 0.47 (12534) hydrogen bonds : bond 0.08519 / 6.61 ( 697) hydrogen bonds : angle 4.14878 / 3.34 ( 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 : 0.191 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0352 time to fit residues: 1.3073 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 : 0.190 ------------------------------------------------------------------------------- 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: 30.0000 chunk 60 optimal weight: 30.0000 chunk 87 optimal weight: 50.0000 chunk 8 optimal weight: 50.0000 chunk 48 optimal weight: 7.9990 chunk 91 optimal weight: 50.0000 chunk 51 optimal weight: 30.0000 chunk 10 optimal weight: 0.1980 chunk 62 optimal weight: 30.0000 chunk 64 optimal weight: 50.0000 chunk 70 optimal weight: 40.0000 overall best weight: 19.6394 ------------------------------------------------------------------------------- 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 = 0.3535 r_free = 0.3535 target = 0.072177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.049980 restraints weight = 57624.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.049933 restraints weight = 46929.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.049750 restraints weight = 41369.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.049867 restraints weight = 39878.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.049878 restraints weight = 37986.109| |-----------------------------------------------------------------------------| r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8782 Z= 0.326 Angle : 0.867 7.029 12534 Z= 0.525 Chirality : 0.064 0.318 936 Planarity : 0.005 0.020 1077 Dihedral : 32.512 157.099 3470 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 21.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % 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: 0.24 (0.28), residues: 833 helix: 1.10 (0.20), residues: 586 sheet: None (None), residues: 0 loop : -2.18 (0.34), residues: 247 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.33 ( 8782) covalent geometry : angle 0.86725 / 0.53 (12534) hydrogen bonds : bond 0.12136 / 9.43 ( 697) hydrogen bonds : angle 4.79132 / 3.85 ( 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 : 0.200 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0354 time to fit residues: 1.3327 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 : 0.195 ------------------------------------------------------------------------------- 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: 50.0000 chunk 22 optimal weight: 50.0000 chunk 52 optimal weight: 30.0000 chunk 66 optimal weight: 9.9990 chunk 15 optimal weight: 30.0000 chunk 80 optimal weight: 50.0000 chunk 88 optimal weight: 50.0000 chunk 98 optimal weight: 0.0030 chunk 60 optimal weight: 40.0000 chunk 30 optimal weight: 30.0000 chunk 70 optimal weight: 30.0000 overall best weight: 20.0004 ------------------------------------------------------------------------------- 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 = 0.3526 r_free = 0.3526 target = 0.071888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.049961 restraints weight = 57122.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.049882 restraints weight = 47283.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.049761 restraints weight = 41502.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.049894 restraints weight = 39155.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.049903 restraints weight = 37890.763| |-----------------------------------------------------------------------------| r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.5236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 8782 Z= 0.318 Angle : 0.872 7.772 12534 Z= 0.526 Chirality : 0.064 0.311 936 Planarity : 0.005 0.020 1077 Dihedral : 32.776 162.116 3470 Min Nonbonded Distance : 2.045 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: -0.28 (0.28), residues: 833 helix: 0.90 (0.20), residues: 576 sheet: None (None), residues: 0 loop : -2.76 (0.34), residues: 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.32 ( 8782) covalent geometry : angle 0.87164 / 0.53 (12534) hydrogen bonds : bond 0.10567 / 8.22 ( 697) hydrogen bonds : angle 4.92111 / 3.96 ( 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 : 0.155 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0361 time to fit residues: 1.3534 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 : 0.200 ------------------------------------------------------------------------------- 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: 40.0000 chunk 22 optimal weight: 50.0000 chunk 51 optimal weight: 30.0000 chunk 93 optimal weight: 50.0000 chunk 17 optimal weight: 50.0000 chunk 75 optimal weight: 50.0000 chunk 0 optimal weight: 80.0000 chunk 15 optimal weight: 30.0000 chunk 29 optimal weight: 10.0000 chunk 60 optimal weight: 40.0000 chunk 69 optimal weight: 20.0000 overall best weight: 26.0000 ------------------------------------------------------------------------------- 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 = 0.3474 r_free = 0.3474 target = 0.069714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.047235 restraints weight = 58552.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.047735 restraints weight = 45683.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.047722 restraints weight = 33237.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.047815 restraints weight = 34651.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.047855 restraints weight = 31096.680| |-----------------------------------------------------------------------------| r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.5819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 8782 Z= 0.419 Angle : 1.012 9.372 12534 Z= 0.600 Chirality : 0.071 0.326 936 Planarity : 0.006 0.023 1077 Dihedral : 32.876 161.961 3470 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 33.19 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.80 % Favored : 88.96 % 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: -1.44 (0.27), residues: 833 helix: -0.01 (0.20), residues: 579 sheet: None (None), residues: 0 loop : -3.16 (0.36), residues: 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.42 ( 8782) covalent geometry : angle 1.01194 / 0.60 (12534) hydrogen bonds : bond 0.15041 / 11.70 ( 697) hydrogen bonds : angle 5.78285 / 4.65 ( 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 : 0.200 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0359 time to fit residues: 1.3371 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 ------------------------------------------------------------------------------- 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: 50.0000 chunk 28 optimal weight: 50.0000 chunk 101 optimal weight: 50.0000 chunk 80 optimal weight: 50.0000 chunk 32 optimal weight: 6.9990 chunk 0 optimal weight: 60.0000 chunk 90 optimal weight: 50.0000 chunk 82 optimal weight: 50.0000 chunk 42 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 23 optimal weight: 30.0000 overall best weight: 23.3998 ------------------------------------------------------------------------------- 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 = 0.3486 r_free = 0.3486 target = 0.070265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.047530 restraints weight = 57608.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.047805 restraints weight = 46191.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.047790 restraints weight = 37821.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.047977 restraints weight = 34498.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.047946 restraints weight = 34406.508| |-----------------------------------------------------------------------------| r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.6003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 8782 Z= 0.365 Angle : 0.943 9.201 12534 Z= 0.562 Chirality : 0.068 0.311 936 Planarity : 0.005 0.021 1077 Dihedral : 33.005 167.140 3470 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 27.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % 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: -1.36 (0.28), residues: 833 helix: 0.14 (0.20), residues: 566 sheet: None (None), residues: 0 loop : -3.21 (0.35), residues: 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.36 ( 8782) covalent geometry : angle 0.94329 / 0.56 (12534) hydrogen bonds : bond 0.12086 / 9.43 ( 697) hydrogen bonds : angle 5.47060 / 4.40 ( 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 : 0.204 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0367 time to fit residues: 1.3810 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 : 0.171 ------------------------------------------------------------------------------- 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: 10.0000 chunk 82 optimal weight: 50.0000 chunk 74 optimal weight: 50.0000 chunk 86 optimal weight: 50.0000 chunk 68 optimal weight: 6.9990 chunk 5 optimal weight: 30.0000 chunk 8 optimal weight: 30.0000 chunk 84 optimal weight: 50.0000 chunk 96 optimal weight: 60.0000 chunk 11 optimal weight: 20.0000 chunk 91 optimal weight: 50.0000 overall best weight: 19.3998 ------------------------------------------------------------------------------- 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 = 0.3497 r_free = 0.3497 target = 0.070812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.047486 restraints weight = 57628.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.047768 restraints weight = 44177.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.047964 restraints weight = 35467.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.048130 restraints weight = 30149.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.048170 restraints weight = 28876.397| |-----------------------------------------------------------------------------| r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.6141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8782 Z= 0.324 Angle : 0.892 8.511 12534 Z= 0.533 Chirality : 0.065 0.323 936 Planarity : 0.005 0.021 1077 Dihedral : 32.952 167.613 3470 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 25.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % 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: -0.93 (0.28), residues: 833 helix: 0.54 (0.21), residues: 567 sheet: None (None), residues: 0 loop : -3.24 (0.35), residues: 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.32 ( 8782) covalent geometry : angle 0.89178 / 0.53 (12534) hydrogen bonds : bond 0.11516 / 8.99 ( 697) hydrogen bonds : angle 5.11540 / 4.11 ( 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 : 0.122 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0339 time to fit residues: 1.2650 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 : 0.220 ------------------------------------------------------------------------------- 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: 50.0000 chunk 20 optimal weight: 10.0000 chunk 76 optimal weight: 50.0000 chunk 13 optimal weight: 7.9990 chunk 17 optimal weight: 50.0000 chunk 88 optimal weight: 50.0000 chunk 90 optimal weight: 50.0000 chunk 10 optimal weight: 3.9990 chunk 32 optimal weight: 30.0000 chunk 38 optimal weight: 10.0000 chunk 0 optimal weight: 60.0000 overall best weight: 12.3996 ------------------------------------------------------------------------------- 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 = 0.3537 r_free = 0.3537 target = 0.072626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.049518 restraints weight = 56582.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.049604 restraints weight = 46984.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.049778 restraints weight = 36194.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.049883 restraints weight = 34500.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.049964 restraints weight = 30501.610| |-----------------------------------------------------------------------------| r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.6052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 8782 Z= 0.240 Angle : 0.795 7.253 12534 Z= 0.479 Chirality : 0.060 0.328 936 Planarity : 0.004 0.019 1077 Dihedral : 32.914 167.335 3470 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 17.66 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: 0.31 (0.30), residues: 833 helix: 1.59 (0.21), residues: 567 sheet: None (None), residues: 0 loop : -3.04 (0.35), residues: 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.24 ( 8782) covalent geometry : angle 0.79474 / 0.48 (12534) hydrogen bonds : bond 0.08897 / 6.95 ( 697) hydrogen bonds : angle 4.30991 / 3.47 ( 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 : 0.201 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0363 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 : 0.197 ------------------------------------------------------------------------------- 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: 50.0000 chunk 46 optimal weight: 40.0000 chunk 4 optimal weight: 20.0000 chunk 5 optimal weight: 30.0000 chunk 74 optimal weight: 60.0000 chunk 9 optimal weight: 50.0000 chunk 89 optimal weight: 50.0000 chunk 95 optimal weight: 50.0000 chunk 2 optimal weight: 0.6980 chunk 81 optimal weight: 50.0000 overall best weight: 22.1396 ------------------------------------------------------------------------------- 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 = 0.3490 r_free = 0.3490 target = 0.070409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.047642 restraints weight = 57947.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.048043 restraints weight = 46949.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.047984 restraints weight = 36986.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.048171 restraints weight = 35741.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.048172 restraints weight = 32304.631| |-----------------------------------------------------------------------------| r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.6341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 8782 Z= 0.359 Angle : 0.920 8.288 12534 Z= 0.549 Chirality : 0.065 0.334 936 Planarity : 0.005 0.020 1077 Dihedral : 32.865 165.354 3470 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 26.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.40 % Favored : 88.60 % 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: -0.82 (0.28), residues: 833 helix: 0.67 (0.21), residues: 567 sheet: None (None), residues: 0 loop : -3.33 (0.35), residues: 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.36 ( 8782) covalent geometry : angle 0.92014 / 0.55 (12534) hydrogen bonds : bond 0.12530 / 9.76 ( 697) hydrogen bonds : angle 5.21196 / 4.19 ( 1797) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1074.62 seconds wall clock time: 19 minutes 17.27 seconds (1157.27 seconds total)