Starting phenix.real_space_refine on Mon Feb 19 06:02:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v96_31810/02_2024/7v96_31810.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v96_31810/02_2024/7v96_31810.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v96_31810/02_2024/7v96_31810.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v96_31810/02_2024/7v96_31810.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v96_31810/02_2024/7v96_31810.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v96_31810/02_2024/7v96_31810.pdb" } resolution = 3.92 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= 0.000 sd= 0.004 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 549 5.49 5 S 28 5.16 5 C 13350 2.51 5 N 4535 2.21 5 O 5506 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 73": "OE1" <-> "OE2" Residue "C ARG 20": "NH1" <-> "NH2" Residue "C GLU 41": "OE1" <-> "OE2" Residue "C GLU 56": "OE1" <-> "OE2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "D GLU 32": "OE1" <-> "OE2" Residue "D GLU 90": "OE1" <-> "OE2" Residue "D GLU 102": "OE1" <-> "OE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "E GLU 50": "OE1" <-> "OE2" Residue "E GLU 59": "OE1" <-> "OE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "F ARG 19": "NH1" <-> "NH2" Residue "F ARG 23": "NH1" <-> "NH2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "F GLU 53": "OE1" <-> "OE2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "H GLU 90": "OE1" <-> "OE2" Residue "H GLU 102": "OE1" <-> "OE2" Residue "H GLU 110": "OE1" <-> "OE2" Residue "K GLU 59": "OE1" <-> "OE2" Residue "K GLU 97": "OE1" <-> "OE2" Residue "K GLU 105": "OE1" <-> "OE2" Residue "L ARG 19": "NH1" <-> "NH2" Residue "L ASP 24": "OD1" <-> "OD2" Residue "L GLU 52": "OE1" <-> "OE2" Residue "L GLU 53": "OE1" <-> "OE2" Residue "L GLU 63": "OE1" <-> "OE2" Residue "M ARG 20": "NH1" <-> "NH2" Residue "N GLU 32": "OE1" <-> "OE2" Residue "N GLU 102": "OE1" <-> "OE2" Residue "N GLU 110": "OE1" <-> "OE2" Residue "O ARG 40": "NH1" <-> "NH2" Residue "O GLU 133": "OE1" <-> "OE2" Residue "P GLU 53": "OE1" <-> "OE2" Residue "Q GLU 41": "OE1" <-> "OE2" Residue "Q GLU 92": "OE1" <-> "OE2" Residue "R TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 90": "OE1" <-> "OE2" Residue "R GLU 110": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 23968 Number of models: 1 Model: "" Number of chains: 18 Chain: "I" Number of atoms: 5818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 5818 Classifications: {'DNA': 275} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 274} Chain: "J" Number of atoms: 5454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 5454 Classifications: {'DNA': 275} Link IDs: {'rna3p': 274} Chain: "A" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 826 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "B" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 673 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "C" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 783 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain: "E" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 825 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "F" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "G" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 927 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "H" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 773 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "K" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 819 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "L" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "M" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 921 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 5, 'TRANS': 113} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "N" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 783 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain: "O" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 825 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "P" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 673 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "Q" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 849 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "R" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 773 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Time building chain proxies: 11.89, per 1000 atoms: 0.50 Number of scatterers: 23968 At special positions: 0 Unit cell: (136.422, 141.57, 120.12, 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 28 16.00 P 549 15.00 O 5506 8.00 N 4535 7.00 C 13350 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 - 3.50 Amino acid : False - 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: 10.75 Conformation dependent library (CDL) restraints added in 2.2 seconds 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2974 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 13 sheets defined 58.9% alpha, 1.6% beta 188 base pairs and 478 stacking pairs defined. Time for finding SS restraints: 11.10 Creating SS restraints... Processing helix chain 'A' and resid 64 through 68 Processing helix chain 'A' and resid 69 through 74 Processing helix chain 'A' and resid 92 through 96 Processing helix chain 'A' and resid 99 through 103 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.906A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLN A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG A 129 " --> pdb=" O GLN A 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 27 Processing helix chain 'B' and resid 31 through 35 Processing helix chain 'B' and resid 49 through 57 removed outlier: 3.842A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 66 Processing helix chain 'B' and resid 69 through 76 removed outlier: 3.524A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.757A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS B 91 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG B 92 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 28 through 37 Processing helix chain 'C' and resid 45 through 74 removed outlier: 4.300A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU C 58 " --> pdb=" O VAL C 54 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA C 69 " --> pdb=" O LEU C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 88 removed outlier: 3.554A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.822A pdb=" N VAL D 38 " --> pdb=" O TYR D 34 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS D 40 " --> pdb=" O VAL D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 82 removed outlier: 3.541A pdb=" N ILE D 58 " --> pdb=" O LYS D 54 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE D 67 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLU D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY D 72 " --> pdb=" O GLU D 68 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG D 76 " --> pdb=" O GLY D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 99 removed outlier: 3.858A pdb=" N VAL D 95 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU D 99 " --> pdb=" O VAL D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 121 removed outlier: 3.927A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N HIS D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA D 107 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU D 110 " --> pdb=" O HIS D 106 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 55 removed outlier: 3.761A pdb=" N ARG E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.518A pdb=" N ARG E 69 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL E 71 " --> pdb=" O PHE E 67 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.764A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.921A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLN E 125 " --> pdb=" O PRO E 121 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 28 removed outlier: 3.987A pdb=" N ILE F 26 " --> pdb=" O ARG F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 36 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.869A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU F 58 " --> pdb=" O THR F 54 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU F 63 " --> pdb=" O LYS F 59 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS F 75 " --> pdb=" O THR F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.719A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR F 88 " --> pdb=" O MET F 84 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ARG F 92 " --> pdb=" O TYR F 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 31 through 36 Processing helix chain 'G' and resid 46 through 61 removed outlier: 3.841A pdb=" N TYR G 50 " --> pdb=" O GLY G 46 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA G 53 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU G 55 " --> pdb=" O LEU G 51 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU G 56 " --> pdb=" O ALA G 52 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU G 61 " --> pdb=" O TYR G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 72 removed outlier: 3.817A pdb=" N ASP G 72 " --> pdb=" O ASN G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 88 removed outlier: 3.675A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN G 84 " --> pdb=" O PRO G 80 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA G 86 " --> pdb=" O HIS G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.540A pdb=" N LEU G 115 " --> pdb=" O GLN G 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 46 removed outlier: 3.522A pdb=" N TYR H 39 " --> pdb=" O SER H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.986A pdb=" N PHE H 62 " --> pdb=" O ILE H 58 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER H 75 " --> pdb=" O ALA H 71 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ARG H 76 " --> pdb=" O GLY H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.527A pdb=" N ALA H 94 " --> pdb=" O GLU H 90 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL H 95 " --> pdb=" O ILE H 91 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU H 99 " --> pdb=" O VAL H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 120 removed outlier: 3.913A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 56 removed outlier: 3.840A pdb=" N ARG K 49 " --> pdb=" O THR K 45 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS K 56 " --> pdb=" O ARG K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 79 removed outlier: 3.559A pdb=" N ARG K 69 " --> pdb=" O LEU K 65 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASP K 77 " --> pdb=" O GLU K 73 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N PHE K 78 " --> pdb=" O ILE K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 114 removed outlier: 3.758A pdb=" N VAL K 89 " --> pdb=" O GLN K 85 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS K 113 " --> pdb=" O LEU K 109 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA K 114 " --> pdb=" O CYS K 110 " (cutoff:3.500A) Processing helix chain 'K' and resid 120 through 131 removed outlier: 3.875A pdb=" N ILE K 124 " --> pdb=" O MET K 120 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLN K 125 " --> pdb=" O PRO K 121 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU K 126 " --> pdb=" O LYS K 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 42 removed outlier: 4.160A pdb=" N ARG L 39 " --> pdb=" O ARG L 35 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 77 removed outlier: 3.809A pdb=" N GLU L 53 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU L 58 " --> pdb=" O THR L 54 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS L 59 " --> pdb=" O ARG L 55 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASN L 64 " --> pdb=" O VAL L 60 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP L 68 " --> pdb=" O ASN L 64 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS L 75 " --> pdb=" O THR L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 94 removed outlier: 3.646A pdb=" N VAL L 86 " --> pdb=" O THR L 82 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG L 92 " --> pdb=" O TYR L 88 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN L 93 " --> pdb=" O ALA L 89 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 21 removed outlier: 3.753A pdb=" N ALA M 21 " --> pdb=" O ARG M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 36 removed outlier: 3.551A pdb=" N ARG M 32 " --> pdb=" O GLY M 28 " (cutoff:3.500A) Processing helix chain 'M' and resid 46 through 51 removed outlier: 3.806A pdb=" N TYR M 50 " --> pdb=" O GLY M 46 " (cutoff:3.500A) Processing helix chain 'M' and resid 55 through 66 removed outlier: 3.557A pdb=" N LEU M 63 " --> pdb=" O THR M 59 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLU M 64 " --> pdb=" O ALA M 60 " (cutoff:3.500A) Processing helix chain 'M' and resid 67 through 72 removed outlier: 3.821A pdb=" N ASP M 72 " --> pdb=" O ASN M 68 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 88 removed outlier: 3.680A pdb=" N LEU M 83 " --> pdb=" O ILE M 79 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN M 84 " --> pdb=" O PRO M 80 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA M 86 " --> pdb=" O HIS M 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 112 through 116 removed outlier: 3.546A pdb=" N LEU M 115 " --> pdb=" O GLN M 112 " (cutoff:3.500A) Processing helix chain 'N' and resid 41 through 46 removed outlier: 3.724A pdb=" N VAL N 45 " --> pdb=" O VAL N 41 " (cutoff:3.500A) Processing helix chain 'N' and resid 52 through 64 removed outlier: 4.221A pdb=" N PHE N 62 " --> pdb=" O ILE N 58 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN N 64 " --> pdb=" O ASN N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 76 through 81 Processing helix chain 'N' and resid 87 through 99 removed outlier: 3.993A pdb=" N VAL N 95 " --> pdb=" O ILE N 91 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU N 99 " --> pdb=" O VAL N 95 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 121 removed outlier: 3.938A pdb=" N SER N 109 " --> pdb=" O LYS N 105 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLU N 110 " --> pdb=" O HIS N 106 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR N 118 " --> pdb=" O ALA N 114 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 55 Processing helix chain 'O' and resid 64 through 68 Processing helix chain 'O' and resid 70 through 74 removed outlier: 3.581A pdb=" N ILE O 74 " --> pdb=" O VAL O 71 " (cutoff:3.500A) Processing helix chain 'O' and resid 99 through 112 removed outlier: 4.388A pdb=" N GLU O 105 " --> pdb=" O VAL O 101 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP O 106 " --> pdb=" O GLY O 102 " (cutoff:3.500A) Processing helix chain 'O' and resid 120 through 132 removed outlier: 3.860A pdb=" N ILE O 124 " --> pdb=" O MET O 120 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN O 125 " --> pdb=" O PRO O 121 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU O 126 " --> pdb=" O LYS O 122 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG O 129 " --> pdb=" O GLN O 125 " (cutoff:3.500A) Processing helix chain 'P' and resid 23 through 28 Processing helix chain 'P' and resid 31 through 34 Processing helix chain 'P' and resid 35 through 40 Processing helix chain 'P' and resid 49 through 76 removed outlier: 3.876A pdb=" N ARG P 55 " --> pdb=" O TYR P 51 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY P 56 " --> pdb=" O GLU P 52 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU P 58 " --> pdb=" O THR P 54 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP P 68 " --> pdb=" O ASN P 64 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS P 75 " --> pdb=" O THR P 71 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA P 76 " --> pdb=" O TYR P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 93 removed outlier: 3.755A pdb=" N VAL P 86 " --> pdb=" O THR P 82 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS P 91 " --> pdb=" O VAL P 87 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG P 92 " --> pdb=" O TYR P 88 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN P 93 " --> pdb=" O ALA P 89 " (cutoff:3.500A) Processing helix chain 'Q' and resid 16 through 22 Processing helix chain 'Q' and resid 28 through 37 Processing helix chain 'Q' and resid 45 through 74 removed outlier: 4.326A pdb=" N VAL Q 49 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR Q 50 " --> pdb=" O GLY Q 46 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU Q 58 " --> pdb=" O VAL Q 54 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA Q 69 " --> pdb=" O LEU Q 65 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 88 removed outlier: 3.553A pdb=" N LEU Q 83 " --> pdb=" O ILE Q 79 " (cutoff:3.500A) Processing helix chain 'Q' and resid 91 through 95 Processing helix chain 'R' and resid 34 through 46 removed outlier: 3.820A pdb=" N VAL R 38 " --> pdb=" O TYR R 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 64 Processing helix chain 'R' and resid 68 through 82 removed outlier: 3.758A pdb=" N ALA R 74 " --> pdb=" O ILE R 70 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG R 76 " --> pdb=" O GLY R 72 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN R 81 " --> pdb=" O LEU R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 92 Processing helix chain 'R' and resid 101 through 121 removed outlier: 3.883A pdb=" N LYS R 105 " --> pdb=" O GLY R 101 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N HIS R 106 " --> pdb=" O GLU R 102 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA R 107 " --> pdb=" O LEU R 103 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU R 110 " --> pdb=" O HIS R 106 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS R 113 " --> pdb=" O SER R 109 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA R 114 " --> pdb=" O GLU R 110 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.444A 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 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.597A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.089A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.781A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'K' and resid 83 through 84 removed outlier: 7.234A pdb=" N ARG K 83 " --> pdb=" O VAL L 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'L' and resid 97 through 98 removed outlier: 3.668A pdb=" N TYR L 98 " --> pdb=" O THR Q 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'M' and resid 101 through 102 removed outlier: 6.431A pdb=" N THR M 101 " --> pdb=" O TYR P 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'O' and resid 83 through 84 removed outlier: 7.460A pdb=" N ARG O 83 " --> pdb=" O VAL P 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'O' and resid 118 through 119 Processing sheet with id=AB4, first strand: chain 'Q' and resid 77 through 78 506 hydrogen bonds defined for protein. 1449 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 451 hydrogen bonds 856 hydrogen bond angles 0 basepair planarities 188 basepair parallelities 478 stacking parallelities Total time for adding SS restraints: 8.46 Time building geometry restraints manager: 11.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2681 1.31 - 1.43: 8755 1.43 - 1.56: 12926 1.56 - 1.68: 1097 1.68 - 1.81: 48 Bond restraints: 25507 Sorted by residual: bond pdb=" N MET O 120 " pdb=" CA MET O 120 " ideal model delta sigma weight residual 1.453 1.492 -0.039 8.30e-03 1.45e+04 2.25e+01 bond pdb=" N MET A 120 " pdb=" CA MET A 120 " ideal model delta sigma weight residual 1.453 1.492 -0.039 8.30e-03 1.45e+04 2.24e+01 bond pdb=" CA SER H 35 " pdb=" CB SER H 35 " ideal model delta sigma weight residual 1.536 1.471 0.064 1.42e-02 4.96e+03 2.06e+01 bond pdb=" CA SER H 84 " pdb=" CB SER H 84 " ideal model delta sigma weight residual 1.536 1.465 0.071 1.58e-02 4.01e+03 2.02e+01 bond pdb=" CA SER H 61 " pdb=" CB SER H 61 " ideal model delta sigma weight residual 1.528 1.460 0.069 1.56e-02 4.11e+03 1.93e+01 ... (remaining 25502 not shown) Histogram of bond angle deviations from ideal: 98.04 - 104.95: 2317 104.95 - 111.85: 12232 111.85 - 118.76: 9650 118.76 - 125.66: 10732 125.66 - 132.56: 1826 Bond angle restraints: 36757 Sorted by residual: angle pdb=" O3' DC J 213 " pdb=" C3' DC J 213 " pdb=" C2' DC J 213 " ideal model delta sigma weight residual 111.50 127.13 -15.63 1.50e+00 4.44e-01 1.09e+02 angle pdb=" N VAL O 89 " pdb=" CA VAL O 89 " pdb=" C VAL O 89 " ideal model delta sigma weight residual 112.90 104.09 8.81 9.60e-01 1.09e+00 8.42e+01 angle pdb=" O3' DA J 242 " pdb=" C3' DA J 242 " pdb=" C2' DA J 242 " ideal model delta sigma weight residual 111.50 125.11 -13.61 1.50e+00 4.44e-01 8.24e+01 angle pdb=" O3' DT J 102 " pdb=" C3' DT J 102 " pdb=" C2' DT J 102 " ideal model delta sigma weight residual 111.50 124.97 -13.47 1.50e+00 4.44e-01 8.07e+01 angle pdb=" N VAL A 89 " pdb=" CA VAL A 89 " pdb=" C VAL A 89 " ideal model delta sigma weight residual 112.17 103.71 8.46 9.50e-01 1.11e+00 7.93e+01 ... (remaining 36752 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.66: 10735 35.66 - 71.33: 3252 71.33 - 106.99: 74 106.99 - 142.66: 8 142.66 - 178.32: 8 Dihedral angle restraints: 14077 sinusoidal: 9466 harmonic: 4611 Sorted by residual: dihedral pdb=" C ARG E 128 " pdb=" N ARG E 128 " pdb=" CA ARG E 128 " pdb=" CB ARG E 128 " ideal model delta harmonic sigma weight residual -122.60 -137.84 15.24 0 2.50e+00 1.60e-01 3.71e+01 dihedral pdb=" C HIS H 79 " pdb=" N HIS H 79 " pdb=" CA HIS H 79 " pdb=" CB HIS H 79 " ideal model delta harmonic sigma weight residual -122.60 -137.11 14.51 0 2.50e+00 1.60e-01 3.37e+01 dihedral pdb=" C ASN L 64 " pdb=" N ASN L 64 " pdb=" CA ASN L 64 " pdb=" CB ASN L 64 " ideal model delta harmonic sigma weight residual -122.60 -136.89 14.29 0 2.50e+00 1.60e-01 3.27e+01 ... (remaining 14074 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.240: 4001 0.240 - 0.480: 150 0.480 - 0.719: 7 0.719 - 0.959: 2 0.959 - 1.199: 1 Chirality restraints: 4161 Sorted by residual: chirality pdb=" C3' DC J 213 " pdb=" C4' DC J 213 " pdb=" O3' DC J 213 " pdb=" C2' DC J 213 " both_signs ideal model delta sigma weight residual False -2.66 -1.46 -1.20 2.00e-01 2.50e+01 3.59e+01 chirality pdb=" C3' DT J 102 " pdb=" C4' DT J 102 " pdb=" O3' DT J 102 " pdb=" C2' DT J 102 " both_signs ideal model delta sigma weight residual False -2.66 -1.70 -0.96 2.00e-01 2.50e+01 2.29e+01 chirality pdb=" C3' DA J 242 " pdb=" C4' DA J 242 " pdb=" O3' DA J 242 " pdb=" C2' DA J 242 " both_signs ideal model delta sigma weight residual False -2.66 -1.71 -0.95 2.00e-01 2.50e+01 2.25e+01 ... (remaining 4158 not shown) Planarity restraints: 2744 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Q 10 " 0.015 2.00e-02 2.50e+03 3.01e-02 9.09e+00 pdb=" C ALA Q 10 " -0.052 2.00e-02 2.50e+03 pdb=" O ALA Q 10 " 0.019 2.00e-02 2.50e+03 pdb=" N ARG Q 11 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA J 80 " 0.010 2.00e-02 2.50e+03 1.73e-02 8.18e+00 pdb=" N9 DA J 80 " -0.036 2.00e-02 2.50e+03 pdb=" C8 DA J 80 " 0.012 2.00e-02 2.50e+03 pdb=" N7 DA J 80 " 0.016 2.00e-02 2.50e+03 pdb=" C5 DA J 80 " -0.019 2.00e-02 2.50e+03 pdb=" C6 DA J 80 " -0.010 2.00e-02 2.50e+03 pdb=" N6 DA J 80 " 0.014 2.00e-02 2.50e+03 pdb=" N1 DA J 80 " -0.017 2.00e-02 2.50e+03 pdb=" C2 DA J 80 " 0.014 2.00e-02 2.50e+03 pdb=" N3 DA J 80 " 0.017 2.00e-02 2.50e+03 pdb=" C4 DA J 80 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA J 242 " 0.036 2.00e-02 2.50e+03 1.70e-02 7.96e+00 pdb=" N9 DA J 242 " -0.040 2.00e-02 2.50e+03 pdb=" C8 DA J 242 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DA J 242 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA J 242 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DA J 242 " 0.004 2.00e-02 2.50e+03 pdb=" N6 DA J 242 " 0.012 2.00e-02 2.50e+03 pdb=" N1 DA J 242 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DA J 242 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DA J 242 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DA J 242 " -0.008 2.00e-02 2.50e+03 ... (remaining 2741 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 25 2.49 - 3.09: 14461 3.09 - 3.70: 37263 3.70 - 4.30: 59383 4.30 - 4.90: 83199 Nonbonded interactions: 194331 Sorted by model distance: nonbonded pdb=" O4' DC J 173 " pdb=" OP1 DT J 174 " model vdw 1.891 3.040 nonbonded pdb=" OP1 DC J 173 " pdb=" O4' DC J 173 " model vdw 2.099 3.040 nonbonded pdb=" O ASN M 73 " pdb=" OD1 ASN M 73 " model vdw 2.113 3.040 nonbonded pdb=" C4 DC J 173 " pdb=" O4 DT J 174 " model vdw 2.295 3.260 nonbonded pdb=" C1' DC J 173 " pdb=" OP1 DT J 174 " model vdw 2.329 3.470 ... (remaining 194326 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 36 through 134) selection = (chain 'E' and resid 36 through 134) selection = chain 'K' selection = (chain 'O' and resid 36 through 134) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 19 through 102) selection = (chain 'L' and resid 19 through 102) selection = chain 'P' } ncs_group { reference = (chain 'C' and ((resid 11 and (name N or name CA or name C or name CB or name CG \ or name CD or name NE or name CZ or name NH1 or name NH2)) or resid 12 through \ 118)) selection = (chain 'G' and ((resid 11 and (name N or name CA or name C or name CB or name CG \ or name CD or name NE or name CZ or name NH1 or name NH2)) or resid 12 through \ 118)) selection = (chain 'M' and resid 11 through 118) selection = (chain 'Q' and ((resid 11 and (name N or name CA or name C or name CB or name CG \ or name CD or name NE or name CZ or name NH1 or name NH2)) or resid 12 through \ 118)) } ncs_group { reference = (chain 'D' and resid 24 through 121) selection = chain 'H' selection = (chain 'N' and resid 24 through 121) selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.150 Check model and map are aligned: 0.390 Set scattering table: 0.250 Process input model: 67.380 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.100 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 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 : 0.011 0.071 25507 Z= 0.679 Angle : 1.593 15.632 36757 Z= 1.150 Chirality : 0.111 1.199 4161 Planarity : 0.007 0.030 2744 Dihedral : 30.755 178.319 11103 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.77 % Allowed : 4.74 % Favored : 94.49 % Rotamer: Outliers : 15.66 % Allowed : 16.04 % Favored : 68.30 % Cbeta Deviations : 2.35 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.38 (0.20), residues: 1561 helix: -0.33 (0.16), residues: 957 sheet: None (None), residues: 0 loop : -1.79 (0.22), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS O 113 PHE 0.022 0.003 PHE K 78 TYR 0.029 0.003 TYR N 34 ARG 0.007 0.001 ARG R 76 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 256 time to evaluate : 1.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG M 11 " (corrupted residue). Skipping it. REVERT: B 27 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7099 (mp10) REVERT: B 79 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8332 (mttp) REVERT: B 88 TYR cc_start: 0.8358 (m-10) cc_final: 0.8100 (m-10) REVERT: B 92 ARG cc_start: 0.9041 (OUTLIER) cc_final: 0.7948 (ttp80) REVERT: B 95 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7979 (ttp-110) REVERT: C 13 LYS cc_start: 0.7599 (OUTLIER) cc_final: 0.6634 (tptt) REVERT: C 74 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.7959 (mtpt) REVERT: D 30 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7328 (mtp-110) REVERT: D 56 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7751 (tpt) REVERT: E 42 ARG cc_start: 0.7665 (mtp85) cc_final: 0.7448 (mtm-85) REVERT: E 50 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.7080 (tt0) REVERT: E 70 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8620 (tt) REVERT: G 24 GLN cc_start: 0.7607 (mm110) cc_final: 0.7202 (mp10) REVERT: G 73 ASN cc_start: 0.8012 (m-40) cc_final: 0.7806 (t0) REVERT: G 78 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8579 (mm) REVERT: G 94 ASN cc_start: 0.9311 (t0) cc_final: 0.8772 (t0) REVERT: G 99 ARG cc_start: 0.7143 (OUTLIER) cc_final: 0.6613 (mmt180) REVERT: G 110 ASN cc_start: 0.8227 (t0) cc_final: 0.7302 (p0) REVERT: H 90 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7597 (mm-30) REVERT: H 103 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8902 (mt) REVERT: K 36 LYS cc_start: -0.0587 (OUTLIER) cc_final: -0.2574 (mmtt) REVERT: L 44 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8204 (tttt) REVERT: L 95 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.8207 (mtp85) REVERT: M 13 LYS cc_start: 0.6495 (OUTLIER) cc_final: 0.6148 (ptmm) REVERT: M 24 GLN cc_start: 0.7485 (mm-40) cc_final: 0.7222 (mp10) REVERT: M 29 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8239 (mmm160) REVERT: M 34 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8735 (mp) REVERT: M 110 ASN cc_start: 0.8484 (t0) cc_final: 0.7443 (p0) REVERT: N 66 ILE cc_start: 0.9321 (OUTLIER) cc_final: 0.9099 (mt) REVERT: N 76 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7800 (mtt90) REVERT: O 37 LYS cc_start: 0.5090 (OUTLIER) cc_final: 0.3972 (ttmt) REVERT: O 123 ASP cc_start: 0.9039 (m-30) cc_final: 0.8511 (m-30) REVERT: P 29 ILE cc_start: 0.9186 (OUTLIER) cc_final: 0.8778 (mt) REVERT: P 53 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.7135 (tm-30) REVERT: P 88 TYR cc_start: 0.8519 (m-10) cc_final: 0.8115 (m-10) REVERT: P 92 ARG cc_start: 0.9101 (OUTLIER) cc_final: 0.7953 (ttp80) REVERT: R 81 ASN cc_start: 0.8392 (m-40) cc_final: 0.8069 (m-40) outliers start: 208 outliers final: 59 residues processed: 416 average time/residue: 0.4814 time to fit residues: 281.0518 Evaluate side-chains 277 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 192 time to evaluate : 1.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain E residue 36 LYS Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 25 PHE Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 36 LYS Chi-restraints excluded: chain K residue 37 LYS Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 76 GLN Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 122 LYS Chi-restraints excluded: chain K residue 129 ARG Chi-restraints excluded: chain L residue 44 LYS Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 95 ARG Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 98 TYR Chi-restraints excluded: chain L residue 100 PHE Chi-restraints excluded: chain M residue 11 ARG Chi-restraints excluded: chain M residue 13 LYS Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 29 ARG Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 64 GLU Chi-restraints excluded: chain M residue 115 LEU Chi-restraints excluded: chain M residue 118 LYS Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain N residue 76 ARG Chi-restraints excluded: chain N residue 88 SER Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain O residue 37 LYS Chi-restraints excluded: chain O residue 39 HIS Chi-restraints excluded: chain O residue 43 PRO Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 77 ASP Chi-restraints excluded: chain O residue 131 ARG Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain P residue 26 ILE Chi-restraints excluded: chain P residue 29 ILE Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain P residue 73 THR Chi-restraints excluded: chain P residue 92 ARG Chi-restraints excluded: chain Q residue 59 THR Chi-restraints excluded: chain Q residue 84 GLN Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 86 ILE Chi-restraints excluded: chain R residue 89 ARG Chi-restraints excluded: chain R residue 102 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 0.1980 chunk 155 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 83 optimal weight: 0.7980 chunk 160 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 186 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN B 25 ASN B 64 ASN B 75 HIS ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 60 ASN D 81 ASN F 93 GLN G 84 GLN G 104 GLN G 110 ASN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 GLN K 125 GLN M 84 GLN M 110 ASN ** M 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 81 ASN R 92 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25507 Z= 0.199 Angle : 0.645 7.532 36757 Z= 0.386 Chirality : 0.037 0.153 4161 Planarity : 0.005 0.049 2744 Dihedral : 32.651 178.198 8090 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.63 % Favored : 97.12 % Rotamer: Outliers : 6.02 % Allowed : 20.41 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.87 (0.21), residues: 1561 helix: 0.01 (0.17), residues: 995 sheet: None (None), residues: 0 loop : -1.53 (0.23), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.014 0.001 PHE D 67 TYR 0.018 0.001 TYR R 80 ARG 0.011 0.001 ARG F 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 186 time to evaluate : 1.950 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG M 11 " (corrupted residue). Skipping it. REVERT: B 27 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.7771 (mp10) REVERT: B 75 HIS cc_start: 0.9127 (t70) cc_final: 0.8784 (t-90) REVERT: B 79 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8367 (mtmp) REVERT: C 13 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.6668 (tptt) REVERT: C 74 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.7578 (tmtt) REVERT: D 30 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.7005 (mtp-110) REVERT: E 122 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7808 (mtmt) REVERT: H 80 TYR cc_start: 0.7041 (m-10) cc_final: 0.6823 (m-10) REVERT: H 113 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.6996 (ttpt) REVERT: K 122 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7606 (mtmt) REVERT: K 129 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.7316 (ttm-80) REVERT: M 13 LYS cc_start: 0.6762 (OUTLIER) cc_final: 0.6366 (ptmt) REVERT: M 34 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8907 (mp) REVERT: O 37 LYS cc_start: 0.5503 (OUTLIER) cc_final: 0.4702 (tttt) REVERT: P 29 ILE cc_start: 0.9234 (mm) cc_final: 0.8902 (mt) REVERT: R 110 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7453 (tm-30) REVERT: R 117 LYS cc_start: 0.7950 (mtpp) cc_final: 0.7455 (mtmt) outliers start: 80 outliers final: 31 residues processed: 246 average time/residue: 0.4165 time to fit residues: 150.0345 Evaluate side-chains 194 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 150 time to evaluate : 1.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 58 THR Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 122 LYS Chi-restraints excluded: chain K residue 129 ARG Chi-restraints excluded: chain L residue 100 PHE Chi-restraints excluded: chain M residue 11 ARG Chi-restraints excluded: chain M residue 13 LYS Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 29 ARG Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain O residue 37 LYS Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain O residue 131 ARG Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain Q residue 118 LYS Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 110 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 103 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 126 optimal weight: 6.9990 chunk 51 optimal weight: 20.0000 chunk 186 optimal weight: 4.9990 chunk 201 optimal weight: 2.9990 chunk 166 optimal weight: 10.0000 chunk 184 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN E 108 ASN G 104 GLN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25507 Z= 0.228 Angle : 0.617 8.273 36757 Z= 0.367 Chirality : 0.036 0.145 4161 Planarity : 0.004 0.043 2744 Dihedral : 32.114 179.496 7949 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.16 % Favored : 95.64 % Rotamer: Outliers : 4.67 % Allowed : 22.74 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.07 (0.21), residues: 1561 helix: -0.14 (0.17), residues: 1004 sheet: None (None), residues: 0 loop : -1.64 (0.23), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS M 123 PHE 0.013 0.001 PHE E 78 TYR 0.019 0.002 TYR N 34 ARG 0.005 0.000 ARG R 26 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 157 time to evaluate : 1.967 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ARG M 11 " (corrupted residue). Skipping it. REVERT: B 27 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.7839 (mp10) REVERT: B 75 HIS cc_start: 0.9056 (t70) cc_final: 0.8809 (t-90) REVERT: C 13 LYS cc_start: 0.7720 (OUTLIER) cc_final: 0.6729 (tptt) REVERT: C 74 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7961 (mtpt) REVERT: D 30 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.7047 (mtp-110) REVERT: D 56 MET cc_start: 0.7657 (tpp) cc_final: 0.7381 (tpp) REVERT: H 59 MET cc_start: 0.9005 (OUTLIER) cc_final: 0.8798 (tpp) REVERT: H 113 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7220 (ttpp) REVERT: K 129 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.7393 (tpm170) REVERT: L 26 ILE cc_start: 0.7373 (tp) cc_final: 0.7172 (tp) REVERT: M 13 LYS cc_start: 0.6741 (OUTLIER) cc_final: 0.6429 (ptmm) REVERT: O 37 LYS cc_start: 0.6043 (OUTLIER) cc_final: 0.5164 (tttt) REVERT: O 87 SER cc_start: 0.8438 (OUTLIER) cc_final: 0.8134 (t) REVERT: R 110 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7666 (tm-30) outliers start: 62 outliers final: 38 residues processed: 202 average time/residue: 0.4495 time to fit residues: 134.0284 Evaluate side-chains 188 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 139 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 59 MET Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 58 THR Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 122 LYS Chi-restraints excluded: chain K residue 129 ARG Chi-restraints excluded: chain L residue 100 PHE Chi-restraints excluded: chain M residue 11 ARG Chi-restraints excluded: chain M residue 13 LYS Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 29 ARG Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 115 LEU Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain O residue 37 LYS Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 77 ASP Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain O residue 131 ARG Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 110 GLU Chi-restraints excluded: chain R residue 112 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 184 optimal weight: 1.9990 chunk 140 optimal weight: 0.0050 chunk 96 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 89 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 chunk 187 optimal weight: 6.9990 chunk 198 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 chunk 177 optimal weight: 0.9990 chunk 53 optimal weight: 20.0000 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 ASN F 27 GLN G 104 GLN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 73 ASN ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.4633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25507 Z= 0.177 Angle : 0.560 6.020 36757 Z= 0.336 Chirality : 0.033 0.172 4161 Planarity : 0.004 0.031 2744 Dihedral : 31.747 176.229 7935 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.07 % Favored : 96.73 % Rotamer: Outliers : 4.22 % Allowed : 23.57 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.80 (0.21), residues: 1561 helix: 0.03 (0.17), residues: 1007 sheet: None (None), residues: 0 loop : -1.45 (0.24), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.008 0.001 PHE P 100 TYR 0.011 0.001 TYR N 80 ARG 0.008 0.000 ARG E 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 155 time to evaluate : 1.940 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG M 11 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 86 SER cc_start: 0.7538 (t) cc_final: 0.6602 (m) REVERT: B 27 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.7817 (mp10) REVERT: C 13 LYS cc_start: 0.7700 (OUTLIER) cc_final: 0.6664 (tptt) REVERT: C 74 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7725 (mtpt) REVERT: C 112 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7108 (mt0) REVERT: D 30 ARG cc_start: 0.7367 (OUTLIER) cc_final: 0.7049 (mtp-110) REVERT: D 56 MET cc_start: 0.7435 (tpp) cc_final: 0.7118 (tpp) REVERT: D 68 GLU cc_start: 0.7370 (tt0) cc_final: 0.7168 (mt-10) REVERT: H 35 SER cc_start: 0.8829 (m) cc_final: 0.8535 (t) REVERT: H 113 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7111 (ttpt) REVERT: K 129 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7142 (ttm170) REVERT: M 13 LYS cc_start: 0.6650 (OUTLIER) cc_final: 0.6431 (ptmm) REVERT: M 29 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.8102 (mmm160) REVERT: N 76 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7596 (mtt180) REVERT: O 86 SER cc_start: 0.7237 (t) cc_final: 0.6800 (m) REVERT: O 123 ASP cc_start: 0.8726 (m-30) cc_final: 0.8498 (m-30) REVERT: R 56 MET cc_start: 0.8132 (tpp) cc_final: 0.7915 (tpp) REVERT: R 80 TYR cc_start: 0.7454 (m-80) cc_final: 0.6782 (m-10) REVERT: R 110 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7479 (tm-30) outliers start: 56 outliers final: 33 residues processed: 200 average time/residue: 0.4319 time to fit residues: 125.3384 Evaluate side-chains 181 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 137 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 25 PHE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 59 MET Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 58 THR Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 122 LYS Chi-restraints excluded: chain K residue 129 ARG Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 100 PHE Chi-restraints excluded: chain M residue 11 ARG Chi-restraints excluded: chain M residue 13 LYS Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 29 ARG Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain N residue 76 ARG Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 77 ASP Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain O residue 131 ARG Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain Q residue 34 LEU Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 110 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 165 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 2 optimal weight: 20.0000 chunk 147 optimal weight: 0.1980 chunk 81 optimal weight: 10.0000 chunk 169 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 101 optimal weight: 20.0000 chunk 177 optimal weight: 8.9990 chunk 50 optimal weight: 20.0000 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 104 GLN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 ASN Q 73 ASN Q 84 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.5030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 25507 Z= 0.279 Angle : 0.633 6.788 36757 Z= 0.372 Chirality : 0.037 0.212 4161 Planarity : 0.004 0.035 2744 Dihedral : 31.677 177.747 7927 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.19 % Favored : 94.62 % Rotamer: Outliers : 5.50 % Allowed : 24.02 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.43 (0.21), residues: 1561 helix: -0.42 (0.17), residues: 1017 sheet: None (None), residues: 0 loop : -1.80 (0.24), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 75 PHE 0.012 0.002 PHE E 78 TYR 0.018 0.002 TYR N 34 ARG 0.014 0.000 ARG E 116 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 153 time to evaluate : 1.829 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG M 11 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7623 (mt-10) REVERT: B 27 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.7885 (mp10) REVERT: C 13 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.6856 (tptm) REVERT: C 74 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7883 (mtpt) REVERT: C 112 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7294 (mt0) REVERT: D 30 ARG cc_start: 0.7384 (OUTLIER) cc_final: 0.7106 (mtp-110) REVERT: D 56 MET cc_start: 0.7960 (tpp) cc_final: 0.7625 (tpt) REVERT: D 68 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7161 (mt-10) REVERT: H 35 SER cc_start: 0.9098 (m) cc_final: 0.8688 (t) REVERT: H 59 MET cc_start: 0.9210 (OUTLIER) cc_final: 0.8955 (tpp) REVERT: H 113 LYS cc_start: 0.7721 (OUTLIER) cc_final: 0.7084 (tttt) REVERT: K 42 ARG cc_start: 0.6924 (mmm-85) cc_final: 0.6654 (mmt90) REVERT: K 129 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.6912 (ttm170) REVERT: M 13 LYS cc_start: 0.6879 (OUTLIER) cc_final: 0.6542 (ptmt) REVERT: M 24 GLN cc_start: 0.7397 (mm-40) cc_final: 0.7144 (mp10) REVERT: M 29 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8159 (mmm160) REVERT: O 86 SER cc_start: 0.7298 (t) cc_final: 0.6737 (m) REVERT: O 87 SER cc_start: 0.8568 (OUTLIER) cc_final: 0.8089 (t) REVERT: P 92 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8030 (ttp80) REVERT: R 110 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7798 (tm-30) outliers start: 73 outliers final: 40 residues processed: 215 average time/residue: 0.4624 time to fit residues: 145.1371 Evaluate side-chains 188 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 134 time to evaluate : 1.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 25 PHE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 59 MET Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 58 THR Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 129 ARG Chi-restraints excluded: chain K residue 130 ILE Chi-restraints excluded: chain L residue 100 PHE Chi-restraints excluded: chain M residue 11 ARG Chi-restraints excluded: chain M residue 13 LYS Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 29 ARG Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 115 LEU Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 77 ASP Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain O residue 131 ARG Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 92 ARG Chi-restraints excluded: chain Q residue 18 SER Chi-restraints excluded: chain Q residue 34 LEU Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 110 GLU Chi-restraints excluded: chain R residue 112 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 66 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 116 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 198 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 65 optimal weight: 0.0970 chunk 104 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN C 73 ASN D 46 HIS G 104 GLN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 73 ASN Q 84 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.5421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 25507 Z= 0.183 Angle : 0.557 7.075 36757 Z= 0.332 Chirality : 0.033 0.247 4161 Planarity : 0.004 0.030 2744 Dihedral : 31.452 176.027 7923 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.91 % Favored : 95.96 % Rotamer: Outliers : 4.22 % Allowed : 25.23 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.94 (0.22), residues: 1561 helix: -0.02 (0.17), residues: 1007 sheet: None (None), residues: 0 loop : -1.63 (0.25), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS N 106 PHE 0.010 0.001 PHE K 84 TYR 0.016 0.001 TYR R 80 ARG 0.007 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 147 time to evaluate : 1.815 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ARG M 11 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: B 27 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.7831 (mp10) REVERT: C 13 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.6813 (tptm) REVERT: C 74 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7820 (mtpt) REVERT: D 30 ARG cc_start: 0.7259 (OUTLIER) cc_final: 0.7057 (mtp-110) REVERT: D 68 GLU cc_start: 0.7420 (tt0) cc_final: 0.7103 (mt-10) REVERT: H 35 SER cc_start: 0.8950 (m) cc_final: 0.8517 (t) REVERT: H 113 LYS cc_start: 0.7667 (OUTLIER) cc_final: 0.7161 (ttpt) REVERT: K 42 ARG cc_start: 0.6978 (mmm-85) cc_final: 0.6697 (mmt90) REVERT: K 129 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.7031 (ttm170) REVERT: M 13 LYS cc_start: 0.6578 (OUTLIER) cc_final: 0.6356 (ptmt) REVERT: M 24 GLN cc_start: 0.7392 (mm-40) cc_final: 0.7180 (mp10) REVERT: M 29 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8284 (mmm160) REVERT: O 87 SER cc_start: 0.8446 (OUTLIER) cc_final: 0.8210 (t) REVERT: O 131 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7186 (mtp180) REVERT: Q 84 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8114 (tp-100) REVERT: R 110 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7552 (tm-30) outliers start: 56 outliers final: 37 residues processed: 192 average time/residue: 0.4056 time to fit residues: 114.5808 Evaluate side-chains 184 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 135 time to evaluate : 1.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 25 PHE Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 58 THR Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 129 ARG Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 100 PHE Chi-restraints excluded: chain M residue 11 ARG Chi-restraints excluded: chain M residue 13 LYS Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 29 ARG Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 77 ASP Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain O residue 131 ARG Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain Q residue 18 SER Chi-restraints excluded: chain Q residue 34 LEU Chi-restraints excluded: chain Q residue 84 GLN Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 110 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 191 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 chunk 112 optimal weight: 5.9990 chunk 166 optimal weight: 8.9990 chunk 110 optimal weight: 8.9990 chunk 197 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS F 25 ASN K 68 GLN Q 84 GLN Q 110 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.5534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 25507 Z= 0.304 Angle : 0.648 8.215 36757 Z= 0.376 Chirality : 0.038 0.146 4161 Planarity : 0.004 0.041 2744 Dihedral : 31.580 176.076 7922 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.60 % Favored : 93.27 % Rotamer: Outliers : 5.05 % Allowed : 24.70 % Favored : 70.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.62 (0.21), residues: 1561 helix: -0.53 (0.17), residues: 1019 sheet: None (None), residues: 0 loop : -1.97 (0.24), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 75 PHE 0.012 0.002 PHE E 78 TYR 0.021 0.002 TYR N 34 ARG 0.006 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 144 time to evaluate : 1.771 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG M 11 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 38 PRO cc_start: 0.6801 (Cg_endo) cc_final: 0.6522 (Cg_exo) REVERT: B 27 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.8007 (mp10) REVERT: C 13 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.6895 (tptm) REVERT: C 74 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7944 (mtpt) REVERT: C 112 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7294 (mt0) REVERT: G 99 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.6493 (mmt180) REVERT: H 35 SER cc_start: 0.8975 (m) cc_final: 0.8560 (t) REVERT: H 113 LYS cc_start: 0.7678 (OUTLIER) cc_final: 0.7034 (tttt) REVERT: K 42 ARG cc_start: 0.7106 (mmm-85) cc_final: 0.6854 (mmt90) REVERT: K 129 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.6855 (ttm170) REVERT: M 13 LYS cc_start: 0.6821 (OUTLIER) cc_final: 0.6366 (ptmt) REVERT: O 38 PRO cc_start: 0.6328 (Cg_endo) cc_final: 0.6120 (Cg_exo) REVERT: O 86 SER cc_start: 0.7225 (t) cc_final: 0.6677 (m) REVERT: O 87 SER cc_start: 0.8588 (OUTLIER) cc_final: 0.8035 (t) REVERT: P 92 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.7988 (ttp80) REVERT: R 110 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7818 (tm-30) outliers start: 67 outliers final: 43 residues processed: 198 average time/residue: 0.4245 time to fit residues: 124.5989 Evaluate side-chains 189 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 135 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 58 THR Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 129 ARG Chi-restraints excluded: chain L residue 100 PHE Chi-restraints excluded: chain M residue 11 ARG Chi-restraints excluded: chain M residue 13 LYS Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 29 ARG Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 115 LEU Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 77 ASP Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain O residue 131 ARG Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 92 ARG Chi-restraints excluded: chain Q residue 18 SER Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 64 GLU Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 110 GLU Chi-restraints excluded: chain R residue 112 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 122 optimal weight: 0.5980 chunk 78 optimal weight: 9.9990 chunk 118 optimal weight: 0.3980 chunk 59 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 125 optimal weight: 4.9990 chunk 134 optimal weight: 0.0670 chunk 97 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 155 optimal weight: 10.0000 chunk 179 optimal weight: 2.9990 overall best weight: 1.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN Q 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.5900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25507 Z= 0.168 Angle : 0.549 8.189 36757 Z= 0.327 Chirality : 0.033 0.153 4161 Planarity : 0.004 0.032 2744 Dihedral : 31.289 176.627 7918 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.80 % Favored : 95.07 % Rotamer: Outliers : 3.24 % Allowed : 26.43 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.92 (0.22), residues: 1561 helix: 0.00 (0.17), residues: 1004 sheet: None (None), residues: 0 loop : -1.64 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS N 79 PHE 0.010 0.001 PHE D 67 TYR 0.054 0.001 TYR L 88 ARG 0.006 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 147 time to evaluate : 1.803 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 27 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.7790 (mp10) REVERT: C 13 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.6852 (tptm) REVERT: D 56 MET cc_start: 0.7507 (tpp) cc_final: 0.7253 (tpp) REVERT: D 68 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6824 (mt-10) REVERT: E 131 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.7761 (mtt180) REVERT: H 35 SER cc_start: 0.8756 (m) cc_final: 0.8405 (t) REVERT: H 113 LYS cc_start: 0.7648 (OUTLIER) cc_final: 0.7183 (ttpt) REVERT: K 42 ARG cc_start: 0.6864 (mmm-85) cc_final: 0.6656 (mmt90) REVERT: K 129 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.6965 (ttm170) REVERT: M 13 LYS cc_start: 0.6558 (OUTLIER) cc_final: 0.6282 (ptmt) REVERT: M 24 GLN cc_start: 0.7422 (mm-40) cc_final: 0.7201 (mp10) REVERT: M 29 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8356 (ttm170) REVERT: O 38 PRO cc_start: 0.6247 (Cg_endo) cc_final: 0.6017 (Cg_exo) REVERT: Q 84 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.8026 (tp-100) outliers start: 43 outliers final: 29 residues processed: 181 average time/residue: 0.4093 time to fit residues: 110.1635 Evaluate side-chains 175 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 137 time to evaluate : 1.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 58 THR Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 129 ARG Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 100 PHE Chi-restraints excluded: chain M residue 13 LYS Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 29 ARG Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain N residue 39 TYR Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 77 ASP Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain Q residue 84 GLN Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 49 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 189 optimal weight: 4.9990 chunk 172 optimal weight: 2.9990 chunk 184 optimal weight: 7.9990 chunk 110 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 166 optimal weight: 7.9990 chunk 174 optimal weight: 0.4980 chunk 183 optimal weight: 0.9980 chunk 120 optimal weight: 9.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.5929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25507 Z= 0.225 Angle : 0.580 9.042 36757 Z= 0.341 Chirality : 0.034 0.134 4161 Planarity : 0.004 0.043 2744 Dihedral : 31.329 177.090 7906 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.89 % Favored : 93.98 % Rotamer: Outliers : 3.69 % Allowed : 26.51 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.04 (0.22), residues: 1561 helix: -0.09 (0.17), residues: 1011 sheet: None (None), residues: 0 loop : -1.70 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.017 0.001 HIS A 39 PHE 0.009 0.001 PHE E 67 TYR 0.058 0.002 TYR L 88 ARG 0.005 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 140 time to evaluate : 1.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 PRO cc_start: 0.6709 (Cg_endo) cc_final: 0.6437 (Cg_exo) REVERT: B 27 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.7966 (mp10) REVERT: C 13 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.6844 (tptm) REVERT: D 56 MET cc_start: 0.7602 (tpp) cc_final: 0.7388 (tpp) REVERT: D 68 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6815 (mt-10) REVERT: G 99 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.6436 (mmt180) REVERT: H 35 SER cc_start: 0.8864 (m) cc_final: 0.8484 (t) REVERT: H 113 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7066 (tttt) REVERT: K 42 ARG cc_start: 0.6948 (mmm-85) cc_final: 0.6658 (mmt90) REVERT: K 129 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.6725 (ttm170) REVERT: M 13 LYS cc_start: 0.6608 (OUTLIER) cc_final: 0.6298 (ptmt) REVERT: M 29 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.8195 (mmm160) REVERT: N 98 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8027 (mp) REVERT: O 86 SER cc_start: 0.7102 (t) cc_final: 0.6771 (m) REVERT: O 87 SER cc_start: 0.8514 (OUTLIER) cc_final: 0.8195 (t) REVERT: P 92 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8026 (ttp80) REVERT: R 110 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7645 (tm-30) outliers start: 49 outliers final: 32 residues processed: 179 average time/residue: 0.4099 time to fit residues: 109.2923 Evaluate side-chains 179 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 135 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 58 THR Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 129 ARG Chi-restraints excluded: chain L residue 100 PHE Chi-restraints excluded: chain M residue 13 LYS Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 29 ARG Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain N residue 39 TYR Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 77 ASP Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain P residue 92 ARG Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 110 GLU Chi-restraints excluded: chain R residue 112 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 194 optimal weight: 3.9990 chunk 118 optimal weight: 8.9990 chunk 92 optimal weight: 0.7980 chunk 135 optimal weight: 2.9990 chunk 204 optimal weight: 3.9990 chunk 187 optimal weight: 5.9990 chunk 162 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 125 optimal weight: 4.9990 chunk 99 optimal weight: 0.0050 chunk 129 optimal weight: 0.7980 overall best weight: 1.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.6158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25507 Z= 0.183 Angle : 0.555 8.056 36757 Z= 0.328 Chirality : 0.033 0.139 4161 Planarity : 0.004 0.070 2744 Dihedral : 31.178 177.400 7906 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.55 % Favored : 95.32 % Rotamer: Outliers : 3.31 % Allowed : 26.66 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.89 (0.22), residues: 1561 helix: 0.04 (0.17), residues: 1008 sheet: None (None), residues: 0 loop : -1.68 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS N 79 PHE 0.009 0.001 PHE E 67 TYR 0.059 0.002 TYR N 80 ARG 0.007 0.000 ARG A 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 134 time to evaluate : 2.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 27 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.7887 (mp10) REVERT: C 13 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.6882 (tptm) REVERT: E 131 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.7705 (mtt180) REVERT: F 59 LYS cc_start: 0.8310 (tppt) cc_final: 0.6601 (tttt) REVERT: H 35 SER cc_start: 0.8790 (m) cc_final: 0.8422 (t) REVERT: H 113 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.7191 (ttpt) REVERT: K 42 ARG cc_start: 0.6868 (mmm-85) cc_final: 0.6595 (mmt90) REVERT: K 129 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.6688 (ttm170) REVERT: M 13 LYS cc_start: 0.6554 (OUTLIER) cc_final: 0.6287 (ptmt) REVERT: M 29 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.8263 (mmm160) REVERT: N 98 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8023 (mp) REVERT: O 87 SER cc_start: 0.8526 (OUTLIER) cc_final: 0.8261 (t) REVERT: R 110 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7586 (tm-30) outliers start: 44 outliers final: 30 residues processed: 169 average time/residue: 0.4071 time to fit residues: 102.8034 Evaluate side-chains 171 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 131 time to evaluate : 1.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 58 THR Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 129 ARG Chi-restraints excluded: chain L residue 100 PHE Chi-restraints excluded: chain M residue 13 LYS Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 29 ARG Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain N residue 31 LYS Chi-restraints excluded: chain N residue 39 TYR Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 77 ASP Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain O residue 133 GLU Chi-restraints excluded: chain P residue 26 ILE Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 110 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 149 optimal weight: 0.9990 chunk 24 optimal weight: 20.0000 chunk 45 optimal weight: 20.0000 chunk 162 optimal weight: 0.0470 chunk 68 optimal weight: 0.9990 chunk 167 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 143 optimal weight: 2.9990 overall best weight: 1.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 46 HIS D 81 ASN ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.178683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.138048 restraints weight = 35336.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.137219 restraints weight = 78785.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.137958 restraints weight = 82279.830| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.6446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25507 Z= 0.164 Angle : 0.541 8.762 36757 Z= 0.320 Chirality : 0.032 0.143 4161 Planarity : 0.004 0.071 2744 Dihedral : 31.024 178.683 7906 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.48 % Favored : 95.39 % Rotamer: Outliers : 3.01 % Allowed : 26.96 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.61 (0.22), residues: 1561 helix: 0.28 (0.17), residues: 1008 sheet: None (None), residues: 0 loop : -1.61 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS N 79 PHE 0.006 0.001 PHE E 67 TYR 0.014 0.001 TYR H 80 ARG 0.008 0.000 ARG E 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3544.64 seconds wall clock time: 65 minutes 37.85 seconds (3937.85 seconds total)