Starting phenix.real_space_refine on Sun Jul 5 23:11:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j8o_61233/07_2026/9j8o_61233.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j8o_61233/07_2026/9j8o_61233.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9j8o_61233/07_2026/9j8o_61233.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j8o_61233/07_2026/9j8o_61233.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9j8o_61233/07_2026/9j8o_61233.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j8o_61233/07_2026/9j8o_61233.map" } resolution = 4.05 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= 0.001 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 704 5.49 5 S 54 5.16 5 C 17970 2.51 5 N 5970 2.21 5 O 7418 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32116 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 75} Chain: "C" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 805 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 3591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 3591 Classifications: {'DNA': 176} Link IDs: {'rna3p': 175} Chain: "J" Number of atoms: 3625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 3625 Classifications: {'DNA': 176} Link IDs: {'rna3p': 175} Chain: "K" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 697 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "L" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 697 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "M" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 928 Classifications: {'peptide': 119} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 113} Chain: "N" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 555 Classifications: {'peptide': 78} Link IDs: {'TRANS': 77} Chain: "a" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "b" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 75} Chain: "c" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "d" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "e" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "f" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "g" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 805 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "h" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "i" Number of atoms: 3591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 3591 Classifications: {'DNA': 176} Link IDs: {'rna3p': 175} Chain: "j" Number of atoms: 3625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 3625 Classifications: {'DNA': 176} Link IDs: {'rna3p': 175} Chain: "k" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 697 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "l" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 697 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "m" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 928 Classifications: {'peptide': 119} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 113} Chain: "n" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 555 Classifications: {'peptide': 78} Link IDs: {'TRANS': 77} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ARG M 453 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG M 453 " occ=0.50 residue: pdb=" N ARG m 453 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG m 453 " occ=0.50 Time building chain proxies: 5.99, per 1000 atoms: 0.19 Number of scatterers: 32116 At special positions: 0 Unit cell: (200.34, 168.54, 180.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 54 16.00 P 704 15.00 O 7418 8.00 N 5970 7.00 C 17970 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: 2.63 Conformation dependent library (CDL) restraints added in 795.9 milliseconds 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4148 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 28 sheets defined 65.5% alpha, 6.8% beta 352 base pairs and 582 stacking pairs defined. Time for finding SS restraints: 4.20 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.599A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.536A pdb=" N GLY A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.594A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.853A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.633A pdb=" N ASN C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.507A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 removed outlier: 3.504A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.556A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (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 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.604A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.632A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.687A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.658A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.792A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 13 removed outlier: 4.263A pdb=" N GLU K 13 " --> pdb=" O ASP K 9 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 23 Processing helix chain 'K' and resid 27 through 38 Processing helix chain 'K' and resid 41 through 52 removed outlier: 3.524A pdb=" N LEU K 52 " --> pdb=" O GLN K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 68 Processing helix chain 'K' and resid 70 through 89 Processing helix chain 'L' and resid 4 through 13 removed outlier: 4.197A pdb=" N GLU L 13 " --> pdb=" O ASP L 9 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 23 Processing helix chain 'L' and resid 27 through 38 Processing helix chain 'L' and resid 41 through 52 removed outlier: 3.543A pdb=" N VAL L 45 " --> pdb=" O LYS L 41 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 68 Processing helix chain 'L' and resid 70 through 88 Processing helix chain 'M' and resid 501 through 503 No H-bonds generated for 'chain 'M' and resid 501 through 503' Processing helix chain 'N' and resid 42 through 54 Processing helix chain 'N' and resid 62 through 72 Processing helix chain 'N' and resid 79 through 93 Processing helix chain 'N' and resid 102 through 105 removed outlier: 3.842A pdb=" N SER N 105 " --> pdb=" O THR N 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 102 through 105' Processing helix chain 'N' and resid 113 through 117 Processing helix chain 'a' and resid 44 through 57 Processing helix chain 'a' and resid 63 through 76 removed outlier: 3.501A pdb=" N PHE a 67 " --> pdb=" O ARG a 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 85 through 114 Processing helix chain 'a' and resid 120 through 132 Processing helix chain 'b' and resid 25 through 29 Processing helix chain 'b' and resid 30 through 41 Processing helix chain 'b' and resid 49 through 76 removed outlier: 4.234A pdb=" N ASP b 68 " --> pdb=" O ASN b 64 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 93 removed outlier: 3.637A pdb=" N VAL b 86 " --> pdb=" O THR b 82 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN b 93 " --> pdb=" O ALA b 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 16 through 21 Processing helix chain 'c' and resid 26 through 37 Processing helix chain 'c' and resid 45 through 73 removed outlier: 4.420A pdb=" N VAL c 49 " --> pdb=" O ALA c 45 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN c 73 " --> pdb=" O ALA c 69 " (cutoff:3.500A) Processing helix chain 'c' and resid 79 through 89 Processing helix chain 'c' and resid 90 through 97 Processing helix chain 'd' and resid 37 through 49 Processing helix chain 'd' and resid 55 through 84 removed outlier: 3.540A pdb=" N ASN d 84 " --> pdb=" O LEU d 80 " (cutoff:3.500A) Processing helix chain 'd' and resid 90 through 102 removed outlier: 3.696A pdb=" N ILE d 94 " --> pdb=" O THR d 90 " (cutoff:3.500A) Processing helix chain 'd' and resid 104 through 124 removed outlier: 3.786A pdb=" N LYS d 108 " --> pdb=" O GLY d 104 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA d 124 " --> pdb=" O LYS d 120 " (cutoff:3.500A) Processing helix chain 'e' and resid 44 through 57 Processing helix chain 'e' and resid 63 through 77 removed outlier: 3.601A pdb=" N PHE e 67 " --> pdb=" O ARG e 63 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASP e 77 " --> pdb=" O GLU e 73 " (cutoff:3.500A) Processing helix chain 'e' and resid 85 through 114 Processing helix chain 'e' and resid 120 through 132 Processing helix chain 'f' and resid 25 through 29 Processing helix chain 'f' and resid 30 through 42 Processing helix chain 'f' and resid 49 through 76 removed outlier: 3.721A pdb=" N GLU f 53 " --> pdb=" O LEU f 49 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP f 68 " --> pdb=" O ASN f 64 " (cutoff:3.500A) Processing helix chain 'f' and resid 82 through 93 removed outlier: 3.576A pdb=" N VAL f 86 " --> pdb=" O THR f 82 " (cutoff:3.500A) Processing helix chain 'g' and resid 16 through 21 Processing helix chain 'g' and resid 26 through 37 Processing helix chain 'g' and resid 45 through 72 removed outlier: 4.547A pdb=" N VAL g 49 " --> pdb=" O ALA g 45 " (cutoff:3.500A) Processing helix chain 'g' and resid 79 through 89 removed outlier: 3.501A pdb=" N LEU g 83 " --> pdb=" O ILE g 79 " (cutoff:3.500A) Processing helix chain 'g' and resid 90 through 97 Processing helix chain 'h' and resid 37 through 49 Processing helix chain 'h' and resid 55 through 84 Processing helix chain 'h' and resid 90 through 102 removed outlier: 3.698A pdb=" N ILE h 94 " --> pdb=" O THR h 90 " (cutoff:3.500A) Processing helix chain 'h' and resid 104 through 124 removed outlier: 3.818A pdb=" N LYS h 108 " --> pdb=" O GLY h 104 " (cutoff:3.500A) Processing helix chain 'k' and resid 4 through 13 removed outlier: 4.312A pdb=" N GLU k 13 " --> pdb=" O ASP k 9 " (cutoff:3.500A) Processing helix chain 'k' and resid 19 through 23 Processing helix chain 'k' and resid 27 through 38 Processing helix chain 'k' and resid 41 through 52 removed outlier: 3.614A pdb=" N LEU k 52 " --> pdb=" O GLN k 48 " (cutoff:3.500A) Processing helix chain 'k' and resid 55 through 67 removed outlier: 3.740A pdb=" N PHE k 59 " --> pdb=" O ASP k 55 " (cutoff:3.500A) Processing helix chain 'k' and resid 70 through 89 Processing helix chain 'l' and resid 4 through 13 removed outlier: 4.084A pdb=" N GLU l 13 " --> pdb=" O ASP l 9 " (cutoff:3.500A) Processing helix chain 'l' and resid 19 through 23 Processing helix chain 'l' and resid 27 through 38 Processing helix chain 'l' and resid 41 through 52 removed outlier: 3.524A pdb=" N VAL l 45 " --> pdb=" O LYS l 41 " (cutoff:3.500A) Processing helix chain 'l' and resid 55 through 68 Processing helix chain 'l' and resid 70 through 89 Processing helix chain 'n' and resid 42 through 54 Processing helix chain 'n' and resid 61 through 72 Processing helix chain 'n' and resid 79 through 93 Processing helix chain 'n' and resid 102 through 106 removed outlier: 4.115A pdb=" N SER n 105 " --> pdb=" O THR n 102 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY n 106 " --> pdb=" O GLY n 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 102 through 106' Processing helix chain 'n' and resid 113 through 117 removed outlier: 3.726A pdb=" N VAL n 117 " --> pdb=" O ALA n 114 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.969A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.432A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.951A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.348A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.884A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'M' and resid 430 through 436 Processing sheet with id=AB3, first strand: chain 'M' and resid 440 through 445 removed outlier: 6.745A pdb=" N ARG M 453 " --> pdb=" O GLU M 443 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N VAL M 445 " --> pdb=" O PHE M 451 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N PHE M 451 " --> pdb=" O VAL M 445 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LEU M 512 " --> pdb=" O VAL M 494 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N THR M 496 " --> pdb=" O LEU M 512 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N TRP M 514 " --> pdb=" O THR M 496 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N TRP M 498 " --> pdb=" O TRP M 514 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 462 through 463 Processing sheet with id=AB5, first strand: chain 'N' and resid 60 through 61 removed outlier: 3.531A pdb=" N LYS N 100 " --> pdb=" O SER N 107 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LYS N 109 " --> pdb=" O GLN N 98 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N GLN N 98 " --> pdb=" O LYS N 109 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'a' and resid 83 through 84 removed outlier: 7.312A pdb=" N ARG a 83 " --> pdb=" O VAL b 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'a' and resid 118 through 119 Processing sheet with id=AB8, first strand: chain 'b' and resid 97 through 98 Processing sheet with id=AB9, first strand: chain 'c' and resid 42 through 43 removed outlier: 7.756A pdb=" N ARG c 42 " --> pdb=" O ILE d 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'c' and resid 77 through 78 Processing sheet with id=AC2, first strand: chain 'c' and resid 101 through 102 removed outlier: 6.853A pdb=" N THR c 101 " --> pdb=" O TYR f 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'e' and resid 83 through 84 removed outlier: 7.199A pdb=" N ARG e 83 " --> pdb=" O VAL f 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'e' and resid 118 through 119 Processing sheet with id=AC5, first strand: chain 'g' and resid 42 through 43 removed outlier: 7.696A pdb=" N ARG g 42 " --> pdb=" O ILE h 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'g' and resid 77 through 78 Processing sheet with id=AC7, first strand: chain 'm' and resid 430 through 436 removed outlier: 3.569A pdb=" N ALA m 539 " --> pdb=" O LEU m 530 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'm' and resid 440 through 445 removed outlier: 5.508A pdb=" N VAL m 442 " --> pdb=" O ARG m 455 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ARG m 455 " --> pdb=" O VAL m 442 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N LEU m 512 " --> pdb=" O VAL m 494 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N THR m 496 " --> pdb=" O LEU m 512 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N TRP m 514 " --> pdb=" O THR m 496 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N TRP m 498 " --> pdb=" O TRP m 514 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'm' and resid 462 through 463 Processing sheet with id=AD1, first strand: chain 'n' and resid 96 through 100 removed outlier: 6.399A pdb=" N SER n 107 " --> pdb=" O THR n 99 " (cutoff:3.500A) 1101 hydrogen bonds defined for protein. 3222 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 906 hydrogen bonds 1812 hydrogen bond angles 0 basepair planarities 352 basepair parallelities 582 stacking parallelities Total time for adding SS restraints: 6.05 Time building geometry restraints manager: 3.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5535 1.33 - 1.45: 11295 1.45 - 1.57: 15810 1.57 - 1.69: 1404 1.69 - 1.81: 82 Bond restraints: 34126 Sorted by residual: bond pdb=" C3' DC I 28 " pdb=" C2' DC I 28 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.32e+01 bond pdb=" C3' DG J 175 " pdb=" C2' DG J 175 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.23e+01 bond pdb=" C3' DT j 32 " pdb=" C2' DT j 32 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.18e+01 bond pdb=" C3' DG j 170 " pdb=" O3' DG j 170 " ideal model delta sigma weight residual 1.435 1.391 0.044 1.30e-02 5.92e+03 1.12e+01 bond pdb=" C3' DA J 65 " pdb=" O3' DA J 65 " ideal model delta sigma weight residual 1.435 1.392 0.043 1.30e-02 5.92e+03 1.11e+01 ... (remaining 34121 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 45671 1.58 - 3.16: 3219 3.16 - 4.75: 153 4.75 - 6.33: 28 6.33 - 7.91: 3 Bond angle restraints: 49074 Sorted by residual: angle pdb=" N VAL a 117 " pdb=" CA VAL a 117 " pdb=" C VAL a 117 " ideal model delta sigma weight residual 113.71 108.09 5.62 9.50e-01 1.11e+00 3.50e+01 angle pdb=" O4' DG J 81 " pdb=" C4' DG J 81 " pdb=" C3' DG J 81 " ideal model delta sigma weight residual 106.00 102.89 3.11 6.00e-01 2.78e+00 2.68e+01 angle pdb=" O4' DA i 64 " pdb=" C4' DA i 64 " pdb=" C3' DA i 64 " ideal model delta sigma weight residual 106.00 102.97 3.03 6.00e-01 2.78e+00 2.55e+01 angle pdb=" N VAL E 117 " pdb=" CA VAL E 117 " pdb=" C VAL E 117 " ideal model delta sigma weight residual 113.53 108.75 4.78 9.80e-01 1.04e+00 2.38e+01 angle pdb=" N3 DT I 60 " pdb=" C4 DT I 60 " pdb=" O4 DT I 60 " ideal model delta sigma weight residual 119.90 122.79 -2.89 6.00e-01 2.78e+00 2.33e+01 ... (remaining 49069 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.22: 15360 35.22 - 70.44: 3264 70.44 - 105.66: 28 105.66 - 140.88: 0 140.88 - 176.10: 4 Dihedral angle restraints: 18656 sinusoidal: 12214 harmonic: 6442 Sorted by residual: dihedral pdb=" CA ASN C 73 " pdb=" C ASN C 73 " pdb=" N LYS C 74 " pdb=" CA LYS C 74 " ideal model delta harmonic sigma weight residual 180.00 157.50 22.50 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" C4' DT j 153 " pdb=" C3' DT j 153 " pdb=" O3' DT j 153 " pdb=" P DC j 154 " ideal model delta sinusoidal sigma weight residual 220.00 43.90 176.10 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT J 153 " pdb=" C3' DT J 153 " pdb=" O3' DT J 153 " pdb=" P DC J 154 " ideal model delta sinusoidal sigma weight residual 220.00 53.66 166.34 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 18653 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 3189 0.037 - 0.073: 1562 0.073 - 0.110: 569 0.110 - 0.146: 199 0.146 - 0.183: 19 Chirality restraints: 5538 Sorted by residual: chirality pdb=" C3' DC J 118 " pdb=" C4' DC J 118 " pdb=" O3' DC J 118 " pdb=" C2' DC J 118 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.33e-01 chirality pdb=" C3' DT J 153 " pdb=" C4' DT J 153 " pdb=" O3' DT J 153 " pdb=" C2' DT J 153 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.27e-01 chirality pdb=" C3' DG i 108 " pdb=" C4' DG i 108 " pdb=" O3' DG i 108 " pdb=" C2' DG i 108 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.17e-01 ... (remaining 5535 not shown) Planarity restraints: 3788 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I 86 " -0.029 2.00e-02 2.50e+03 1.30e-02 4.68e+00 pdb=" N9 DA I 86 " 0.029 2.00e-02 2.50e+03 pdb=" C8 DA I 86 " 0.006 2.00e-02 2.50e+03 pdb=" N7 DA I 86 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DA I 86 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DA I 86 " -0.003 2.00e-02 2.50e+03 pdb=" N6 DA I 86 " -0.010 2.00e-02 2.50e+03 pdb=" N1 DA I 86 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 86 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DA I 86 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DA I 86 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 73 " 0.026 2.00e-02 2.50e+03 1.27e-02 4.03e+00 pdb=" N1 DT I 73 " -0.026 2.00e-02 2.50e+03 pdb=" C2 DT I 73 " -0.003 2.00e-02 2.50e+03 pdb=" O2 DT I 73 " -0.007 2.00e-02 2.50e+03 pdb=" N3 DT I 73 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DT I 73 " 0.005 2.00e-02 2.50e+03 pdb=" O4 DT I 73 " 0.011 2.00e-02 2.50e+03 pdb=" C5 DT I 73 " 0.001 2.00e-02 2.50e+03 pdb=" C7 DT I 73 " -0.007 2.00e-02 2.50e+03 pdb=" C6 DT I 73 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG i 146 " 0.028 2.00e-02 2.50e+03 1.12e-02 3.80e+00 pdb=" N9 DG i 146 " -0.024 2.00e-02 2.50e+03 pdb=" C8 DG i 146 " -0.006 2.00e-02 2.50e+03 pdb=" N7 DG i 146 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DG i 146 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG i 146 " 0.002 2.00e-02 2.50e+03 pdb=" O6 DG i 146 " 0.010 2.00e-02 2.50e+03 pdb=" N1 DG i 146 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DG i 146 " 0.001 2.00e-02 2.50e+03 pdb=" N2 DG i 146 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DG i 146 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DG i 146 " -0.002 2.00e-02 2.50e+03 ... (remaining 3785 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 953 2.67 - 3.23: 28559 3.23 - 3.78: 58978 3.78 - 4.34: 73968 4.34 - 4.90: 107675 Nonbonded interactions: 270133 Sorted by model distance: nonbonded pdb=" O THR c 16 " pdb=" OG SER c 19 " model vdw 2.111 3.040 nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 68 " model vdw 2.127 3.040 nonbonded pdb=" OD2 ASP D 68 " pdb=" OH TYR F 98 " model vdw 2.156 3.040 nonbonded pdb=" O THR g 16 " pdb=" OG SER g 19 " model vdw 2.163 3.040 nonbonded pdb=" OH TYR e 99 " pdb=" OE1 GLU e 133 " model vdw 2.169 3.040 ... (remaining 270128 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 38 through 133) selection = chain 'a' selection = (chain 'e' and resid 38 through 133) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 25 through 102) selection = chain 'b' selection = (chain 'f' and resid 25 through 102) } ncs_group { reference = (chain 'C' and resid 15 through 118) selection = chain 'G' selection = (chain 'c' and resid 15 through 118) selection = chain 'g' } ncs_group { reference = (chain 'D' and resid 34 through 124) selection = chain 'H' selection = (chain 'd' and resid 34 through 124) selection = chain 'h' } ncs_group { reference = chain 'I' selection = chain 'i' } ncs_group { reference = chain 'J' selection = chain 'j' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'k' selection = chain 'l' } ncs_group { reference = chain 'M' selection = chain 'm' } ncs_group { reference = chain 'N' selection = chain 'n' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 1.070 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: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 28.380 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6507 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 : 0.008 0.051 34126 Z= 0.610 Angle : 0.800 7.912 49074 Z= 0.670 Chirality : 0.049 0.183 5538 Planarity : 0.004 0.032 3788 Dihedral : 26.588 176.098 14508 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.38 % Allowed : 8.00 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.09 % 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: 1.66 (0.18), residues: 2202 helix: 1.82 (0.14), residues: 1394 sheet: 1.50 (0.49), residues: 120 loop : -0.45 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 55 TYR 0.016 0.002 TYR L 43 PHE 0.009 0.001 PHE b 100 TRP 0.007 0.001 TRP L 84 HIS 0.006 0.001 HIS f 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00812 / 0.61 (34126) covalent geometry : angle 0.80009 / 0.67 (49074) hydrogen bonds : bond 0.10256 / 7.18 ( 2007) hydrogen bonds : angle 4.16498 / 2.97 ( 5034) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 412 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 15 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.7338 (mtp) REVERT: b 97 LEU cc_start: 0.8316 (tp) cc_final: 0.8071 (tt) REVERT: e 130 ILE cc_start: 0.8056 (mt) cc_final: 0.7809 (mt) REVERT: k 32 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.8162 (tppp) outliers start: 63 outliers final: 9 residues processed: 456 average time/residue: 0.2012 time to fit residues: 145.5644 Evaluate side-chains 152 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 141 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 50.0000 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 0.2980 chunk 183 optimal weight: 30.0000 chunk 111 optimal weight: 8.9990 overall best weight: 5.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN D 109 HIS E 39 HIS E 68 GLN F 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN K 48 GLN N 98 GLN a 76 GLN b 93 GLN c 112 GLN d 84 ASN d 95 GLN d 109 HIS e 93 GLN g 112 GLN ** h 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 95 GLN l 48 GLN m 433 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.044288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.030473 restraints weight = 394531.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.030816 restraints weight = 194695.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.031136 restraints weight = 131261.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.031341 restraints weight = 107278.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.031406 restraints weight = 97243.201| |-----------------------------------------------------------------------------| r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2898 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2898 r_free = 0.2898 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.2897 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 34126 Z= 0.190 Angle : 0.674 8.481 49074 Z= 0.396 Chirality : 0.044 0.257 5538 Planarity : 0.005 0.062 3788 Dihedral : 30.196 177.884 10138 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.09 % 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: 1.91 (0.18), residues: 2202 helix: 1.99 (0.14), residues: 1404 sheet: 1.89 (0.51), residues: 114 loop : -0.34 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG a 131 TYR 0.027 0.002 TYR b 98 PHE 0.025 0.002 PHE M 451 TRP 0.016 0.002 TRP m 467 HIS 0.022 0.003 HIS d 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.19 (34126) covalent geometry : angle 0.67395 / 0.40 (49074) hydrogen bonds : bond 0.05605 / 3.83 ( 2007) hydrogen bonds : angle 3.53916 / 2.52 ( 5034) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8495 (tm-30) cc_final: 0.8257 (tm-30) REVERT: B 59 LYS cc_start: 0.9503 (tppt) cc_final: 0.9256 (tppt) REVERT: B 85 ASP cc_start: 0.8341 (m-30) cc_final: 0.8060 (m-30) REVERT: C 72 ASP cc_start: 0.8441 (m-30) cc_final: 0.8041 (m-30) REVERT: D 93 GLU cc_start: 0.9381 (mp0) cc_final: 0.9158 (mp0) REVERT: E 93 GLN cc_start: 0.9321 (tt0) cc_final: 0.8894 (tm-30) REVERT: E 120 MET cc_start: 0.8879 (mmp) cc_final: 0.8521 (mmm) REVERT: F 84 MET cc_start: 0.8730 (tpp) cc_final: 0.8191 (mmm) REVERT: H 59 MET cc_start: 0.8966 (tpp) cc_final: 0.8704 (tpp) REVERT: H 62 MET cc_start: 0.9486 (mmm) cc_final: 0.9020 (mmm) REVERT: K 76 ASP cc_start: 0.8905 (t0) cc_final: 0.8603 (t0) REVERT: L 83 GLU cc_start: 0.9452 (tp30) cc_final: 0.8811 (tp30) REVERT: a 105 GLU cc_start: 0.9231 (tm-30) cc_final: 0.8884 (tm-30) REVERT: a 112 ILE cc_start: 0.9107 (mt) cc_final: 0.8884 (mt) REVERT: a 120 MET cc_start: 0.8676 (mtp) cc_final: 0.8279 (mtt) REVERT: b 49 LEU cc_start: 0.9685 (mp) cc_final: 0.8640 (mm) REVERT: b 53 GLU cc_start: 0.9649 (mm-30) cc_final: 0.9212 (mm-30) REVERT: b 85 ASP cc_start: 0.8136 (m-30) cc_final: 0.7587 (t0) REVERT: c 90 ASP cc_start: 0.9043 (t70) cc_final: 0.8801 (t0) REVERT: d 76 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8580 (mm-30) REVERT: e 105 GLU cc_start: 0.8881 (tm-30) cc_final: 0.8675 (tm-30) REVERT: e 120 MET cc_start: 0.8985 (mmp) cc_final: 0.8660 (mmm) REVERT: e 124 ILE cc_start: 0.9716 (tt) cc_final: 0.9299 (tt) REVERT: h 59 MET cc_start: 0.9186 (tpp) cc_final: 0.8975 (tpp) REVERT: h 62 MET cc_start: 0.9432 (mmm) cc_final: 0.9192 (mmm) REVERT: k 15 MET cc_start: 0.8960 (ptm) cc_final: 0.8685 (ppp) REVERT: l 15 MET cc_start: 0.8468 (ptp) cc_final: 0.7956 (mtp) REVERT: l 89 LEU cc_start: 0.7824 (tt) cc_final: 0.7203 (tt) REVERT: m 526 LEU cc_start: 0.9685 (mt) cc_final: 0.9446 (mt) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.1783 time to fit residues: 67.7743 Evaluate side-chains 144 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 44 optimal weight: 0.1980 chunk 174 optimal weight: 20.0000 chunk 19 optimal weight: 2.9990 chunk 108 optimal weight: 9.9990 chunk 147 optimal weight: 3.9990 chunk 134 optimal weight: 30.0000 chunk 25 optimal weight: 20.0000 chunk 132 optimal weight: 40.0000 chunk 1 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 chunk 57 optimal weight: 0.0470 overall best weight: 2.8484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 48 GLN a 68 GLN c 112 GLN ** h 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.044329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.030514 restraints weight = 393254.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.030857 restraints weight = 194473.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.031174 restraints weight = 130668.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.031386 restraints weight = 106965.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.031497 restraints weight = 97086.470| |-----------------------------------------------------------------------------| r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2902 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2902 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 34126 Z= 0.148 Angle : 0.595 6.836 49074 Z= 0.361 Chirality : 0.041 0.259 5538 Planarity : 0.004 0.045 3788 Dihedral : 30.177 178.231 10138 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.05 % Allowed : 1.56 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.09 % 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: 2.26 (0.18), residues: 2202 helix: 2.22 (0.14), residues: 1414 sheet: 1.90 (0.49), residues: 114 loop : -0.11 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG m 545 TYR 0.013 0.001 TYR G 50 PHE 0.016 0.001 PHE e 67 TRP 0.012 0.001 TRP K 62 HIS 0.010 0.001 HIS f 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.15 (34126) covalent geometry : angle 0.59457 / 0.36 (49074) hydrogen bonds : bond 0.04479 / 3.05 ( 2007) hydrogen bonds : angle 3.28271 / 2.35 ( 5034) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 197 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8373 (tm-30) REVERT: A 120 MET cc_start: 0.9001 (mmp) cc_final: 0.8770 (mmm) REVERT: B 59 LYS cc_start: 0.9540 (tppt) cc_final: 0.9303 (tppt) REVERT: B 85 ASP cc_start: 0.8301 (m-30) cc_final: 0.8038 (m-30) REVERT: C 72 ASP cc_start: 0.8445 (m-30) cc_final: 0.8037 (m-30) REVERT: E 93 GLN cc_start: 0.9314 (tt0) cc_final: 0.8937 (tm-30) REVERT: E 120 MET cc_start: 0.8930 (mmp) cc_final: 0.8554 (mmm) REVERT: K 76 ASP cc_start: 0.8930 (t0) cc_final: 0.8639 (t70) REVERT: L 83 GLU cc_start: 0.9437 (tp30) cc_final: 0.8760 (tp30) REVERT: M 443 GLU cc_start: 0.9253 (tt0) cc_final: 0.8886 (pt0) REVERT: a 105 GLU cc_start: 0.9250 (tm-30) cc_final: 0.8958 (tm-30) REVERT: a 120 MET cc_start: 0.8609 (mtp) cc_final: 0.8194 (mtt) REVERT: b 49 LEU cc_start: 0.9495 (mp) cc_final: 0.8653 (mm) REVERT: b 52 GLU cc_start: 0.8899 (pm20) cc_final: 0.8341 (pm20) REVERT: b 53 GLU cc_start: 0.9660 (mm-30) cc_final: 0.9221 (mm-30) REVERT: b 84 MET cc_start: 0.8755 (mmm) cc_final: 0.8400 (mmm) REVERT: b 85 ASP cc_start: 0.8117 (m-30) cc_final: 0.7518 (t0) REVERT: c 90 ASP cc_start: 0.8984 (t70) cc_final: 0.8726 (t0) REVERT: d 76 GLU cc_start: 0.8837 (mm-30) cc_final: 0.8538 (mm-30) REVERT: e 120 MET cc_start: 0.9088 (mmp) cc_final: 0.8759 (mmm) REVERT: h 62 MET cc_start: 0.9441 (mmm) cc_final: 0.9231 (mmm) REVERT: l 15 MET cc_start: 0.8482 (ptp) cc_final: 0.8281 (ptp) REVERT: l 89 LEU cc_start: 0.7539 (tt) cc_final: 0.7038 (tt) REVERT: m 455 ARG cc_start: 0.9407 (ttt-90) cc_final: 0.9190 (tpt-90) REVERT: m 530 LEU cc_start: 0.9443 (tp) cc_final: 0.9211 (tp) outliers start: 1 outliers final: 0 residues processed: 198 average time/residue: 0.1642 time to fit residues: 55.1220 Evaluate side-chains 136 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 0 optimal weight: 50.0000 chunk 97 optimal weight: 50.0000 chunk 257 optimal weight: 20.0000 chunk 186 optimal weight: 8.9990 chunk 250 optimal weight: 20.0000 chunk 33 optimal weight: 10.0000 chunk 178 optimal weight: 6.9990 chunk 135 optimal weight: 20.0000 chunk 200 optimal weight: 20.0000 chunk 205 optimal weight: 10.0000 chunk 139 optimal weight: 60.0000 overall best weight: 11.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS C 31 HIS ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.042368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.028564 restraints weight = 400248.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.028918 restraints weight = 210463.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.029085 restraints weight = 145579.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.029310 restraints weight = 125354.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 68)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.029413 restraints weight = 114310.886| |-----------------------------------------------------------------------------| r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2815 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2815 r_free = 0.2815 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2815 r_free = 0.2815 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2815 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 34126 Z= 0.269 Angle : 0.712 9.912 49074 Z= 0.410 Chirality : 0.042 0.242 5538 Planarity : 0.005 0.099 3788 Dihedral : 30.459 177.150 10138 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.11 % Allowed : 3.33 % Favored : 96.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.09 % 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: 1.96 (0.18), residues: 2202 helix: 1.97 (0.13), residues: 1422 sheet: 1.37 (0.50), residues: 120 loop : -0.12 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG g 42 TYR 0.021 0.002 TYR D 40 PHE 0.017 0.002 PHE L 39 TRP 0.017 0.002 TRP K 62 HIS 0.013 0.002 HIS f 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.27 (34126) covalent geometry : angle 0.71176 / 0.41 (49074) hydrogen bonds : bond 0.07849 / 5.35 ( 2007) hydrogen bonds : angle 3.69476 / 2.64 ( 5034) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 161 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8486 (tm-30) REVERT: A 120 MET cc_start: 0.9093 (mmp) cc_final: 0.8848 (mmm) REVERT: B 59 LYS cc_start: 0.9590 (tttp) cc_final: 0.9283 (tptm) REVERT: B 62 LEU cc_start: 0.9610 (mt) cc_final: 0.9390 (mt) REVERT: B 85 ASP cc_start: 0.8588 (m-30) cc_final: 0.8345 (m-30) REVERT: C 72 ASP cc_start: 0.8627 (m-30) cc_final: 0.8254 (m-30) REVERT: D 71 GLU cc_start: 0.9148 (tp30) cc_final: 0.8859 (tp30) REVERT: D 93 GLU cc_start: 0.9462 (mp0) cc_final: 0.9230 (mp0) REVERT: D 105 GLU cc_start: 0.8730 (tp30) cc_final: 0.8458 (tp30) REVERT: H 59 MET cc_start: 0.9248 (tpp) cc_final: 0.8833 (tpp) REVERT: K 15 MET cc_start: 0.9014 (ptm) cc_final: 0.8580 (ptm) REVERT: K 57 ASP cc_start: 0.9648 (m-30) cc_final: 0.9330 (t70) REVERT: L 83 GLU cc_start: 0.9497 (tp30) cc_final: 0.8903 (tp30) REVERT: M 443 GLU cc_start: 0.9191 (tt0) cc_final: 0.8825 (pt0) REVERT: a 105 GLU cc_start: 0.9291 (tm-30) cc_final: 0.8985 (tm-30) REVERT: b 49 LEU cc_start: 0.9489 (mp) cc_final: 0.8849 (mm) REVERT: b 52 GLU cc_start: 0.8912 (pm20) cc_final: 0.8606 (pm20) REVERT: b 53 GLU cc_start: 0.9688 (mm-30) cc_final: 0.9233 (mm-30) REVERT: b 84 MET cc_start: 0.8945 (mmm) cc_final: 0.8560 (mmm) REVERT: b 85 ASP cc_start: 0.8406 (m-30) cc_final: 0.8052 (m-30) REVERT: c 90 ASP cc_start: 0.8918 (t70) cc_final: 0.8658 (t0) REVERT: e 120 MET cc_start: 0.9238 (mmp) cc_final: 0.8765 (mmm) REVERT: l 15 MET cc_start: 0.8785 (ptp) cc_final: 0.8304 (ptp) REVERT: m 526 LEU cc_start: 0.9650 (mp) cc_final: 0.9308 (mt) outliers start: 2 outliers final: 0 residues processed: 161 average time/residue: 0.1671 time to fit residues: 45.4471 Evaluate side-chains 109 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 166 optimal weight: 8.9990 chunk 90 optimal weight: 50.0000 chunk 170 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 99 optimal weight: 50.0000 chunk 39 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 206 optimal weight: 7.9990 chunk 271 optimal weight: 9.9990 chunk 167 optimal weight: 30.0000 chunk 207 optimal weight: 0.9980 overall best weight: 6.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 84 ASN F 75 HIS ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.042730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.028934 restraints weight = 399584.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.029231 restraints weight = 201079.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.029534 restraints weight = 136096.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.029726 restraints weight = 112085.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.029810 restraints weight = 102133.527| |-----------------------------------------------------------------------------| r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2833 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2833 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 34126 Z= 0.181 Angle : 0.610 8.505 49074 Z= 0.364 Chirality : 0.041 0.265 5538 Planarity : 0.004 0.048 3788 Dihedral : 30.526 176.057 10138 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.09 % 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: 2.29 (0.18), residues: 2202 helix: 2.27 (0.14), residues: 1414 sheet: 1.66 (0.50), residues: 114 loop : -0.13 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG g 29 TYR 0.017 0.002 TYR D 40 PHE 0.012 0.001 PHE K 78 TRP 0.012 0.001 TRP K 62 HIS 0.011 0.002 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.18 (34126) covalent geometry : angle 0.60984 / 0.36 (49074) hydrogen bonds : bond 0.04861 / 3.30 ( 2007) hydrogen bonds : angle 3.42631 / 2.45 ( 5034) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8273 (tm-30) REVERT: A 120 MET cc_start: 0.9150 (mmp) cc_final: 0.8860 (mmm) REVERT: B 63 GLU cc_start: 0.8513 (mp0) cc_final: 0.8114 (mm-30) REVERT: B 85 ASP cc_start: 0.8503 (m-30) cc_final: 0.7333 (t0) REVERT: C 72 ASP cc_start: 0.8614 (m-30) cc_final: 0.8223 (m-30) REVERT: E 120 MET cc_start: 0.8700 (mmm) cc_final: 0.8363 (mmm) REVERT: H 59 MET cc_start: 0.9269 (tpp) cc_final: 0.8856 (tpp) REVERT: K 15 MET cc_start: 0.8917 (ptm) cc_final: 0.8525 (ptm) REVERT: L 15 MET cc_start: 0.7942 (mtp) cc_final: 0.7679 (mpp) REVERT: L 83 GLU cc_start: 0.9498 (tp30) cc_final: 0.8916 (tp30) REVERT: M 443 GLU cc_start: 0.9294 (tt0) cc_final: 0.8914 (pt0) REVERT: M 447 GLU cc_start: 0.8816 (pm20) cc_final: 0.8271 (tm-30) REVERT: a 105 GLU cc_start: 0.9242 (tm-30) cc_final: 0.8956 (tm-30) REVERT: b 49 LEU cc_start: 0.9505 (mp) cc_final: 0.8879 (mm) REVERT: b 52 GLU cc_start: 0.8921 (pm20) cc_final: 0.8703 (pm20) REVERT: b 53 GLU cc_start: 0.9656 (mm-30) cc_final: 0.9234 (mm-30) REVERT: b 84 MET cc_start: 0.8886 (mmm) cc_final: 0.8415 (mmm) REVERT: b 85 ASP cc_start: 0.8360 (m-30) cc_final: 0.7632 (t0) REVERT: e 105 GLU cc_start: 0.9033 (tm-30) cc_final: 0.8715 (tm-30) REVERT: e 120 MET cc_start: 0.9248 (mmp) cc_final: 0.8767 (mmm) REVERT: f 84 MET cc_start: 0.9337 (mmm) cc_final: 0.9111 (tpp) REVERT: h 62 MET cc_start: 0.9488 (mmm) cc_final: 0.9263 (mmm) REVERT: h 71 GLU cc_start: 0.9221 (tp30) cc_final: 0.8965 (tp30) REVERT: m 526 LEU cc_start: 0.9616 (mp) cc_final: 0.9227 (mt) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.1793 time to fit residues: 48.7327 Evaluate side-chains 112 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 180 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 187 optimal weight: 5.9990 chunk 130 optimal weight: 50.0000 chunk 238 optimal weight: 50.0000 chunk 268 optimal weight: 8.9990 chunk 254 optimal weight: 0.6980 chunk 246 optimal weight: 0.0870 chunk 273 optimal weight: 10.0000 chunk 93 optimal weight: 40.0000 chunk 215 optimal weight: 50.0000 overall best weight: 3.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** N 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 93 GLN f 75 HIS ** h 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.043068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.029302 restraints weight = 395838.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.029605 restraints weight = 204365.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.029910 restraints weight = 140593.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.030108 restraints weight = 116824.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.030146 restraints weight = 106564.074| |-----------------------------------------------------------------------------| r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2855 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2855 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 34126 Z= 0.143 Angle : 0.572 7.223 49074 Z= 0.347 Chirality : 0.040 0.266 5538 Planarity : 0.004 0.041 3788 Dihedral : 30.415 175.886 10138 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.05 % Allowed : 0.97 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.09 % 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 (0.18), residues: 2202 helix: 2.43 (0.14), residues: 1410 sheet: 1.30 (0.50), residues: 120 loop : -0.06 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 79 TYR 0.012 0.001 TYR D 40 PHE 0.010 0.001 PHE b 100 TRP 0.015 0.001 TRP K 62 HIS 0.006 0.001 HIS c 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.14 (34126) covalent geometry : angle 0.57209 / 0.35 (49074) hydrogen bonds : bond 0.04154 / 2.81 ( 2007) hydrogen bonds : angle 3.24755 / 2.32 ( 5034) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8288 (tm-30) REVERT: A 120 MET cc_start: 0.9101 (mmp) cc_final: 0.8837 (mmm) REVERT: B 59 LYS cc_start: 0.9595 (tttt) cc_final: 0.9324 (tptm) REVERT: B 62 LEU cc_start: 0.9571 (mt) cc_final: 0.9314 (mt) REVERT: B 85 ASP cc_start: 0.8469 (m-30) cc_final: 0.8227 (m-30) REVERT: C 72 ASP cc_start: 0.8649 (m-30) cc_final: 0.8263 (m-30) REVERT: D 93 GLU cc_start: 0.9416 (mp0) cc_final: 0.9213 (mp0) REVERT: K 57 ASP cc_start: 0.9619 (m-30) cc_final: 0.9241 (t70) REVERT: L 15 MET cc_start: 0.7641 (mtp) cc_final: 0.7399 (mpp) REVERT: L 83 GLU cc_start: 0.9485 (tp30) cc_final: 0.8927 (tp30) REVERT: M 443 GLU cc_start: 0.9271 (tt0) cc_final: 0.8901 (pt0) REVERT: M 447 GLU cc_start: 0.8817 (pm20) cc_final: 0.8320 (tp30) REVERT: a 105 GLU cc_start: 0.9296 (tm-30) cc_final: 0.9015 (tm-30) REVERT: a 120 MET cc_start: 0.8580 (mtp) cc_final: 0.8281 (mtp) REVERT: b 49 LEU cc_start: 0.9498 (mp) cc_final: 0.8857 (mm) REVERT: b 53 GLU cc_start: 0.9714 (mm-30) cc_final: 0.9255 (mm-30) REVERT: b 84 MET cc_start: 0.8941 (mmm) cc_final: 0.8464 (mmm) REVERT: b 85 ASP cc_start: 0.8301 (m-30) cc_final: 0.7602 (t0) REVERT: c 39 TYR cc_start: 0.9360 (m-80) cc_final: 0.9048 (m-80) REVERT: e 120 MET cc_start: 0.9287 (mmp) cc_final: 0.8771 (mmm) REVERT: h 62 MET cc_start: 0.9515 (mmm) cc_final: 0.9284 (mmm) REVERT: h 71 GLU cc_start: 0.9271 (tp30) cc_final: 0.9034 (tp30) REVERT: l 15 MET cc_start: 0.8354 (ptp) cc_final: 0.8000 (ptp) REVERT: m 526 LEU cc_start: 0.9560 (mp) cc_final: 0.9017 (mt) outliers start: 1 outliers final: 0 residues processed: 158 average time/residue: 0.1737 time to fit residues: 46.9145 Evaluate side-chains 110 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 187 optimal weight: 8.9990 chunk 25 optimal weight: 20.0000 chunk 43 optimal weight: 2.9990 chunk 258 optimal weight: 20.0000 chunk 158 optimal weight: 9.9990 chunk 154 optimal weight: 2.9990 chunk 84 optimal weight: 50.0000 chunk 15 optimal weight: 2.9990 chunk 166 optimal weight: 20.0000 chunk 112 optimal weight: 10.0000 chunk 95 optimal weight: 50.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 31 HIS a 68 GLN e 93 GLN ** h 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.042603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.028850 restraints weight = 401973.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.029156 restraints weight = 202719.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.029462 restraints weight = 136832.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.029656 restraints weight = 113003.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.029695 restraints weight = 103163.504| |-----------------------------------------------------------------------------| r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2835 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2835 r_free = 0.2835 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2835 r_free = 0.2835 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2835 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34126 Z= 0.170 Angle : 0.597 11.493 49074 Z= 0.356 Chirality : 0.040 0.255 5538 Planarity : 0.004 0.041 3788 Dihedral : 30.456 175.942 10138 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.09 % 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: 2.51 (0.18), residues: 2202 helix: 2.49 (0.14), residues: 1408 sheet: 1.25 (0.50), residues: 120 loop : -0.05 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG f 92 TYR 0.017 0.001 TYR D 40 PHE 0.011 0.001 PHE e 104 TRP 0.011 0.001 TRP K 62 HIS 0.007 0.001 HIS b 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.17 (34126) covalent geometry : angle 0.59665 / 0.36 (49074) hydrogen bonds : bond 0.04865 / 3.30 ( 2007) hydrogen bonds : angle 3.26747 / 2.33 ( 5034) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8234 (tm-30) REVERT: B 49 LEU cc_start: 0.9658 (mp) cc_final: 0.9396 (mp) REVERT: B 59 LYS cc_start: 0.9537 (tttt) cc_final: 0.9190 (tptm) REVERT: B 85 ASP cc_start: 0.8478 (m-30) cc_final: 0.7348 (t0) REVERT: C 72 ASP cc_start: 0.8649 (m-30) cc_final: 0.8253 (m-30) REVERT: E 120 MET cc_start: 0.8716 (mmm) cc_final: 0.8416 (mmm) REVERT: H 59 MET cc_start: 0.9285 (tpp) cc_final: 0.8903 (tpp) REVERT: K 15 MET cc_start: 0.8979 (ptm) cc_final: 0.8432 (ptm) REVERT: K 57 ASP cc_start: 0.9594 (m-30) cc_final: 0.9220 (t70) REVERT: L 15 MET cc_start: 0.7691 (mtp) cc_final: 0.7472 (mpp) REVERT: L 83 GLU cc_start: 0.9510 (tp30) cc_final: 0.8933 (tp30) REVERT: M 443 GLU cc_start: 0.9224 (tt0) cc_final: 0.8854 (pt0) REVERT: M 447 GLU cc_start: 0.8828 (pm20) cc_final: 0.8572 (tp30) REVERT: a 105 GLU cc_start: 0.9249 (tm-30) cc_final: 0.8924 (tm-30) REVERT: a 120 MET cc_start: 0.8728 (mtp) cc_final: 0.8410 (mtp) REVERT: b 49 LEU cc_start: 0.9607 (mp) cc_final: 0.8826 (mm) REVERT: b 53 GLU cc_start: 0.9695 (mm-30) cc_final: 0.9265 (mm-30) REVERT: b 84 MET cc_start: 0.8933 (mmm) cc_final: 0.8460 (mmm) REVERT: b 85 ASP cc_start: 0.8330 (m-30) cc_final: 0.7643 (t0) REVERT: c 39 TYR cc_start: 0.9331 (m-80) cc_final: 0.8953 (m-80) REVERT: e 120 MET cc_start: 0.9318 (mmp) cc_final: 0.8815 (mmm) REVERT: f 63 GLU cc_start: 0.9184 (pm20) cc_final: 0.8915 (pm20) REVERT: h 62 MET cc_start: 0.9438 (mmm) cc_final: 0.9215 (mmm) REVERT: h 71 GLU cc_start: 0.9177 (tp30) cc_final: 0.8908 (tp30) REVERT: l 15 MET cc_start: 0.8416 (ptp) cc_final: 0.8076 (ptp) REVERT: m 526 LEU cc_start: 0.9536 (mp) cc_final: 0.8978 (mt) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.1766 time to fit residues: 44.2324 Evaluate side-chains 111 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 86 optimal weight: 50.0000 chunk 146 optimal weight: 20.0000 chunk 244 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 chunk 161 optimal weight: 5.9990 chunk 100 optimal weight: 50.0000 chunk 242 optimal weight: 60.0000 chunk 143 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 75 optimal weight: 50.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** N 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 93 GLN g 110 ASN ** h 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 433 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.042623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.028879 restraints weight = 402230.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.029174 restraints weight = 202753.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.029489 restraints weight = 137672.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.029695 restraints weight = 113225.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.029760 restraints weight = 102895.604| |-----------------------------------------------------------------------------| r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2838 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2838 r_free = 0.2838 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2838 r_free = 0.2838 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2838 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 34126 Z= 0.162 Angle : 0.581 8.314 49074 Z= 0.351 Chirality : 0.040 0.259 5538 Planarity : 0.004 0.044 3788 Dihedral : 30.482 175.837 10138 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.05 % Allowed : 0.48 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.09 % 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: 2.54 (0.18), residues: 2202 helix: 2.51 (0.14), residues: 1410 sheet: 1.24 (0.50), residues: 120 loop : -0.04 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 92 TYR 0.015 0.001 TYR h 83 PHE 0.026 0.001 PHE e 67 TRP 0.011 0.001 TRP K 62 HIS 0.015 0.001 HIS d 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.16 (34126) covalent geometry : angle 0.58078 / 0.35 (49074) hydrogen bonds : bond 0.04460 / 3.02 ( 2007) hydrogen bonds : angle 3.26804 / 2.34 ( 5034) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8632 (tm-30) cc_final: 0.8264 (tm-30) REVERT: A 120 MET cc_start: 0.9175 (mmp) cc_final: 0.8761 (mmm) REVERT: B 58 LEU cc_start: 0.9595 (tp) cc_final: 0.9381 (tt) REVERT: B 59 LYS cc_start: 0.9609 (tttt) cc_final: 0.9297 (ttpp) REVERT: B 62 LEU cc_start: 0.9514 (mt) cc_final: 0.9138 (mt) REVERT: B 85 ASP cc_start: 0.8494 (m-30) cc_final: 0.7346 (t0) REVERT: C 72 ASP cc_start: 0.8670 (m-30) cc_final: 0.8270 (m-30) REVERT: D 93 GLU cc_start: 0.9382 (mp0) cc_final: 0.9170 (mp0) REVERT: E 120 MET cc_start: 0.8732 (mmm) cc_final: 0.8390 (mmm) REVERT: H 59 MET cc_start: 0.9257 (tpp) cc_final: 0.8851 (tpp) REVERT: K 15 MET cc_start: 0.8944 (ptm) cc_final: 0.8269 (ptm) REVERT: L 15 MET cc_start: 0.7662 (mtp) cc_final: 0.7441 (mpp) REVERT: M 443 GLU cc_start: 0.9245 (tt0) cc_final: 0.8876 (pt0) REVERT: M 447 GLU cc_start: 0.8836 (pm20) cc_final: 0.8564 (tp30) REVERT: a 105 GLU cc_start: 0.9276 (tm-30) cc_final: 0.9004 (tm-30) REVERT: a 120 MET cc_start: 0.8726 (mtp) cc_final: 0.8411 (mtp) REVERT: b 49 LEU cc_start: 0.9618 (mp) cc_final: 0.8915 (mp) REVERT: b 53 GLU cc_start: 0.9706 (mm-30) cc_final: 0.9272 (mm-30) REVERT: b 84 MET cc_start: 0.8947 (mmm) cc_final: 0.8480 (mmm) REVERT: b 85 ASP cc_start: 0.8292 (m-30) cc_final: 0.7593 (t0) REVERT: c 39 TYR cc_start: 0.9350 (m-80) cc_final: 0.8965 (m-80) REVERT: e 120 MET cc_start: 0.9324 (mmp) cc_final: 0.8821 (mmm) REVERT: f 84 MET cc_start: 0.9132 (mmm) cc_final: 0.8895 (tpp) REVERT: h 62 MET cc_start: 0.9426 (mmm) cc_final: 0.9218 (mmm) REVERT: h 71 GLU cc_start: 0.9171 (tp30) cc_final: 0.8939 (tp30) REVERT: m 526 LEU cc_start: 0.9549 (mp) cc_final: 0.8994 (mt) outliers start: 1 outliers final: 0 residues processed: 143 average time/residue: 0.1629 time to fit residues: 39.8438 Evaluate side-chains 107 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 33 optimal weight: 7.9990 chunk 157 optimal weight: 10.0000 chunk 62 optimal weight: 20.0000 chunk 228 optimal weight: 50.0000 chunk 156 optimal weight: 8.9990 chunk 152 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 277 optimal weight: 50.0000 chunk 189 optimal weight: 7.9990 chunk 174 optimal weight: 30.0000 chunk 14 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 472 GLN ** N 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.042350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.028287 restraints weight = 398339.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.028621 restraints weight = 201383.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.028942 restraints weight = 137981.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.029090 restraints weight = 113795.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 64)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.029190 restraints weight = 104374.066| |-----------------------------------------------------------------------------| r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2785 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2785 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34126 Z= 0.170 Angle : 0.595 9.479 49074 Z= 0.355 Chirality : 0.040 0.254 5538 Planarity : 0.004 0.043 3788 Dihedral : 30.508 176.016 10138 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.09 % 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: 2.49 (0.18), residues: 2202 helix: 2.45 (0.14), residues: 1414 sheet: 1.25 (0.50), residues: 120 loop : -0.02 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 82 TYR 0.015 0.001 TYR D 40 PHE 0.029 0.002 PHE e 67 TRP 0.012 0.001 TRP K 62 HIS 0.007 0.001 HIS b 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.17 (34126) covalent geometry : angle 0.59525 / 0.35 (49074) hydrogen bonds : bond 0.04751 / 3.22 ( 2007) hydrogen bonds : angle 3.31619 / 2.37 ( 5034) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8824 (tm-30) cc_final: 0.8472 (tm-30) REVERT: A 120 MET cc_start: 0.9086 (mmp) cc_final: 0.8673 (mmm) REVERT: B 58 LEU cc_start: 0.9587 (tp) cc_final: 0.9386 (tt) REVERT: B 59 LYS cc_start: 0.9731 (tttt) cc_final: 0.9436 (ttpp) REVERT: B 62 LEU cc_start: 0.9543 (mt) cc_final: 0.9272 (mt) REVERT: B 63 GLU cc_start: 0.9096 (pm20) cc_final: 0.8805 (pm20) REVERT: B 84 MET cc_start: 0.9129 (mmm) cc_final: 0.8791 (mmm) REVERT: B 85 ASP cc_start: 0.8578 (m-30) cc_final: 0.7389 (t0) REVERT: E 37 LYS cc_start: 0.9183 (tppt) cc_final: 0.8825 (mmmt) REVERT: E 120 MET cc_start: 0.8707 (mmm) cc_final: 0.8363 (mmm) REVERT: H 59 MET cc_start: 0.9315 (tpp) cc_final: 0.8899 (tpp) REVERT: K 15 MET cc_start: 0.8987 (ptm) cc_final: 0.8050 (ptm) REVERT: M 443 GLU cc_start: 0.9215 (tt0) cc_final: 0.8874 (tm-30) REVERT: M 447 GLU cc_start: 0.8865 (pm20) cc_final: 0.8319 (tp30) REVERT: a 105 GLU cc_start: 0.9396 (tm-30) cc_final: 0.9115 (tm-30) REVERT: a 120 MET cc_start: 0.8651 (mtp) cc_final: 0.8341 (mtp) REVERT: b 49 LEU cc_start: 0.9594 (mp) cc_final: 0.8955 (mp) REVERT: b 53 GLU cc_start: 0.9767 (mm-30) cc_final: 0.9328 (mm-30) REVERT: b 84 MET cc_start: 0.9096 (mmm) cc_final: 0.8604 (mmm) REVERT: b 85 ASP cc_start: 0.8336 (m-30) cc_final: 0.7663 (t0) REVERT: c 39 TYR cc_start: 0.9518 (m-80) cc_final: 0.9135 (m-80) REVERT: e 120 MET cc_start: 0.9369 (mmp) cc_final: 0.8833 (mmm) REVERT: f 84 MET cc_start: 0.9282 (mmm) cc_final: 0.8856 (tpt) REVERT: h 59 MET cc_start: 0.9182 (tpt) cc_final: 0.8947 (tpt) REVERT: h 62 MET cc_start: 0.9578 (mmm) cc_final: 0.9364 (mmm) REVERT: h 71 GLU cc_start: 0.9360 (tp30) cc_final: 0.9098 (tp30) REVERT: l 15 MET cc_start: 0.8199 (ptp) cc_final: 0.7900 (ptp) REVERT: m 526 LEU cc_start: 0.9547 (mp) cc_final: 0.8988 (mt) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.1756 time to fit residues: 40.1476 Evaluate side-chains 104 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 67 optimal weight: 6.9990 chunk 243 optimal weight: 70.0000 chunk 162 optimal weight: 5.9990 chunk 272 optimal weight: 30.0000 chunk 125 optimal weight: 2.9990 chunk 102 optimal weight: 50.0000 chunk 22 optimal weight: 8.9990 chunk 123 optimal weight: 30.0000 chunk 220 optimal weight: 50.0000 chunk 260 optimal weight: 50.0000 chunk 275 optimal weight: 0.6980 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** N 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 47 GLN e 93 GLN ** f 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.042375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.028316 restraints weight = 399253.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.028640 restraints weight = 200713.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.028952 restraints weight = 137016.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.029157 restraints weight = 112972.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.029191 restraints weight = 102964.474| |-----------------------------------------------------------------------------| r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2791 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2791 r_free = 0.2791 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2791 r_free = 0.2791 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (22 function evaluations) r_final: 0.2791 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34126 Z= 0.157 Angle : 0.579 8.054 49074 Z= 0.348 Chirality : 0.039 0.255 5538 Planarity : 0.004 0.041 3788 Dihedral : 30.512 176.045 10138 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.09 % 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: 2.53 (0.18), residues: 2202 helix: 2.50 (0.14), residues: 1416 sheet: 1.28 (0.50), residues: 120 loop : -0.04 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 82 TYR 0.014 0.001 TYR D 40 PHE 0.011 0.001 PHE E 104 TRP 0.013 0.001 TRP L 84 HIS 0.005 0.001 HIS b 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.16 (34126) covalent geometry : angle 0.57865 / 0.35 (49074) hydrogen bonds : bond 0.04386 / 2.96 ( 2007) hydrogen bonds : angle 3.26457 / 2.32 ( 5034) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8817 (tm-30) cc_final: 0.8456 (tm-30) REVERT: A 120 MET cc_start: 0.9114 (mmp) cc_final: 0.8680 (mmm) REVERT: B 58 LEU cc_start: 0.9583 (tp) cc_final: 0.9377 (tt) REVERT: B 59 LYS cc_start: 0.9719 (tttt) cc_final: 0.9453 (ttpp) REVERT: B 62 LEU cc_start: 0.9540 (mt) cc_final: 0.9249 (mt) REVERT: B 63 GLU cc_start: 0.8944 (pm20) cc_final: 0.8739 (pm20) REVERT: B 84 MET cc_start: 0.9124 (mmm) cc_final: 0.8885 (mmm) REVERT: B 85 ASP cc_start: 0.8567 (m-30) cc_final: 0.7351 (t0) REVERT: B 88 TYR cc_start: 0.9044 (m-10) cc_final: 0.8546 (m-10) REVERT: D 93 GLU cc_start: 0.9485 (mp0) cc_final: 0.9182 (mp0) REVERT: E 37 LYS cc_start: 0.9196 (tppt) cc_final: 0.8838 (mmmt) REVERT: E 120 MET cc_start: 0.8729 (mmm) cc_final: 0.8171 (mmm) REVERT: H 59 MET cc_start: 0.9312 (tpp) cc_final: 0.8871 (tpp) REVERT: K 15 MET cc_start: 0.8984 (ptm) cc_final: 0.8137 (ptm) REVERT: K 65 ASP cc_start: 0.9364 (m-30) cc_final: 0.8981 (p0) REVERT: M 443 GLU cc_start: 0.9203 (tt0) cc_final: 0.8871 (tm-30) REVERT: M 447 GLU cc_start: 0.8835 (pm20) cc_final: 0.8284 (tp30) REVERT: a 105 GLU cc_start: 0.9392 (tm-30) cc_final: 0.9107 (tm-30) REVERT: a 120 MET cc_start: 0.8661 (mtp) cc_final: 0.8341 (mtp) REVERT: b 49 LEU cc_start: 0.9590 (mp) cc_final: 0.8965 (mp) REVERT: b 53 GLU cc_start: 0.9772 (mm-30) cc_final: 0.9331 (mm-30) REVERT: b 84 MET cc_start: 0.9085 (mmm) cc_final: 0.8570 (mmm) REVERT: b 85 ASP cc_start: 0.8324 (m-30) cc_final: 0.7508 (t0) REVERT: c 39 TYR cc_start: 0.9513 (m-80) cc_final: 0.9158 (m-80) REVERT: e 120 MET cc_start: 0.9371 (mmp) cc_final: 0.8829 (mmm) REVERT: h 59 MET cc_start: 0.9091 (tpt) cc_final: 0.8870 (tpt) REVERT: h 62 MET cc_start: 0.9581 (mmm) cc_final: 0.9351 (mmm) REVERT: h 71 GLU cc_start: 0.9364 (tp30) cc_final: 0.9121 (tp30) REVERT: l 15 MET cc_start: 0.8129 (ptp) cc_final: 0.7818 (ptp) REVERT: m 526 LEU cc_start: 0.9519 (mp) cc_final: 0.8965 (mt) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.1797 time to fit residues: 42.8425 Evaluate side-chains 107 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 57 optimal weight: 10.0000 chunk 163 optimal weight: 6.9990 chunk 91 optimal weight: 50.0000 chunk 183 optimal weight: 10.0000 chunk 247 optimal weight: 0.3980 chunk 157 optimal weight: 5.9990 chunk 113 optimal weight: 8.9990 chunk 155 optimal weight: 20.0000 chunk 198 optimal weight: 20.0000 chunk 100 optimal weight: 50.0000 chunk 262 optimal weight: 30.0000 overall best weight: 6.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** N 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.042021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.027984 restraints weight = 402087.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.028400 restraints weight = 203696.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.028656 restraints weight = 136952.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.028791 restraints weight = 113080.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.028879 restraints weight = 104377.225| |-----------------------------------------------------------------------------| r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2775 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2775 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 34126 Z= 0.182 Angle : 0.602 9.739 49074 Z= 0.358 Chirality : 0.039 0.248 5538 Planarity : 0.004 0.041 3788 Dihedral : 30.574 176.234 10138 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.09 % 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: 2.47 (0.18), residues: 2202 helix: 2.44 (0.14), residues: 1416 sheet: 1.27 (0.50), residues: 120 loop : -0.05 (0.25), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 92 TYR 0.023 0.001 TYR K 43 PHE 0.015 0.002 PHE E 104 TRP 0.011 0.001 TRP K 62 HIS 0.007 0.001 HIS b 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.18 (34126) covalent geometry : angle 0.60222 / 0.36 (49074) hydrogen bonds : bond 0.05159 / 3.50 ( 2007) hydrogen bonds : angle 3.35493 / 2.39 ( 5034) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5898.51 seconds wall clock time: 102 minutes 4.91 seconds (6124.91 seconds total)