Starting phenix.real_space_refine on Wed May 28 18:36:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j8o_61233/05_2025/9j8o_61233.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j8o_61233/05_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_61233/05_2025/9j8o_61233.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j8o_61233/05_2025/9j8o_61233.map" model { file = "/net/cci-nas-00/data/ceres_data/9j8o_61233/05_2025/9j8o_61233.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j8o_61233/05_2025/9j8o_61233.cif" } resolution = 4.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 18.18, per 1000 atoms: 0.57 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: 8.55 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 14.51 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: 13.91 Time building geometry restraints manager: 9.91 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: 0.01 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: 0.690 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: 0.030 Extract box with map and model: 1.200 Check model and map are aligned: 0.230 Set scattering table: 0.280 Process input model: 79.110 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.630 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.007 0.001 TRP L 84 HIS 0.006 0.001 HIS f 75 PHE 0.009 0.001 PHE b 100 TYR 0.016 0.002 TYR L 43 ARG 0.004 0.001 ARG F 55 Details of bonding type rmsd hydrogen bonds : bond 0.10256 ( 2007) hydrogen bonds : angle 4.16498 ( 5034) covalent geometry : bond 0.00708 (34126) covalent geometry : angle 0.66962 (49074) *********************** 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 : 3.672 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: 0.4466 time to fit residues: 318.9807 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 : 2.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 234 optimal weight: 10.0000 chunk 210 optimal weight: 80.0000 chunk 116 optimal weight: 5.9990 chunk 71 optimal weight: 60.0000 chunk 142 optimal weight: 7.9990 chunk 112 optimal weight: 9.9990 chunk 217 optimal weight: 10.0000 chunk 84 optimal weight: 20.0000 chunk 132 optimal weight: 0.9990 chunk 162 optimal weight: 5.9990 chunk 252 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 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 d 84 ASN d 95 GLN d 109 HIS ** 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.044054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.030274 restraints weight = 395695.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.030637 restraints weight = 195444.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.030951 restraints weight = 129983.005| |-----------------------------------------------------------------------------| r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2878 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2878 r_free = 0.2878 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2876 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2120 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= 0.200 Angle : 0.604 9.041 49074 Z= 0.356 Chirality : 0.036 0.191 5538 Planarity : 0.005 0.056 3788 Dihedral : 29.825 178.144 10138 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.18), residues: 2202 helix: 2.17 (0.14), residues: 1410 sheet: 1.72 (0.50), residues: 116 loop : -0.29 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP m 467 HIS 0.014 0.002 HIS f 75 PHE 0.017 0.002 PHE c 25 TYR 0.021 0.002 TYR b 98 ARG 0.007 0.001 ARG d 33 Details of bonding type rmsd hydrogen bonds : bond 0.04765 ( 2007) hydrogen bonds : angle 3.37979 ( 5034) covalent geometry : bond 0.00429 (34126) covalent geometry : angle 0.60414 (49074) *********************** 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 230 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 2.485 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: 0.8669 (tm-30) cc_final: 0.8447 (tm-30) REVERT: A 119 ILE cc_start: 0.9606 (pt) cc_final: 0.9369 (pt) REVERT: B 59 LYS cc_start: 0.9596 (tppt) cc_final: 0.9370 (tppt) REVERT: B 84 MET cc_start: 0.8955 (mmm) cc_final: 0.8754 (mmm) REVERT: B 85 ASP cc_start: 0.8238 (m-30) cc_final: 0.8009 (m-30) REVERT: C 72 ASP cc_start: 0.8440 (m-30) cc_final: 0.8067 (m-30) REVERT: D 93 GLU cc_start: 0.9381 (mp0) cc_final: 0.9141 (mp0) REVERT: E 90 MET cc_start: 0.9138 (mmm) cc_final: 0.8935 (mmp) REVERT: E 93 GLN cc_start: 0.9343 (tt0) cc_final: 0.8913 (tm-30) REVERT: K 65 ASP cc_start: 0.9338 (m-30) cc_final: 0.9031 (m-30) REVERT: K 76 ASP cc_start: 0.8977 (t0) cc_final: 0.8653 (t0) REVERT: L 52 LEU cc_start: 0.9270 (mt) cc_final: 0.9019 (mp) REVERT: L 83 GLU cc_start: 0.9465 (tp30) cc_final: 0.8839 (tp30) REVERT: a 105 GLU cc_start: 0.9236 (tm-30) cc_final: 0.8956 (tm-30) REVERT: a 112 ILE cc_start: 0.9095 (mt) cc_final: 0.8861 (mt) REVERT: a 120 MET cc_start: 0.8653 (mtp) cc_final: 0.8263 (mtt) REVERT: b 49 LEU cc_start: 0.9653 (mp) cc_final: 0.8812 (mm) REVERT: b 53 GLU cc_start: 0.9643 (mm-30) cc_final: 0.9230 (mm-30) REVERT: b 84 MET cc_start: 0.8744 (mmm) cc_final: 0.8504 (mmm) REVERT: b 85 ASP cc_start: 0.8150 (m-30) cc_final: 0.7517 (t0) REVERT: c 39 TYR cc_start: 0.9014 (m-80) cc_final: 0.6583 (m-80) REVERT: c 90 ASP cc_start: 0.9020 (t70) cc_final: 0.8769 (t0) REVERT: d 71 GLU cc_start: 0.9062 (tt0) cc_final: 0.8854 (tp30) REVERT: d 76 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8602 (mm-30) REVERT: e 120 MET cc_start: 0.8973 (mmp) cc_final: 0.8618 (mmm) REVERT: e 124 ILE cc_start: 0.9719 (tt) cc_final: 0.9292 (tt) REVERT: h 59 MET cc_start: 0.9227 (tpp) cc_final: 0.8991 (tpp) REVERT: h 62 MET cc_start: 0.9401 (mmm) cc_final: 0.9162 (mmm) REVERT: k 15 MET cc_start: 0.9006 (ptm) cc_final: 0.8659 (ppp) REVERT: l 15 MET cc_start: 0.8511 (ptp) cc_final: 0.7997 (mtp) REVERT: l 56 GLU cc_start: 0.9298 (pm20) cc_final: 0.8913 (pm20) REVERT: l 57 ASP cc_start: 0.9478 (p0) cc_final: 0.9222 (p0) REVERT: l 89 LEU cc_start: 0.7606 (tt) cc_final: 0.7087 (tt) REVERT: m 526 LEU cc_start: 0.9662 (mt) cc_final: 0.9391 (mt) REVERT: m 530 LEU cc_start: 0.9391 (tp) cc_final: 0.9183 (tp) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.3946 time to fit residues: 149.1543 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 : 2.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 233 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 212 optimal weight: 30.0000 chunk 52 optimal weight: 20.0000 chunk 248 optimal weight: 5.9990 chunk 197 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 chunk 226 optimal weight: 30.0000 chunk 14 optimal weight: 2.9990 chunk 111 optimal weight: 30.0000 chunk 58 optimal weight: 10.0000 overall best weight: 6.9992 ------------------------------------------------------------------------------- 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 ** f 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.042945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.029235 restraints weight = 400610.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.029539 restraints weight = 207117.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.029831 restraints weight = 142114.994| |-----------------------------------------------------------------------------| r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2832 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 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 = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2832 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 34126 Z= 0.231 Angle : 0.601 7.310 49074 Z= 0.354 Chirality : 0.035 0.190 5538 Planarity : 0.004 0.058 3788 Dihedral : 29.864 179.037 10138 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.05 % Allowed : 2.09 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.18), residues: 2202 helix: 2.31 (0.14), residues: 1418 sheet: 1.49 (0.51), residues: 120 loop : -0.01 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 84 HIS 0.010 0.002 HIS f 75 PHE 0.019 0.002 PHE e 67 TYR 0.018 0.002 TYR D 40 ARG 0.010 0.001 ARG H 86 Details of bonding type rmsd hydrogen bonds : bond 0.05173 ( 2007) hydrogen bonds : angle 3.38652 ( 5034) covalent geometry : bond 0.00495 (34126) covalent geometry : angle 0.60098 (49074) *********************** 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 174 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 173 time to evaluate : 2.287 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: 0.8755 (tm-30) cc_final: 0.8492 (tm-30) REVERT: A 120 MET cc_start: 0.8882 (mmp) cc_final: 0.8660 (mmm) REVERT: B 85 ASP cc_start: 0.8515 (m-30) cc_final: 0.8250 (m-30) REVERT: C 72 ASP cc_start: 0.8595 (m-30) cc_final: 0.8215 (m-30) REVERT: D 93 GLU cc_start: 0.9412 (mp0) cc_final: 0.9210 (mp0) REVERT: D 105 GLU cc_start: 0.8800 (tp30) cc_final: 0.8427 (tp30) REVERT: H 59 MET cc_start: 0.9219 (tpp) cc_final: 0.8712 (tpp) REVERT: L 15 MET cc_start: 0.8263 (mtp) cc_final: 0.8029 (mtp) REVERT: L 83 GLU cc_start: 0.9496 (tp30) cc_final: 0.8900 (tp30) REVERT: M 443 GLU cc_start: 0.9200 (tt0) cc_final: 0.8869 (pt0) REVERT: M 447 GLU cc_start: 0.8846 (pm20) cc_final: 0.8137 (tm-30) REVERT: a 105 GLU cc_start: 0.9270 (tm-30) cc_final: 0.9004 (tm-30) REVERT: b 49 LEU cc_start: 0.9521 (mp) cc_final: 0.8935 (mm) REVERT: b 52 GLU cc_start: 0.8969 (pm20) cc_final: 0.8747 (pm20) REVERT: b 53 GLU cc_start: 0.9683 (mm-30) cc_final: 0.9256 (mm-30) REVERT: b 84 MET cc_start: 0.8919 (mmm) cc_final: 0.8644 (mmm) REVERT: b 85 ASP cc_start: 0.8238 (m-30) cc_final: 0.7562 (t0) REVERT: d 76 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8402 (mm-30) REVERT: e 120 MET cc_start: 0.9103 (mmp) cc_final: 0.8775 (mmm) REVERT: h 62 MET cc_start: 0.9448 (mmm) cc_final: 0.9246 (mmm) REVERT: l 15 MET cc_start: 0.8652 (ptp) cc_final: 0.8172 (mtp) REVERT: m 526 LEU cc_start: 0.9526 (mt) cc_final: 0.9318 (mp) outliers start: 1 outliers final: 0 residues processed: 173 average time/residue: 0.3785 time to fit residues: 109.4661 Evaluate side-chains 120 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 2.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 178 optimal weight: 2.9990 chunk 161 optimal weight: 20.0000 chunk 156 optimal weight: 9.9990 chunk 103 optimal weight: 30.0000 chunk 208 optimal weight: 20.0000 chunk 241 optimal weight: 20.0000 chunk 243 optimal weight: 60.0000 chunk 13 optimal weight: 3.9990 chunk 211 optimal weight: 50.0000 chunk 129 optimal weight: 0.1980 chunk 180 optimal weight: 4.9990 overall best weight: 4.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 47 GLN D 84 ASN E 39 HIS ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 433 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.043093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.029393 restraints weight = 400509.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.029692 restraints weight = 205883.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.029985 restraints weight = 141264.746| |-----------------------------------------------------------------------------| r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2842 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 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 = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2842 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 34126 Z= 0.172 Angle : 0.551 6.345 49074 Z= 0.328 Chirality : 0.034 0.146 5538 Planarity : 0.004 0.041 3788 Dihedral : 29.873 179.549 10138 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.18), residues: 2202 helix: 2.51 (0.14), residues: 1416 sheet: 1.52 (0.50), residues: 120 loop : 0.06 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 62 HIS 0.007 0.001 HIS f 75 PHE 0.016 0.001 PHE e 67 TYR 0.014 0.001 TYR D 40 ARG 0.008 0.000 ARG m 455 Details of bonding type rmsd hydrogen bonds : bond 0.03798 ( 2007) hydrogen bonds : angle 3.17737 ( 5034) covalent geometry : bond 0.00368 (34126) covalent geometry : angle 0.55132 (49074) *********************** 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 171 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 2.720 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: 0.8675 (tm-30) cc_final: 0.8330 (tm-30) REVERT: A 120 MET cc_start: 0.9100 (mmp) cc_final: 0.8868 (mmm) REVERT: B 85 ASP cc_start: 0.8480 (m-30) cc_final: 0.8222 (m-30) REVERT: C 72 ASP cc_start: 0.8636 (m-30) cc_final: 0.8259 (m-30) REVERT: D 93 GLU cc_start: 0.9408 (mp0) cc_final: 0.9203 (mp0) REVERT: D 105 GLU cc_start: 0.8786 (tp30) cc_final: 0.8407 (tp30) REVERT: K 15 MET cc_start: 0.8884 (ptm) cc_final: 0.8457 (ptm) REVERT: K 65 ASP cc_start: 0.9279 (m-30) cc_final: 0.8865 (p0) REVERT: L 57 ASP cc_start: 0.9469 (m-30) cc_final: 0.9153 (m-30) REVERT: L 83 GLU cc_start: 0.9498 (tp30) cc_final: 0.8928 (tp30) REVERT: M 443 GLU cc_start: 0.9257 (tt0) cc_final: 0.8934 (pt0) REVERT: a 105 GLU cc_start: 0.9305 (tm-30) cc_final: 0.9053 (tm-30) REVERT: b 49 LEU cc_start: 0.9515 (mp) cc_final: 0.8910 (mm) REVERT: b 52 GLU cc_start: 0.8948 (pm20) cc_final: 0.8741 (pm20) REVERT: b 53 GLU cc_start: 0.9701 (mm-30) cc_final: 0.9252 (mm-30) REVERT: b 84 MET cc_start: 0.9049 (mmm) cc_final: 0.8635 (mmm) REVERT: b 85 ASP cc_start: 0.8215 (m-30) cc_final: 0.7960 (m-30) REVERT: e 120 MET cc_start: 0.9174 (mmp) cc_final: 0.8775 (mmm) REVERT: h 71 GLU cc_start: 0.9281 (tp30) cc_final: 0.9050 (tp30) REVERT: h 95 GLN cc_start: 0.9598 (tt0) cc_final: 0.9290 (tm-30) REVERT: l 15 MET cc_start: 0.8693 (ptp) cc_final: 0.8089 (mtp) REVERT: m 526 LEU cc_start: 0.9532 (mt) cc_final: 0.9320 (mp) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.3872 time to fit residues: 112.3156 Evaluate side-chains 118 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 2.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 175 optimal weight: 7.9990 chunk 251 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 199 optimal weight: 0.5980 chunk 248 optimal weight: 5.9990 chunk 211 optimal weight: 50.0000 chunk 74 optimal weight: 20.0000 chunk 53 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 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 = 0.3389 r_free = 0.3389 target = 0.043114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.029383 restraints weight = 398581.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.029729 restraints weight = 198623.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.030033 restraints weight = 133987.876| |-----------------------------------------------------------------------------| r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2844 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2844 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34126 Z= 0.159 Angle : 0.539 8.114 49074 Z= 0.323 Chirality : 0.033 0.140 5538 Planarity : 0.003 0.041 3788 Dihedral : 29.829 179.524 10138 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.18), residues: 2202 helix: 2.57 (0.14), residues: 1414 sheet: 1.54 (0.50), residues: 120 loop : 0.14 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 62 HIS 0.010 0.001 HIS D 109 PHE 0.011 0.001 PHE L 78 TYR 0.011 0.001 TYR K 43 ARG 0.004 0.000 ARG m 455 Details of bonding type rmsd hydrogen bonds : bond 0.03753 ( 2007) hydrogen bonds : angle 3.11387 ( 5034) covalent geometry : bond 0.00340 (34126) covalent geometry : angle 0.53912 (49074) *********************** 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 167 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 2.624 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: 0.8665 (tm-30) cc_final: 0.8278 (tm-30) REVERT: B 85 ASP cc_start: 0.8461 (m-30) cc_final: 0.8208 (m-30) REVERT: C 72 ASP cc_start: 0.8601 (m-30) cc_final: 0.8214 (m-30) REVERT: D 105 GLU cc_start: 0.8881 (tp30) cc_final: 0.8676 (tp30) REVERT: E 37 LYS cc_start: 0.9175 (tppt) cc_final: 0.8855 (mmmt) REVERT: E 93 GLN cc_start: 0.9280 (tt0) cc_final: 0.8975 (tm-30) REVERT: K 15 MET cc_start: 0.8661 (ptm) cc_final: 0.8378 (ptm) REVERT: K 65 ASP cc_start: 0.9279 (m-30) cc_final: 0.8870 (p0) REVERT: L 83 GLU cc_start: 0.9509 (tp30) cc_final: 0.8930 (tp30) REVERT: M 443 GLU cc_start: 0.9225 (tt0) cc_final: 0.8891 (pt0) REVERT: M 447 GLU cc_start: 0.8825 (pm20) cc_final: 0.8193 (tm-30) REVERT: a 105 GLU cc_start: 0.9270 (tm-30) cc_final: 0.9033 (tm-30) REVERT: a 120 MET cc_start: 0.8740 (mtp) cc_final: 0.8409 (mtp) REVERT: b 49 LEU cc_start: 0.9464 (mp) cc_final: 0.8832 (mm) REVERT: b 52 GLU cc_start: 0.8967 (pm20) cc_final: 0.8759 (pm20) REVERT: b 53 GLU cc_start: 0.9703 (mm-30) cc_final: 0.9281 (mm-30) REVERT: b 84 MET cc_start: 0.9018 (mmm) cc_final: 0.8619 (mmm) REVERT: b 85 ASP cc_start: 0.8168 (m-30) cc_final: 0.7935 (m-30) REVERT: c 39 TYR cc_start: 0.9303 (m-80) cc_final: 0.8983 (m-80) REVERT: e 120 MET cc_start: 0.9166 (mmp) cc_final: 0.8769 (mmm) REVERT: g 41 GLU cc_start: 0.9024 (pm20) cc_final: 0.8701 (pm20) REVERT: h 62 MET cc_start: 0.9472 (mmm) cc_final: 0.9187 (mmm) REVERT: h 71 GLU cc_start: 0.9245 (tp30) cc_final: 0.9005 (tp30) REVERT: h 95 GLN cc_start: 0.9549 (tt0) cc_final: 0.9297 (tm-30) REVERT: l 15 MET cc_start: 0.8687 (ptp) cc_final: 0.8047 (mtp) REVERT: m 526 LEU cc_start: 0.9526 (mt) cc_final: 0.9281 (mp) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.3965 time to fit residues: 111.6036 Evaluate side-chains 117 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 2.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 105 optimal weight: 20.0000 chunk 244 optimal weight: 7.9990 chunk 173 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 222 optimal weight: 10.0000 chunk 145 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 139 optimal weight: 50.0000 chunk 271 optimal weight: 8.9990 chunk 36 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 47 GLN e 68 GLN e 93 GLN ** h 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.042379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.028715 restraints weight = 403886.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.029036 restraints weight = 203070.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.029335 restraints weight = 136921.353| |-----------------------------------------------------------------------------| r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2817 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2817 r_free = 0.2817 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2817 r_free = 0.2817 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2817 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3582 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= 0.209 Angle : 0.568 7.727 49074 Z= 0.337 Chirality : 0.034 0.241 5538 Planarity : 0.004 0.049 3788 Dihedral : 29.889 178.953 10138 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.05 % Allowed : 1.72 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.67 (0.18), residues: 2202 helix: 2.55 (0.14), residues: 1420 sheet: 1.41 (0.50), residues: 120 loop : 0.11 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 62 HIS 0.008 0.002 HIS f 75 PHE 0.014 0.001 PHE e 104 TYR 0.016 0.001 TYR D 40 ARG 0.008 0.000 ARG L 60 Details of bonding type rmsd hydrogen bonds : bond 0.04835 ( 2007) hydrogen bonds : angle 3.20770 ( 5034) covalent geometry : bond 0.00447 (34126) covalent geometry : angle 0.56844 (49074) *********************** 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 150 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 149 time to evaluate : 2.447 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: 0.8684 (tm-30) cc_final: 0.8343 (tm-30) REVERT: A 120 MET cc_start: 0.9148 (mmp) cc_final: 0.8740 (mmm) REVERT: B 85 ASP cc_start: 0.8513 (m-30) cc_final: 0.7439 (t0) REVERT: C 72 ASP cc_start: 0.8657 (m-30) cc_final: 0.8265 (m-30) REVERT: D 105 GLU cc_start: 0.8821 (tp30) cc_final: 0.8517 (tp30) REVERT: E 37 LYS cc_start: 0.9153 (tppt) cc_final: 0.8855 (mmmt) REVERT: K 65 ASP cc_start: 0.9274 (m-30) cc_final: 0.8923 (p0) REVERT: L 15 MET cc_start: 0.8418 (mtp) cc_final: 0.8192 (mtt) REVERT: M 443 GLU cc_start: 0.9220 (tt0) cc_final: 0.8883 (pt0) REVERT: M 447 GLU cc_start: 0.8826 (pm20) cc_final: 0.8163 (tm-30) REVERT: a 105 GLU cc_start: 0.9257 (tm-30) cc_final: 0.9050 (tm-30) REVERT: a 120 MET cc_start: 0.8817 (mtp) cc_final: 0.8502 (mtp) REVERT: b 49 LEU cc_start: 0.9294 (mp) cc_final: 0.8771 (mp) REVERT: b 53 GLU cc_start: 0.9673 (mm-30) cc_final: 0.9242 (mm-30) REVERT: b 84 MET cc_start: 0.9085 (mmm) cc_final: 0.8674 (mmm) REVERT: b 85 ASP cc_start: 0.8268 (m-30) cc_final: 0.7998 (m-30) REVERT: c 39 TYR cc_start: 0.9330 (m-80) cc_final: 0.8924 (m-80) REVERT: e 120 MET cc_start: 0.9269 (mmp) cc_final: 0.8851 (mmm) REVERT: g 41 GLU cc_start: 0.8964 (pm20) cc_final: 0.8683 (pm20) REVERT: h 62 MET cc_start: 0.9431 (mmm) cc_final: 0.9182 (mmm) REVERT: h 71 GLU cc_start: 0.9194 (tp30) cc_final: 0.8956 (tp30) REVERT: l 15 MET cc_start: 0.8761 (ptp) cc_final: 0.8249 (mtp) REVERT: m 526 LEU cc_start: 0.9485 (mt) cc_final: 0.9202 (mp) outliers start: 1 outliers final: 0 residues processed: 150 average time/residue: 0.4000 time to fit residues: 100.9316 Evaluate side-chains 105 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 2.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 33 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 264 optimal weight: 40.0000 chunk 220 optimal weight: 10.0000 chunk 140 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 31 HIS M 472 GLN a 68 GLN f 75 HIS ** h 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.042802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.029191 restraints weight = 400932.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.029476 restraints weight = 208070.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.029773 restraints weight = 143419.120| |-----------------------------------------------------------------------------| r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2839 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2839 r_free = 0.2839 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 = 0.2839 r_free = 0.2839 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2839 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 34126 Z= 0.159 Angle : 0.543 8.045 49074 Z= 0.323 Chirality : 0.033 0.153 5538 Planarity : 0.003 0.040 3788 Dihedral : 29.881 178.984 10138 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.74 (0.18), residues: 2202 helix: 2.58 (0.14), residues: 1418 sheet: 1.45 (0.50), residues: 120 loop : 0.21 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 84 HIS 0.006 0.001 HIS b 75 PHE 0.008 0.001 PHE e 67 TYR 0.011 0.001 TYR G 50 ARG 0.005 0.000 ARG L 82 Details of bonding type rmsd hydrogen bonds : bond 0.03581 ( 2007) hydrogen bonds : angle 3.08790 ( 5034) covalent geometry : bond 0.00337 (34126) covalent geometry : angle 0.54328 (49074) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 2.537 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: 0.8716 (tm-30) cc_final: 0.8351 (tm-30) REVERT: A 120 MET cc_start: 0.9086 (mmp) cc_final: 0.8794 (mmm) REVERT: B 85 ASP cc_start: 0.8511 (m-30) cc_final: 0.7347 (t0) REVERT: C 72 ASP cc_start: 0.8681 (m-30) cc_final: 0.8298 (m-30) REVERT: D 105 GLU cc_start: 0.8884 (tp30) cc_final: 0.8569 (tp30) REVERT: E 37 LYS cc_start: 0.9168 (tppt) cc_final: 0.8815 (mmmt) REVERT: K 15 MET cc_start: 0.8793 (ptm) cc_final: 0.8386 (ptm) REVERT: K 65 ASP cc_start: 0.9290 (m-30) cc_final: 0.8928 (p0) REVERT: L 83 GLU cc_start: 0.9531 (tp30) cc_final: 0.8906 (tp30) REVERT: M 443 GLU cc_start: 0.9251 (tt0) cc_final: 0.8870 (pt0) REVERT: M 447 GLU cc_start: 0.8814 (pm20) cc_final: 0.8175 (tm-30) REVERT: a 105 GLU cc_start: 0.9293 (tm-30) cc_final: 0.9059 (tm-30) REVERT: a 120 MET cc_start: 0.8782 (mtp) cc_final: 0.8450 (mtp) REVERT: b 49 LEU cc_start: 0.9366 (mp) cc_final: 0.8814 (mp) REVERT: b 53 GLU cc_start: 0.9653 (mm-30) cc_final: 0.9229 (mm-30) REVERT: b 84 MET cc_start: 0.9129 (mmm) cc_final: 0.8687 (mmm) REVERT: b 85 ASP cc_start: 0.8188 (m-30) cc_final: 0.7936 (m-30) REVERT: c 39 TYR cc_start: 0.9363 (m-80) cc_final: 0.9001 (m-80) REVERT: e 120 MET cc_start: 0.9278 (mmp) cc_final: 0.8840 (mmm) REVERT: f 84 MET cc_start: 0.9290 (mmm) cc_final: 0.9050 (tpp) REVERT: g 41 GLU cc_start: 0.9003 (pm20) cc_final: 0.8802 (pm20) REVERT: h 62 MET cc_start: 0.9447 (mmm) cc_final: 0.9215 (mmm) REVERT: h 71 GLU cc_start: 0.9226 (tp30) cc_final: 0.8984 (tp30) REVERT: l 15 MET cc_start: 0.8726 (ptp) cc_final: 0.8152 (mtp) REVERT: m 526 LEU cc_start: 0.9406 (mt) cc_final: 0.9152 (mp) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.4110 time to fit residues: 101.5706 Evaluate side-chains 105 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 2.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 36 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 111 optimal weight: 8.9990 chunk 189 optimal weight: 8.9990 chunk 54 optimal weight: 20.0000 chunk 245 optimal weight: 10.0000 chunk 12 optimal weight: 0.7980 chunk 145 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 227 optimal weight: 40.0000 chunk 238 optimal weight: 10.0000 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN D 47 GLN e 93 GLN ** h 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.042364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.028769 restraints weight = 403304.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.029075 restraints weight = 203976.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.029365 restraints weight = 138327.945| |-----------------------------------------------------------------------------| r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2822 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2822 r_free = 0.2822 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 = 0.2822 r_free = 0.2822 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2822 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 34126 Z= 0.194 Angle : 0.559 12.342 49074 Z= 0.332 Chirality : 0.034 0.139 5538 Planarity : 0.004 0.045 3788 Dihedral : 29.877 178.941 10138 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.18), residues: 2202 helix: 2.51 (0.14), residues: 1420 sheet: 1.44 (0.50), residues: 120 loop : 0.18 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 84 HIS 0.007 0.001 HIS b 75 PHE 0.018 0.001 PHE L 78 TYR 0.012 0.001 TYR D 40 ARG 0.015 0.000 ARG L 82 Details of bonding type rmsd hydrogen bonds : bond 0.04367 ( 2007) hydrogen bonds : angle 3.17506 ( 5034) covalent geometry : bond 0.00415 (34126) covalent geometry : angle 0.55860 (49074) *********************** 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 140 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 2.526 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: 0.8667 (tm-30) cc_final: 0.8315 (tm-30) REVERT: A 120 MET cc_start: 0.9113 (mmp) cc_final: 0.8811 (mmm) REVERT: B 85 ASP cc_start: 0.8550 (m-30) cc_final: 0.7410 (t0) REVERT: C 72 ASP cc_start: 0.8682 (m-30) cc_final: 0.8287 (m-30) REVERT: E 37 LYS cc_start: 0.9148 (tppt) cc_final: 0.8795 (mmmt) REVERT: K 15 MET cc_start: 0.8787 (ptm) cc_final: 0.8332 (ptm) REVERT: K 65 ASP cc_start: 0.9296 (m-30) cc_final: 0.8948 (p0) REVERT: L 15 MET cc_start: 0.8390 (mtp) cc_final: 0.7987 (mtt) REVERT: M 443 GLU cc_start: 0.9220 (tt0) cc_final: 0.8876 (pt0) REVERT: M 447 GLU cc_start: 0.8845 (pm20) cc_final: 0.8214 (tm-30) REVERT: a 105 GLU cc_start: 0.9285 (tm-30) cc_final: 0.9077 (tm-30) REVERT: a 120 MET cc_start: 0.8713 (mtp) cc_final: 0.8387 (mtp) REVERT: b 49 LEU cc_start: 0.9312 (mp) cc_final: 0.8746 (mp) REVERT: b 53 GLU cc_start: 0.9651 (mm-30) cc_final: 0.9234 (mm-30) REVERT: b 84 MET cc_start: 0.9131 (mmm) cc_final: 0.8731 (mmm) REVERT: b 85 ASP cc_start: 0.8280 (m-30) cc_final: 0.8020 (m-30) REVERT: c 39 TYR cc_start: 0.9361 (m-80) cc_final: 0.9003 (m-80) REVERT: e 120 MET cc_start: 0.9300 (mmp) cc_final: 0.8869 (mmm) REVERT: f 63 GLU cc_start: 0.9014 (pm20) cc_final: 0.8735 (pm20) REVERT: h 62 MET cc_start: 0.9422 (mmm) cc_final: 0.9201 (mmm) REVERT: h 71 GLU cc_start: 0.9190 (tp30) cc_final: 0.8958 (tp30) REVERT: l 15 MET cc_start: 0.8849 (ptp) cc_final: 0.8309 (mtp) REVERT: m 526 LEU cc_start: 0.9386 (mt) cc_final: 0.9077 (mp) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.3904 time to fit residues: 92.2033 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 : 2.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 192 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 235 optimal weight: 20.0000 chunk 155 optimal weight: 20.0000 chunk 57 optimal weight: 9.9990 chunk 63 optimal weight: 8.9990 chunk 156 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 246 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 ** 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 = 0.3350 r_free = 0.3350 target = 0.042361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.028438 restraints weight = 401859.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.028750 restraints weight = 203337.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.029088 restraints weight = 139081.333| |-----------------------------------------------------------------------------| r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 34126 Z= 0.181 Angle : 0.552 7.564 49074 Z= 0.329 Chirality : 0.033 0.137 5538 Planarity : 0.004 0.042 3788 Dihedral : 29.911 178.875 10138 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.18), residues: 2202 helix: 2.48 (0.14), residues: 1420 sheet: 1.50 (0.50), residues: 120 loop : 0.18 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 84 HIS 0.007 0.001 HIS b 75 PHE 0.010 0.001 PHE E 104 TYR 0.021 0.001 TYR K 43 ARG 0.013 0.000 ARG L 82 Details of bonding type rmsd hydrogen bonds : bond 0.03999 ( 2007) hydrogen bonds : angle 3.16224 ( 5034) covalent geometry : bond 0.00386 (34126) covalent geometry : angle 0.55161 (49074) *********************** 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 : 2.473 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: 0.8828 (tm-30) cc_final: 0.8467 (tm-30) REVERT: A 120 MET cc_start: 0.8951 (mmp) cc_final: 0.8676 (mmm) REVERT: B 84 MET cc_start: 0.9050 (mmm) cc_final: 0.8807 (mmm) REVERT: B 85 ASP cc_start: 0.8609 (m-30) cc_final: 0.7383 (t0) REVERT: B 88 TYR cc_start: 0.9066 (m-10) cc_final: 0.8512 (m-10) REVERT: E 37 LYS cc_start: 0.9163 (tppt) cc_final: 0.8763 (mmmt) REVERT: K 15 MET cc_start: 0.8868 (ptm) cc_final: 0.8306 (ptm) REVERT: K 65 ASP cc_start: 0.9368 (m-30) cc_final: 0.9001 (p0) REVERT: L 15 MET cc_start: 0.8298 (mtp) cc_final: 0.7807 (mtt) REVERT: M 443 GLU cc_start: 0.9253 (tt0) cc_final: 0.8871 (tm-30) REVERT: M 447 GLU cc_start: 0.8859 (pm20) cc_final: 0.8179 (tm-30) REVERT: a 105 GLU cc_start: 0.9383 (tm-30) cc_final: 0.9135 (tm-30) REVERT: a 120 MET cc_start: 0.8665 (mtp) cc_final: 0.8347 (mtp) REVERT: b 49 LEU cc_start: 0.9311 (mp) cc_final: 0.8749 (mp) REVERT: b 53 GLU cc_start: 0.9716 (mm-30) cc_final: 0.9258 (mm-30) REVERT: b 63 GLU cc_start: 0.8841 (tm-30) cc_final: 0.8640 (tm-30) REVERT: b 85 ASP cc_start: 0.8291 (m-30) cc_final: 0.8001 (m-30) REVERT: c 39 TYR cc_start: 0.9502 (m-80) cc_final: 0.9169 (m-80) REVERT: e 120 MET cc_start: 0.9300 (mmp) cc_final: 0.8824 (mmm) REVERT: f 84 MET cc_start: 0.9408 (mmm) cc_final: 0.9171 (tpp) REVERT: h 59 MET cc_start: 0.9273 (tpp) cc_final: 0.8995 (tpp) REVERT: h 62 MET cc_start: 0.9555 (mmm) cc_final: 0.9325 (mmm) REVERT: h 71 GLU cc_start: 0.9334 (tp30) cc_final: 0.9075 (tp30) REVERT: l 15 MET cc_start: 0.8722 (ptp) cc_final: 0.8178 (mtp) REVERT: m 526 LEU cc_start: 0.9308 (mt) cc_final: 0.8993 (mp) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.4001 time to fit residues: 92.3851 Evaluate side-chains 99 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 2.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 270 optimal weight: 40.0000 chunk 126 optimal weight: 8.9990 chunk 193 optimal weight: 8.9990 chunk 90 optimal weight: 20.0000 chunk 257 optimal weight: 0.0370 chunk 153 optimal weight: 20.0000 chunk 5 optimal weight: 2.9990 chunk 246 optimal weight: 4.9990 chunk 172 optimal weight: 5.9990 chunk 169 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 overall best weight: 3.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS ** 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 = 0.3376 r_free = 0.3376 target = 0.042637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.029086 restraints weight = 400613.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.029378 restraints weight = 208802.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.029685 restraints weight = 145454.258| |-----------------------------------------------------------------------------| r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2839 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2839 r_free = 0.2839 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 = 0.2839 r_free = 0.2839 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2839 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 34126 Z= 0.156 Angle : 0.542 9.689 49074 Z= 0.322 Chirality : 0.033 0.139 5538 Planarity : 0.003 0.041 3788 Dihedral : 29.859 179.066 10138 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.18), residues: 2202 helix: 2.49 (0.14), residues: 1422 sheet: 1.56 (0.50), residues: 120 loop : 0.21 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 62 HIS 0.007 0.001 HIS b 75 PHE 0.017 0.001 PHE e 67 TYR 0.018 0.001 TYR K 43 ARG 0.010 0.000 ARG L 82 Details of bonding type rmsd hydrogen bonds : bond 0.03605 ( 2007) hydrogen bonds : angle 3.08028 ( 5034) covalent geometry : bond 0.00331 (34126) covalent geometry : angle 0.54232 (49074) ********************** 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 138 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 2.303 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: 0.8706 (tm-30) cc_final: 0.8340 (tm-30) REVERT: A 120 MET cc_start: 0.9090 (mmp) cc_final: 0.8782 (mmm) REVERT: B 84 MET cc_start: 0.8939 (mmm) cc_final: 0.8702 (mmm) REVERT: B 85 ASP cc_start: 0.8532 (m-30) cc_final: 0.7293 (t0) REVERT: B 88 TYR cc_start: 0.8978 (m-10) cc_final: 0.8493 (m-10) REVERT: E 37 LYS cc_start: 0.9138 (tppt) cc_final: 0.8762 (mmmt) REVERT: H 76 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8709 (mm-30) REVERT: K 15 MET cc_start: 0.8688 (ptm) cc_final: 0.8165 (ptm) REVERT: K 65 ASP cc_start: 0.9307 (m-30) cc_final: 0.8955 (p0) REVERT: L 15 MET cc_start: 0.8280 (mtp) cc_final: 0.7910 (mtp) REVERT: M 443 GLU cc_start: 0.9275 (tt0) cc_final: 0.8847 (tm-30) REVERT: M 447 GLU cc_start: 0.8861 (pm20) cc_final: 0.8226 (tm-30) REVERT: a 105 GLU cc_start: 0.9293 (tm-30) cc_final: 0.9047 (tm-30) REVERT: a 120 MET cc_start: 0.8731 (mtp) cc_final: 0.8400 (mtp) REVERT: b 49 LEU cc_start: 0.9319 (mp) cc_final: 0.8729 (mp) REVERT: b 53 GLU cc_start: 0.9669 (mm-30) cc_final: 0.9232 (mm-30) REVERT: b 63 GLU cc_start: 0.8781 (tm-30) cc_final: 0.8514 (tm-30) REVERT: b 85 ASP cc_start: 0.8206 (m-30) cc_final: 0.7980 (m-30) REVERT: c 39 TYR cc_start: 0.9397 (m-80) cc_final: 0.9085 (m-80) REVERT: e 120 MET cc_start: 0.9315 (mmp) cc_final: 0.8838 (mmm) REVERT: f 63 GLU cc_start: 0.9004 (pm20) cc_final: 0.8760 (pm20) REVERT: f 84 MET cc_start: 0.9286 (mmm) cc_final: 0.9050 (tpp) REVERT: h 62 MET cc_start: 0.9447 (mmm) cc_final: 0.9224 (mmm) REVERT: h 71 GLU cc_start: 0.9237 (tp30) cc_final: 0.8988 (tp30) REVERT: l 15 MET cc_start: 0.8690 (ptp) cc_final: 0.8202 (mtp) REVERT: m 526 LEU cc_start: 0.9316 (mt) cc_final: 0.9000 (mp) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.3858 time to fit residues: 90.0760 Evaluate side-chains 102 residues out of total 1862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 2.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 217 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 chunk 215 optimal weight: 20.0000 chunk 181 optimal weight: 1.9990 chunk 213 optimal weight: 20.0000 chunk 189 optimal weight: 7.9990 chunk 276 optimal weight: 30.0000 chunk 148 optimal weight: 6.9990 chunk 258 optimal weight: 5.9990 chunk 168 optimal weight: 10.0000 chunk 212 optimal weight: 30.0000 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** ** 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 = 0.3339 r_free = 0.3339 target = 0.042028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.028136 restraints weight = 402185.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.028452 restraints weight = 204347.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.028777 restraints weight = 139075.054| |-----------------------------------------------------------------------------| r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2766 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2766 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.4422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 34126 Z= 0.202 Angle : 0.564 9.684 49074 Z= 0.334 Chirality : 0.034 0.142 5538 Planarity : 0.004 0.040 3788 Dihedral : 29.899 178.793 10138 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.18), residues: 2202 helix: 2.42 (0.14), residues: 1424 sheet: 1.55 (0.51), residues: 120 loop : 0.21 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 62 HIS 0.006 0.001 HIS b 75 PHE 0.018 0.001 PHE e 104 TYR 0.018 0.001 TYR K 43 ARG 0.009 0.000 ARG L 82 Details of bonding type rmsd hydrogen bonds : bond 0.04568 ( 2007) hydrogen bonds : angle 3.21127 ( 5034) covalent geometry : bond 0.00433 (34126) covalent geometry : angle 0.56448 (49074) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10238.66 seconds wall clock time: 179 minutes 16.00 seconds (10756.00 seconds total)