Starting phenix.real_space_refine on Mon Aug 25 21:58:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j8o_61233/08_2025/9j8o_61233.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j8o_61233/08_2025/9j8o_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9j8o_61233/08_2025/9j8o_61233.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j8o_61233/08_2025/9j8o_61233.map" model { file = "/net/cci-nas-00/data/ceres_data/9j8o_61233/08_2025/9j8o_61233.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j8o_61233/08_2025/9j8o_61233.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 7.12, per 1000 atoms: 0.22 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: 2.87 Conformation dependent library (CDL) restraints added in 793.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 4.77 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: 7.05 Time building geometry restraints manager: 3.78 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=" CA ILE G 79 " pdb=" CB ILE G 79 " ideal model delta sigma weight residual 1.546 1.533 0.013 8.80e-03 1.29e+04 2.27e+00 bond pdb=" CA ILE F 29 " pdb=" CB ILE F 29 " ideal model delta sigma weight residual 1.540 1.520 0.020 1.36e-02 5.41e+03 2.11e+00 bond pdb=" CG LEU c 51 " pdb=" CD1 LEU c 51 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.07e+00 bond pdb=" CB ASN d 63 " pdb=" CG ASN d 63 " ideal model delta sigma weight residual 1.516 1.481 0.035 2.50e-02 1.60e+03 2.01e+00 bond pdb=" CA ILE c 79 " pdb=" CB ILE c 79 " ideal model delta sigma weight residual 1.547 1.531 0.016 1.10e-02 8.26e+03 2.00e+00 ... (remaining 34121 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 47124 1.58 - 3.16: 1810 3.16 - 4.75: 110 4.75 - 6.33: 27 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=" 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=" C3' DC I 72 " pdb=" C2' DC I 72 " pdb=" C1' DC I 72 " ideal model delta sigma weight residual 101.60 97.63 3.97 1.50e+00 4.44e-01 7.01e+00 angle pdb=" N GLY D 104 " pdb=" CA GLY D 104 " pdb=" C GLY D 104 " ideal model delta sigma weight residual 110.95 115.35 -4.40 1.70e+00 3.46e-01 6.70e+00 angle pdb=" N VAL k 11 " pdb=" CA VAL k 11 " pdb=" C VAL k 11 " ideal model delta sigma weight residual 110.72 113.32 -2.60 1.01e+00 9.80e-01 6.64e+00 ... (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 - 0.031: 3253 0.031 - 0.062: 1698 0.062 - 0.093: 458 0.093 - 0.124: 110 0.124 - 0.155: 19 Chirality restraints: 5538 Sorted by residual: chirality pdb=" CA PRO g 80 " pdb=" N PRO g 80 " pdb=" C PRO g 80 " pdb=" CB PRO g 80 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.02e-01 chirality pdb=" CA ILE G 111 " pdb=" N ILE G 111 " pdb=" C ILE G 111 " pdb=" CB ILE G 111 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.62e-01 chirality pdb=" CA PRO C 80 " pdb=" N PRO C 80 " pdb=" C PRO C 80 " pdb=" CB PRO C 80 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.33e-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: 1.090 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: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 31.880 Find NCS groups from input model: 0.440 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: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6557 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 34126 Z= 0.309 Angle : 0.670 7.912 49074 Z= 0.397 Chirality : 0.039 0.155 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 aren 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 covalent geometry : bond 0.00708 (34126) covalent geometry : angle 0.66962 (49074) hydrogen bonds : bond 0.10256 ( 2007) hydrogen bonds : angle 4.16498 ( 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 : 1.224 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: 0.2112 time to fit residues: 151.3394 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 : 0.842 ------------------------------------------------------------------------------- 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: 20.0000 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... Flipped N/Q/H residues before XYZ refinement: 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 L 48 GLN N 98 GLN a 68 GLN a 76 GLN b 93 GLN c 112 GLN d 84 ASN d 95 GLN d 109 HIS e 93 GLN ** f 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.043974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.030196 restraints weight = 397488.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.030543 restraints weight = 196364.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.030871 restraints weight = 131311.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.031083 restraints weight = 106980.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.031165 restraints weight = 96845.242| |-----------------------------------------------------------------------------| r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2887 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 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 = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2886 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 34126 Z= 0.206 Angle : 0.605 9.450 49074 Z= 0.356 Chirality : 0.036 0.182 5538 Planarity : 0.005 0.062 3788 Dihedral : 29.849 178.138 10138 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % 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 aren not related in a simple way. whole: 2.14 (0.18), residues: 2202 helix: 2.19 (0.14), residues: 1410 sheet: 1.70 (0.50), residues: 116 loop : -0.29 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG d 33 TYR 0.020 0.002 TYR b 98 PHE 0.017 0.002 PHE c 25 TRP 0.021 0.002 TRP m 467 HIS 0.015 0.002 HIS d 109 Details of bonding type rmsd covalent geometry : bond 0.00440 (34126) covalent geometry : angle 0.60485 (49074) hydrogen bonds : bond 0.04906 ( 2007) hydrogen bonds : angle 3.41206 ( 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 228 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.729 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: 0.8699 (tm-30) cc_final: 0.8468 (tm-30) REVERT: B 59 LYS cc_start: 0.9569 (tppt) cc_final: 0.9366 (tppt) REVERT: B 85 ASP cc_start: 0.8243 (m-30) cc_final: 0.8010 (m-30) REVERT: C 72 ASP cc_start: 0.8438 (m-30) cc_final: 0.8063 (m-30) REVERT: D 93 GLU cc_start: 0.9391 (mp0) cc_final: 0.9133 (mp0) REVERT: E 90 MET cc_start: 0.9141 (mmm) cc_final: 0.8939 (mmp) REVERT: E 93 GLN cc_start: 0.9343 (tt0) cc_final: 0.8917 (tm-30) REVERT: E 120 MET cc_start: 0.8873 (mmp) cc_final: 0.8522 (mmm) REVERT: K 76 ASP cc_start: 0.8945 (t0) cc_final: 0.8629 (t0) REVERT: L 83 GLU cc_start: 0.9455 (tp30) cc_final: 0.8836 (tp30) REVERT: a 105 GLU cc_start: 0.9260 (tm-30) cc_final: 0.8972 (tm-30) REVERT: a 112 ILE cc_start: 0.9110 (mt) cc_final: 0.8888 (mt) REVERT: a 120 MET cc_start: 0.8633 (mtp) cc_final: 0.8257 (mtt) REVERT: b 49 LEU cc_start: 0.9667 (mp) cc_final: 0.8838 (mm) REVERT: b 53 GLU cc_start: 0.9655 (mm-30) cc_final: 0.9234 (mm-30) REVERT: b 85 ASP cc_start: 0.8129 (m-30) cc_final: 0.7882 (m-30) REVERT: c 39 TYR cc_start: 0.9054 (m-80) cc_final: 0.6642 (m-80) REVERT: c 90 ASP cc_start: 0.9015 (t70) cc_final: 0.8769 (t0) REVERT: d 71 GLU cc_start: 0.9077 (tt0) cc_final: 0.8855 (tp30) REVERT: d 76 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8596 (mm-30) REVERT: e 105 GLU cc_start: 0.8979 (tm-30) cc_final: 0.8756 (tm-30) REVERT: e 120 MET cc_start: 0.9023 (mmp) cc_final: 0.8659 (mmm) REVERT: e 124 ILE cc_start: 0.9716 (tt) cc_final: 0.9286 (tt) REVERT: h 62 MET cc_start: 0.9421 (mmm) cc_final: 0.9151 (mmm) REVERT: k 15 MET cc_start: 0.9029 (ptm) cc_final: 0.8670 (ppp) REVERT: l 15 MET cc_start: 0.8498 (ptp) cc_final: 0.8013 (mtp) REVERT: l 56 GLU cc_start: 0.9290 (pm20) cc_final: 0.8908 (pm20) REVERT: l 57 ASP cc_start: 0.9478 (p0) cc_final: 0.9227 (p0) REVERT: l 89 LEU cc_start: 0.7616 (tt) cc_final: 0.7091 (tt) REVERT: m 526 LEU cc_start: 0.9652 (mt) cc_final: 0.9376 (mt) REVERT: m 530 LEU cc_start: 0.9409 (tp) cc_final: 0.9197 (tp) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.1925 time to fit residues: 72.4191 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 : 0.836 ------------------------------------------------------------------------------- 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: 10.0000 chunk 174 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 147 optimal weight: 6.9990 chunk 134 optimal weight: 30.0000 chunk 25 optimal weight: 8.9990 chunk 132 optimal weight: 20.0000 chunk 1 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS C 31 HIS ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 93 GLN ** h 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.043015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.029238 restraints weight = 399018.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.029566 restraints weight = 199481.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.029873 restraints weight = 134932.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.030079 restraints weight = 111098.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.030156 restraints weight = 100777.121| |-----------------------------------------------------------------------------| r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2845 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2845 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 34126 Z= 0.222 Angle : 0.596 8.197 49074 Z= 0.352 Chirality : 0.035 0.198 5538 Planarity : 0.004 0.060 3788 Dihedral : 29.860 179.030 10138 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.05 % Allowed : 2.31 % Favored : 97.64 % 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 aren not related in a simple way. whole: 2.37 (0.18), residues: 2202 helix: 2.32 (0.14), residues: 1416 sheet: 1.47 (0.51), residues: 120 loop : -0.04 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 92 TYR 0.018 0.002 TYR D 40 PHE 0.014 0.002 PHE L 39 TRP 0.010 0.001 TRP L 84 HIS 0.010 0.002 HIS f 75 Details of bonding type rmsd covalent geometry : bond 0.00476 (34126) covalent geometry : angle 0.59637 (49074) hydrogen bonds : bond 0.04912 ( 2007) hydrogen bonds : angle 3.36959 ( 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 178 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 177 time to evaluate : 0.863 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: 0.8757 (tm-30) cc_final: 0.8484 (tm-30) REVERT: A 120 MET cc_start: 0.8850 (mmp) cc_final: 0.8627 (mmm) REVERT: B 59 LYS cc_start: 0.9550 (tptm) cc_final: 0.9236 (tppt) REVERT: B 63 GLU cc_start: 0.8684 (mp0) cc_final: 0.8348 (mm-30) REVERT: B 85 ASP cc_start: 0.8505 (m-30) cc_final: 0.8271 (m-30) REVERT: C 72 ASP cc_start: 0.8615 (m-30) cc_final: 0.8241 (m-30) REVERT: D 105 GLU cc_start: 0.8753 (tp30) cc_final: 0.8372 (tp30) REVERT: H 59 MET cc_start: 0.9223 (tpp) cc_final: 0.8700 (tpp) REVERT: L 15 MET cc_start: 0.8227 (mtp) cc_final: 0.8005 (mtp) REVERT: L 56 GLU cc_start: 0.9114 (pp20) cc_final: 0.8907 (pm20) REVERT: L 83 GLU cc_start: 0.9488 (tp30) cc_final: 0.8889 (tp30) REVERT: M 443 GLU cc_start: 0.9231 (tt0) cc_final: 0.8898 (pt0) REVERT: a 105 GLU cc_start: 0.9254 (tm-30) cc_final: 0.8982 (tm-30) REVERT: b 49 LEU cc_start: 0.9527 (mp) cc_final: 0.8931 (mm) REVERT: b 52 GLU cc_start: 0.8939 (pm20) cc_final: 0.8736 (pm20) REVERT: b 53 GLU cc_start: 0.9673 (mm-30) cc_final: 0.9248 (mm-30) REVERT: b 84 MET cc_start: 0.8924 (mmm) cc_final: 0.8416 (mmm) REVERT: b 85 ASP cc_start: 0.8289 (m-30) cc_final: 0.7645 (t0) REVERT: d 76 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8376 (mm-30) REVERT: e 105 GLU cc_start: 0.9025 (tm-30) cc_final: 0.8812 (tm-30) REVERT: e 120 MET cc_start: 0.9201 (mmp) cc_final: 0.8815 (mmm) REVERT: h 62 MET cc_start: 0.9425 (mmm) cc_final: 0.9165 (mmm) REVERT: l 15 MET cc_start: 0.8625 (ptp) cc_final: 0.8140 (mtp) REVERT: m 526 LEU cc_start: 0.9563 (mt) cc_final: 0.9363 (mp) outliers start: 1 outliers final: 0 residues processed: 177 average time/residue: 0.1640 time to fit residues: 49.0595 Evaluate side-chains 114 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.662 ------------------------------------------------------------------------------- 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: 40.0000 chunk 97 optimal weight: 10.0000 chunk 257 optimal weight: 8.9990 chunk 186 optimal weight: 20.0000 chunk 250 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 178 optimal weight: 8.9990 chunk 135 optimal weight: 40.0000 chunk 200 optimal weight: 10.0000 chunk 205 optimal weight: 7.9990 chunk 139 optimal weight: 50.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 433 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.042363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.028641 restraints weight = 402007.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.028927 restraints weight = 202190.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.029226 restraints weight = 138006.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.029429 restraints weight = 113668.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.029487 restraints weight = 103367.636| |-----------------------------------------------------------------------------| r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2825 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2825 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 34126 Z= 0.238 Angle : 0.599 10.180 49074 Z= 0.353 Chirality : 0.035 0.155 5538 Planarity : 0.004 0.043 3788 Dihedral : 29.983 179.130 10138 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.05 % Allowed : 2.36 % Favored : 97.58 % 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 aren not related in a simple way. whole: 2.37 (0.18), residues: 2202 helix: 2.31 (0.14), residues: 1418 sheet: 1.36 (0.51), residues: 120 loop : 0.02 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG g 29 TYR 0.020 0.002 TYR D 40 PHE 0.016 0.002 PHE F 100 TRP 0.009 0.001 TRP K 62 HIS 0.008 0.002 HIS f 75 Details of bonding type rmsd covalent geometry : bond 0.00508 (34126) covalent geometry : angle 0.59888 (49074) hydrogen bonds : bond 0.05220 ( 2007) hydrogen bonds : angle 3.42813 ( 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 157 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 156 time to evaluate : 0.855 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: 0.8651 (tm-30) cc_final: 0.8264 (tm-30) REVERT: A 120 MET cc_start: 0.9134 (mmp) cc_final: 0.8865 (mmm) REVERT: B 59 LYS cc_start: 0.9539 (tptm) cc_final: 0.9006 (tppt) REVERT: B 63 GLU cc_start: 0.8643 (mp0) cc_final: 0.8348 (mp0) REVERT: B 85 ASP cc_start: 0.8532 (m-30) cc_final: 0.7428 (t0) REVERT: C 72 ASP cc_start: 0.8663 (m-30) cc_final: 0.8277 (m-30) REVERT: D 105 GLU cc_start: 0.8694 (tp30) cc_final: 0.8349 (tp30) REVERT: E 106 ASP cc_start: 0.8961 (m-30) cc_final: 0.8517 (m-30) REVERT: E 120 MET cc_start: 0.8781 (mmm) cc_final: 0.8447 (mmm) REVERT: L 83 GLU cc_start: 0.9509 (tp30) cc_final: 0.8942 (tp30) REVERT: M 443 GLU cc_start: 0.9233 (tt0) cc_final: 0.8886 (pt0) REVERT: M 447 GLU cc_start: 0.8829 (pm20) cc_final: 0.8329 (tm-30) REVERT: a 105 GLU cc_start: 0.9260 (tm-30) cc_final: 0.9049 (tm-30) REVERT: a 120 MET cc_start: 0.8735 (mtp) cc_final: 0.8473 (mtp) REVERT: b 49 LEU cc_start: 0.9506 (mp) cc_final: 0.8896 (mm) REVERT: b 52 GLU cc_start: 0.8880 (pm20) cc_final: 0.8642 (pm20) REVERT: b 53 GLU cc_start: 0.9677 (mm-30) cc_final: 0.9243 (mm-30) REVERT: b 84 MET cc_start: 0.8872 (mmm) cc_final: 0.8407 (mmm) REVERT: b 85 ASP cc_start: 0.8376 (m-30) cc_final: 0.7813 (t0) REVERT: e 105 GLU cc_start: 0.8992 (tm-30) cc_final: 0.8719 (tm-30) REVERT: e 120 MET cc_start: 0.9259 (mmp) cc_final: 0.8846 (mmm) REVERT: h 71 GLU cc_start: 0.9243 (tp30) cc_final: 0.9025 (tp30) REVERT: l 15 MET cc_start: 0.8726 (ptp) cc_final: 0.8266 (mtp) REVERT: m 526 LEU cc_start: 0.9514 (mt) cc_final: 0.9290 (mp) outliers start: 1 outliers final: 0 residues processed: 157 average time/residue: 0.1669 time to fit residues: 44.3628 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 : 0.700 ------------------------------------------------------------------------------- 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: 20.0000 chunk 170 optimal weight: 0.2980 chunk 54 optimal weight: 9.9990 chunk 99 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 206 optimal weight: 6.9990 chunk 271 optimal weight: 9.9990 chunk 167 optimal weight: 50.0000 chunk 207 optimal weight: 6.9990 overall best weight: 4.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN e 68 GLN e 93 GLN f 75 HIS ** h 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.042748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.029032 restraints weight = 401324.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.029318 restraints weight = 202122.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.029644 restraints weight = 136787.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.029823 restraints weight = 112832.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.029893 restraints weight = 102636.948| |-----------------------------------------------------------------------------| r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 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 = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 34126 Z= 0.173 Angle : 0.555 5.640 49074 Z= 0.332 Chirality : 0.034 0.138 5538 Planarity : 0.004 0.040 3788 Dihedral : 29.981 179.015 10138 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % 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 aren not related in a simple way. whole: 2.60 (0.18), residues: 2202 helix: 2.52 (0.14), residues: 1414 sheet: 1.36 (0.51), residues: 120 loop : 0.08 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 60 TYR 0.012 0.001 TYR D 40 PHE 0.015 0.001 PHE e 67 TRP 0.008 0.001 TRP K 62 HIS 0.010 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00370 (34126) covalent geometry : angle 0.55479 (49074) hydrogen bonds : bond 0.03815 ( 2007) hydrogen bonds : angle 3.21238 ( 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 : 0.643 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: 0.8631 (tm-30) cc_final: 0.8254 (tm-30) REVERT: B 85 ASP cc_start: 0.8464 (m-30) cc_final: 0.7346 (t0) REVERT: C 72 ASP cc_start: 0.8642 (m-30) cc_final: 0.8253 (m-30) REVERT: H 59 MET cc_start: 0.9299 (tpp) cc_final: 0.8870 (tpp) REVERT: K 15 MET cc_start: 0.8893 (ptm) cc_final: 0.8390 (ptm) REVERT: K 65 ASP cc_start: 0.9305 (m-30) cc_final: 0.8915 (p0) REVERT: L 83 GLU cc_start: 0.9521 (tp30) cc_final: 0.8977 (tp30) REVERT: M 443 GLU cc_start: 0.9248 (tt0) cc_final: 0.8905 (pt0) REVERT: M 447 GLU cc_start: 0.8844 (pm20) cc_final: 0.8314 (tm-30) REVERT: a 105 GLU cc_start: 0.9286 (tm-30) cc_final: 0.9077 (tm-30) REVERT: a 120 MET cc_start: 0.8712 (mtp) cc_final: 0.8375 (mtp) REVERT: b 49 LEU cc_start: 0.9471 (mp) cc_final: 0.9002 (mm) REVERT: b 53 GLU cc_start: 0.9710 (mm-30) cc_final: 0.9313 (mm-30) REVERT: b 84 MET cc_start: 0.8930 (mmm) cc_final: 0.8446 (mmm) REVERT: b 85 ASP cc_start: 0.8341 (m-30) cc_final: 0.7650 (t0) REVERT: e 120 MET cc_start: 0.9266 (mmp) cc_final: 0.8842 (mmm) REVERT: g 41 GLU cc_start: 0.8966 (pm20) cc_final: 0.8654 (pm20) REVERT: h 59 MET cc_start: 0.9371 (tpp) cc_final: 0.9095 (tpp) REVERT: h 62 MET cc_start: 0.9379 (mmm) cc_final: 0.9117 (mmm) REVERT: h 71 GLU cc_start: 0.9211 (tp30) cc_final: 0.8980 (tp30) REVERT: k 15 MET cc_start: 0.9069 (ptm) cc_final: 0.8770 (ppp) REVERT: k 57 ASP cc_start: 0.9392 (p0) cc_final: 0.9068 (p0) REVERT: l 15 MET cc_start: 0.8749 (ptp) cc_final: 0.8149 (mtp) REVERT: m 526 LEU cc_start: 0.9515 (mt) cc_final: 0.9168 (mt) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.1548 time to fit residues: 41.7315 Evaluate side-chains 108 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.724 ------------------------------------------------------------------------------- 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: 0.9990 chunk 131 optimal weight: 6.9990 chunk 187 optimal weight: 10.0000 chunk 130 optimal weight: 0.0870 chunk 238 optimal weight: 10.0000 chunk 268 optimal weight: 0.3980 chunk 254 optimal weight: 40.0000 chunk 246 optimal weight: 20.0000 chunk 273 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 215 optimal weight: 20.0000 overall best weight: 3.6964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 31 HIS a 68 GLN d 47 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.042750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.029134 restraints weight = 398803.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.029418 restraints weight = 207932.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.029712 restraints weight = 142794.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.029803 restraints weight = 118022.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.029969 restraints weight = 109848.395| |-----------------------------------------------------------------------------| r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2853 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2853 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 34126 Z= 0.163 Angle : 0.545 5.906 49074 Z= 0.325 Chirality : 0.033 0.137 5538 Planarity : 0.003 0.041 3788 Dihedral : 29.898 178.946 10138 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.11 % Allowed : 1.13 % Favored : 98.76 % 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 aren not related in a simple way. whole: 2.68 (0.18), residues: 2202 helix: 2.56 (0.14), residues: 1420 sheet: 1.41 (0.50), residues: 120 loop : 0.13 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 63 TYR 0.011 0.001 TYR K 43 PHE 0.014 0.001 PHE L 78 TRP 0.008 0.001 TRP K 62 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00348 (34126) covalent geometry : angle 0.54494 (49074) hydrogen bonds : bond 0.03826 ( 2007) hydrogen bonds : angle 3.12342 ( 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 153 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 151 time to evaluate : 0.589 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: A 105 GLU cc_start: 0.8757 (tm-30) cc_final: 0.8392 (tm-30) REVERT: A 120 MET cc_start: 0.9085 (mmp) cc_final: 0.8672 (mmm) REVERT: B 85 ASP cc_start: 0.8521 (m-30) cc_final: 0.7330 (t0) REVERT: C 72 ASP cc_start: 0.8672 (m-30) cc_final: 0.8281 (m-30) REVERT: E 37 LYS cc_start: 0.9069 (tppt) cc_final: 0.8772 (mmmt) REVERT: H 59 MET cc_start: 0.9307 (tpp) cc_final: 0.8785 (tpp) REVERT: K 15 MET cc_start: 0.8841 (ptm) cc_final: 0.8496 (ptm) REVERT: K 65 ASP cc_start: 0.9282 (m-30) cc_final: 0.8858 (p0) REVERT: L 50 LEU cc_start: 0.9700 (mt) cc_final: 0.9491 (mt) REVERT: L 83 GLU cc_start: 0.9516 (tp30) cc_final: 0.8872 (tp30) REVERT: M 443 GLU cc_start: 0.9227 (tt0) cc_final: 0.8900 (pt0) REVERT: M 447 GLU cc_start: 0.8837 (pm20) cc_final: 0.8310 (tm-30) REVERT: a 105 GLU cc_start: 0.9340 (tm-30) cc_final: 0.9106 (tm-30) REVERT: a 120 MET cc_start: 0.8680 (mtp) cc_final: 0.8281 (mtp) REVERT: b 49 LEU cc_start: 0.9380 (mp) cc_final: 0.8851 (mp) REVERT: b 53 GLU cc_start: 0.9703 (mm-30) cc_final: 0.9253 (mm-30) REVERT: b 84 MET cc_start: 0.9036 (mmm) cc_final: 0.8527 (mmm) REVERT: b 85 ASP cc_start: 0.8280 (m-30) cc_final: 0.7571 (t0) REVERT: c 39 TYR cc_start: 0.9429 (m-80) cc_final: 0.9117 (m-80) REVERT: e 106 ASP cc_start: 0.9404 (m-30) cc_final: 0.8777 (m-30) REVERT: e 120 MET cc_start: 0.9290 (mmp) cc_final: 0.8847 (mmm) REVERT: g 41 GLU cc_start: 0.9009 (pm20) cc_final: 0.8695 (pm20) REVERT: h 59 MET cc_start: 0.9336 (tpp) cc_final: 0.9010 (tpp) REVERT: h 62 MET cc_start: 0.9425 (mmm) cc_final: 0.9162 (mmm) REVERT: h 71 GLU cc_start: 0.9304 (tp30) cc_final: 0.9062 (tp30) REVERT: k 15 MET cc_start: 0.9113 (ptm) cc_final: 0.8852 (ppp) REVERT: k 57 ASP cc_start: 0.9454 (p0) cc_final: 0.9108 (p0) REVERT: l 15 MET cc_start: 0.8701 (ptp) cc_final: 0.8103 (mtp) REVERT: m 526 LEU cc_start: 0.9501 (mt) cc_final: 0.9118 (mt) outliers start: 2 outliers final: 1 residues processed: 153 average time/residue: 0.1669 time to fit residues: 43.0403 Evaluate side-chains 111 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.773 ------------------------------------------------------------------------------- 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: 9.9990 chunk 25 optimal weight: 0.5980 chunk 43 optimal weight: 5.9990 chunk 258 optimal weight: 6.9990 chunk 158 optimal weight: 20.0000 chunk 154 optimal weight: 4.9990 chunk 84 optimal weight: 20.0000 chunk 15 optimal weight: 4.9990 chunk 166 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS F 93 GLN M 472 GLN e 93 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.042497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.028923 restraints weight = 401240.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.029197 restraints weight = 210777.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.029489 restraints weight = 145825.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.029680 restraints weight = 119981.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.029702 restraints weight = 109769.813| |-----------------------------------------------------------------------------| 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 = 0.88 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 = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2838 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 34126 Z= 0.178 Angle : 0.546 6.687 49074 Z= 0.326 Chirality : 0.033 0.147 5538 Planarity : 0.004 0.041 3788 Dihedral : 29.891 178.936 10138 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % 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 aren not related in a simple way. whole: 2.71 (0.18), residues: 2202 helix: 2.56 (0.14), residues: 1422 sheet: 1.48 (0.51), residues: 120 loop : 0.17 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 63 TYR 0.012 0.001 TYR D 40 PHE 0.014 0.001 PHE e 67 TRP 0.008 0.001 TRP K 62 HIS 0.007 0.001 HIS b 75 Details of bonding type rmsd covalent geometry : bond 0.00381 (34126) covalent geometry : angle 0.54578 (49074) hydrogen bonds : bond 0.04059 ( 2007) hydrogen bonds : angle 3.14322 ( 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 148 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.648 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: 0.8742 (tm-30) cc_final: 0.8392 (tm-30) REVERT: A 120 MET cc_start: 0.9067 (mmp) cc_final: 0.8627 (mmm) REVERT: B 84 MET cc_start: 0.9056 (mmm) cc_final: 0.8692 (mmm) REVERT: B 85 ASP cc_start: 0.8547 (m-30) cc_final: 0.7320 (t0) REVERT: C 72 ASP cc_start: 0.8690 (m-30) cc_final: 0.8298 (m-30) REVERT: E 37 LYS cc_start: 0.9088 (tppt) cc_final: 0.8768 (mmmt) REVERT: H 59 MET cc_start: 0.9298 (tpp) cc_final: 0.9075 (tpp) REVERT: K 15 MET cc_start: 0.8671 (ptm) cc_final: 0.8334 (ptm) REVERT: K 65 ASP cc_start: 0.9346 (m-30) cc_final: 0.8988 (p0) REVERT: L 15 MET cc_start: 0.8191 (mtp) cc_final: 0.7873 (mtp) REVERT: M 443 GLU cc_start: 0.9248 (tt0) cc_final: 0.8809 (tm-30) REVERT: M 447 GLU cc_start: 0.8861 (pm20) cc_final: 0.8518 (tp30) REVERT: a 105 GLU cc_start: 0.9351 (tm-30) cc_final: 0.9129 (tm-30) REVERT: a 120 MET cc_start: 0.8538 (mtp) cc_final: 0.8156 (mtp) REVERT: b 49 LEU cc_start: 0.9346 (mp) cc_final: 0.8799 (mp) REVERT: b 53 GLU cc_start: 0.9708 (mm-30) cc_final: 0.9252 (mm-30) REVERT: b 84 MET cc_start: 0.9054 (mmm) cc_final: 0.8553 (mmm) REVERT: b 85 ASP cc_start: 0.8318 (m-30) cc_final: 0.7587 (t0) REVERT: c 39 TYR cc_start: 0.9438 (m-80) cc_final: 0.9084 (m-80) REVERT: e 120 MET cc_start: 0.9302 (mmp) cc_final: 0.8848 (mmm) REVERT: g 41 GLU cc_start: 0.9016 (pm20) cc_final: 0.8772 (pm20) REVERT: h 62 MET cc_start: 0.9403 (mmm) cc_final: 0.9183 (mmm) REVERT: h 71 GLU cc_start: 0.9287 (tp30) cc_final: 0.9046 (tp30) REVERT: k 57 ASP cc_start: 0.9441 (p0) cc_final: 0.9104 (p0) REVERT: l 15 MET cc_start: 0.8747 (ptp) cc_final: 0.8155 (mtp) REVERT: m 526 LEU cc_start: 0.9488 (mt) cc_final: 0.9237 (mp) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.1876 time to fit residues: 46.2918 Evaluate side-chains 98 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.767 ------------------------------------------------------------------------------- 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: 20.0000 chunk 146 optimal weight: 20.0000 chunk 244 optimal weight: 9.9990 chunk 162 optimal weight: 6.9990 chunk 161 optimal weight: 7.9990 chunk 100 optimal weight: 10.0000 chunk 242 optimal weight: 30.0000 chunk 143 optimal weight: 2.9990 chunk 124 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 93 GLN ** 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 = 0.3342 r_free = 0.3342 target = 0.042142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.028226 restraints weight = 402419.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.028526 restraints weight = 202533.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.028836 restraints weight = 138952.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.029022 restraints weight = 113830.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.029095 restraints weight = 103790.679| |-----------------------------------------------------------------------------| r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 34126 Z= 0.199 Angle : 0.564 8.252 49074 Z= 0.336 Chirality : 0.034 0.146 5538 Planarity : 0.004 0.141 3788 Dihedral : 29.944 178.736 10138 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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 aren not related in a simple way. whole: 2.60 (0.18), residues: 2202 helix: 2.46 (0.14), residues: 1420 sheet: 1.44 (0.51), residues: 120 loop : 0.16 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG L 82 TYR 0.021 0.001 TYR K 43 PHE 0.039 0.002 PHE L 78 TRP 0.014 0.001 TRP L 84 HIS 0.007 0.001 HIS b 75 Details of bonding type rmsd covalent geometry : bond 0.00424 (34126) covalent geometry : angle 0.56395 (49074) hydrogen bonds : bond 0.04491 ( 2007) hydrogen bonds : angle 3.24020 ( 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 135 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8840 (tm-30) cc_final: 0.8484 (tm-30) REVERT: A 120 MET cc_start: 0.8961 (mmp) cc_final: 0.8685 (mmm) REVERT: B 84 MET cc_start: 0.9157 (mmm) cc_final: 0.8770 (mmm) REVERT: B 85 ASP cc_start: 0.8602 (m-30) cc_final: 0.7364 (t0) REVERT: E 37 LYS cc_start: 0.9144 (tppt) cc_final: 0.8778 (mmmt) REVERT: H 59 MET cc_start: 0.9309 (tpp) cc_final: 0.9068 (tpp) REVERT: K 65 ASP cc_start: 0.9369 (m-30) cc_final: 0.8988 (p0) REVERT: L 15 MET cc_start: 0.8180 (mtp) cc_final: 0.7712 (mtt) REVERT: L 83 GLU cc_start: 0.9438 (tp30) cc_final: 0.8807 (tp30) REVERT: M 443 GLU cc_start: 0.9214 (tt0) cc_final: 0.8856 (tm-30) REVERT: M 447 GLU cc_start: 0.8908 (pm20) cc_final: 0.8506 (tp30) REVERT: a 105 GLU cc_start: 0.9401 (tm-30) cc_final: 0.9156 (tm-30) REVERT: a 120 MET cc_start: 0.8566 (mtp) cc_final: 0.8174 (mtp) REVERT: b 49 LEU cc_start: 0.9333 (mp) cc_final: 0.8773 (mp) REVERT: b 53 GLU cc_start: 0.9714 (mm-30) cc_final: 0.9263 (mm-30) REVERT: b 84 MET cc_start: 0.9141 (mmm) cc_final: 0.8629 (mmm) REVERT: b 85 ASP cc_start: 0.8354 (m-30) cc_final: 0.7688 (t0) REVERT: c 39 TYR cc_start: 0.9531 (m-80) cc_final: 0.9200 (m-80) REVERT: e 120 MET cc_start: 0.9305 (mmp) cc_final: 0.8812 (mmm) REVERT: f 84 MET cc_start: 0.9327 (mmm) cc_final: 0.9038 (tpt) REVERT: g 41 GLU cc_start: 0.9097 (pm20) cc_final: 0.8844 (pm20) REVERT: h 59 MET cc_start: 0.9360 (tpp) cc_final: 0.9084 (tpp) REVERT: h 62 MET cc_start: 0.9514 (mmm) cc_final: 0.9295 (mmm) REVERT: h 71 GLU cc_start: 0.9379 (tp30) cc_final: 0.9132 (tp30) REVERT: k 57 ASP cc_start: 0.9494 (p0) cc_final: 0.9064 (p0) REVERT: l 15 MET cc_start: 0.8731 (ptp) cc_final: 0.8199 (mtp) REVERT: m 526 LEU cc_start: 0.9392 (mt) cc_final: 0.9129 (mp) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1812 time to fit residues: 41.1431 Evaluate side-chains 96 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.871 ------------------------------------------------------------------------------- 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: 5.9990 chunk 157 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 228 optimal weight: 20.0000 chunk 156 optimal weight: 6.9990 chunk 152 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 chunk 277 optimal weight: 50.0000 chunk 189 optimal weight: 10.0000 chunk 174 optimal weight: 30.0000 chunk 14 optimal weight: 0.9980 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.042073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.028142 restraints weight = 399712.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.028478 restraints weight = 202113.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.028792 restraints weight = 137834.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.028972 restraints weight = 114791.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.029041 restraints weight = 104468.079| |-----------------------------------------------------------------------------| 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 = 0.83 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 | |-----------------------------------------------------------------------------| r_final: 0.2785 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 34126 Z= 0.188 Angle : 0.554 7.505 49074 Z= 0.330 Chirality : 0.034 0.136 5538 Planarity : 0.004 0.100 3788 Dihedral : 29.979 178.618 10138 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % 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 aren not related in a simple way. whole: 2.66 (0.18), residues: 2202 helix: 2.52 (0.14), residues: 1420 sheet: 1.44 (0.51), residues: 120 loop : 0.16 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 86 TYR 0.014 0.001 TYR K 43 PHE 0.047 0.002 PHE e 67 TRP 0.007 0.001 TRP K 62 HIS 0.007 0.001 HIS b 75 Details of bonding type rmsd covalent geometry : bond 0.00401 (34126) covalent geometry : angle 0.55411 (49074) hydrogen bonds : bond 0.04116 ( 2007) hydrogen bonds : angle 3.21099 ( 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 137 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8829 (tm-30) cc_final: 0.8479 (tm-30) REVERT: A 120 MET cc_start: 0.8959 (mmp) cc_final: 0.8670 (mmm) REVERT: B 84 MET cc_start: 0.9148 (mmm) cc_final: 0.8894 (mmm) REVERT: B 85 ASP cc_start: 0.8587 (m-30) cc_final: 0.7336 (t0) REVERT: B 88 TYR cc_start: 0.9062 (m-10) cc_final: 0.8498 (m-10) REVERT: E 37 LYS cc_start: 0.9101 (tppt) cc_final: 0.8752 (mmmt) REVERT: H 59 MET cc_start: 0.9313 (tpp) cc_final: 0.9041 (tpp) REVERT: K 65 ASP cc_start: 0.9368 (m-30) cc_final: 0.9002 (p0) REVERT: L 15 MET cc_start: 0.8155 (mtp) cc_final: 0.7800 (mtp) REVERT: M 443 GLU cc_start: 0.9216 (tt0) cc_final: 0.8845 (tm-30) REVERT: M 447 GLU cc_start: 0.8917 (pm20) cc_final: 0.8319 (tm-30) REVERT: a 105 GLU cc_start: 0.9368 (tm-30) cc_final: 0.9121 (tm-30) REVERT: a 120 MET cc_start: 0.8542 (mtp) cc_final: 0.8148 (mtp) REVERT: b 49 LEU cc_start: 0.9316 (mp) cc_final: 0.8762 (mp) REVERT: b 53 GLU cc_start: 0.9711 (mm-30) cc_final: 0.9251 (mm-30) REVERT: b 63 GLU cc_start: 0.8936 (tm-30) cc_final: 0.8662 (tm-30) REVERT: b 84 MET cc_start: 0.9127 (mmm) cc_final: 0.8590 (mmm) REVERT: b 85 ASP cc_start: 0.8325 (m-30) cc_final: 0.7670 (t0) REVERT: c 39 TYR cc_start: 0.9536 (m-80) cc_final: 0.9236 (m-80) REVERT: d 93 GLU cc_start: 0.9548 (mp0) cc_final: 0.9313 (mp0) REVERT: e 120 MET cc_start: 0.9314 (mmp) cc_final: 0.8819 (mmm) REVERT: f 84 MET cc_start: 0.9281 (mmm) cc_final: 0.8946 (tpt) REVERT: g 41 GLU cc_start: 0.9083 (pm20) cc_final: 0.8806 (pm20) REVERT: h 62 MET cc_start: 0.9503 (mmm) cc_final: 0.9302 (mmm) REVERT: h 71 GLU cc_start: 0.9358 (tp30) cc_final: 0.9112 (tp30) REVERT: k 57 ASP cc_start: 0.9476 (p0) cc_final: 0.9060 (p0) REVERT: l 15 MET cc_start: 0.8620 (ptp) cc_final: 0.8120 (mtp) REVERT: m 526 LEU cc_start: 0.9393 (mt) cc_final: 0.9128 (mp) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.2009 time to fit residues: 46.1473 Evaluate side-chains 100 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.964 ------------------------------------------------------------------------------- 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: 5.9990 chunk 243 optimal weight: 60.0000 chunk 162 optimal weight: 2.9990 chunk 272 optimal weight: 40.0000 chunk 125 optimal weight: 8.9990 chunk 102 optimal weight: 20.0000 chunk 22 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 chunk 220 optimal weight: 10.0000 chunk 260 optimal weight: 40.0000 chunk 275 optimal weight: 0.0030 overall best weight: 4.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 93 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 = 0.3361 r_free = 0.3361 target = 0.042089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.028555 restraints weight = 405227.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.028853 restraints weight = 208031.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.029150 restraints weight = 143223.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.029337 restraints weight = 117536.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.029407 restraints weight = 106864.894| |-----------------------------------------------------------------------------| r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2829 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 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 = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2829 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 34126 Z= 0.182 Angle : 0.550 8.930 49074 Z= 0.328 Chirality : 0.033 0.138 5538 Planarity : 0.004 0.040 3788 Dihedral : 29.966 178.579 10138 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % 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 aren not related in a simple way. whole: 2.66 (0.18), residues: 2202 helix: 2.51 (0.14), residues: 1422 sheet: 1.42 (0.50), residues: 120 loop : 0.18 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 82 TYR 0.014 0.001 TYR K 43 PHE 0.037 0.001 PHE e 67 TRP 0.008 0.001 TRP K 84 HIS 0.008 0.001 HIS b 75 Details of bonding type rmsd covalent geometry : bond 0.00389 (34126) covalent geometry : angle 0.55031 (49074) hydrogen bonds : bond 0.04129 ( 2007) hydrogen bonds : angle 3.18776 ( 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 134 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8729 (tm-30) cc_final: 0.8377 (tm-30) REVERT: A 120 MET cc_start: 0.9057 (mmp) cc_final: 0.8770 (mmm) REVERT: B 84 MET cc_start: 0.9043 (mmm) cc_final: 0.8766 (mmm) REVERT: B 85 ASP cc_start: 0.8554 (m-30) cc_final: 0.7335 (t0) REVERT: B 88 TYR cc_start: 0.9016 (m-10) cc_final: 0.8455 (m-10) REVERT: E 37 LYS cc_start: 0.9036 (tppt) cc_final: 0.8743 (mmmt) REVERT: H 59 MET cc_start: 0.9277 (tpp) cc_final: 0.8996 (tpp) REVERT: H 76 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8735 (mm-30) REVERT: K 65 ASP cc_start: 0.9322 (m-30) cc_final: 0.8963 (p0) REVERT: L 15 MET cc_start: 0.8218 (mtp) cc_final: 0.7662 (mtt) REVERT: M 443 GLU cc_start: 0.9277 (tt0) cc_final: 0.8811 (tm-30) REVERT: M 447 GLU cc_start: 0.8898 (pm20) cc_final: 0.8321 (tm-30) REVERT: M 453 ARG cc_start: 0.9518 (mtt90) cc_final: 0.9252 (mtm-85) REVERT: a 105 GLU cc_start: 0.9308 (tm-30) cc_final: 0.9052 (tm-30) REVERT: a 120 MET cc_start: 0.8671 (mtp) cc_final: 0.8254 (mtp) REVERT: b 49 LEU cc_start: 0.9326 (mp) cc_final: 0.8750 (mp) REVERT: b 53 GLU cc_start: 0.9660 (mm-30) cc_final: 0.9223 (mm-30) REVERT: b 63 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8559 (tm-30) REVERT: b 84 MET cc_start: 0.9042 (mmm) cc_final: 0.8544 (mmm) REVERT: b 85 ASP cc_start: 0.8303 (m-30) cc_final: 0.7686 (t0) REVERT: c 39 TYR cc_start: 0.9455 (m-80) cc_final: 0.9133 (m-80) REVERT: e 120 MET cc_start: 0.9335 (mmp) cc_final: 0.8831 (mmm) REVERT: h 59 MET cc_start: 0.9326 (tpp) cc_final: 0.9065 (tpp) REVERT: h 71 GLU cc_start: 0.9234 (tp30) cc_final: 0.8996 (tp30) REVERT: k 35 GLU cc_start: 0.8877 (pp20) cc_final: 0.8629 (pp20) REVERT: k 57 ASP cc_start: 0.9387 (p0) cc_final: 0.8978 (p0) REVERT: l 15 MET cc_start: 0.8720 (ptp) cc_final: 0.8256 (mtp) REVERT: m 526 LEU cc_start: 0.9403 (mt) cc_final: 0.9136 (mp) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.1956 time to fit residues: 43.2909 Evaluate side-chains 100 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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: 4.9990 chunk 163 optimal weight: 5.9990 chunk 91 optimal weight: 20.0000 chunk 183 optimal weight: 8.9990 chunk 247 optimal weight: 7.9990 chunk 157 optimal weight: 9.9990 chunk 113 optimal weight: 9.9990 chunk 155 optimal weight: 20.0000 chunk 198 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 262 optimal weight: 20.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN C 38 ASN ** N 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 47 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.041479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.027972 restraints weight = 410008.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.028276 restraints weight = 210717.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.028570 restraints weight = 143984.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.028752 restraints weight = 119399.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.028847 restraints weight = 109038.027| |-----------------------------------------------------------------------------| r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2805 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2805 r_free = 0.2805 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2805 r_free = 0.2805 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2805 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.4691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 34126 Z= 0.237 Angle : 0.587 7.658 49074 Z= 0.346 Chirality : 0.035 0.144 5538 Planarity : 0.004 0.044 3788 Dihedral : 30.097 178.068 10138 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.05 % Allowed : 0.27 % 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 aren not related in a simple way. whole: 2.51 (0.18), residues: 2202 helix: 2.41 (0.14), residues: 1424 sheet: 1.30 (0.51), residues: 120 loop : 0.08 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 82 TYR 0.013 0.001 TYR K 43 PHE 0.042 0.002 PHE e 67 TRP 0.009 0.001 TRP K 62 HIS 0.007 0.002 HIS b 75 Details of bonding type rmsd covalent geometry : bond 0.00507 (34126) covalent geometry : angle 0.58701 (49074) hydrogen bonds : bond 0.05469 ( 2007) hydrogen bonds : angle 3.37720 ( 5034) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6117.10 seconds wall clock time: 105 minutes 59.14 seconds (6359.14 seconds total)