Starting phenix.real_space_refine on Sun Feb 25 09:05:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6spc_10281/02_2024/6spc_10281.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6spc_10281/02_2024/6spc_10281.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6spc_10281/02_2024/6spc_10281.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6spc_10281/02_2024/6spc_10281.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6spc_10281/02_2024/6spc_10281.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6spc_10281/02_2024/6spc_10281.pdb" } resolution = 2.95 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= 0.009 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 1518 5.49 5 S 63 5.16 5 C 25750 2.51 5 N 9455 2.21 5 O 13783 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b ARG 35": "NH1" <-> "NH2" Residue "b ARG 113": "NH1" <-> "NH2" Residue "b ARG 115": "NH1" <-> "NH2" Residue "b GLU 118": "OE1" <-> "OE2" Residue "b ARG 139": "NH1" <-> "NH2" Residue "b ARG 170": "NH1" <-> "NH2" Residue "c ARG 59": "NH1" <-> "NH2" Residue "c ARG 88": "NH1" <-> "NH2" Residue "c ARG 156": "NH1" <-> "NH2" Residue "e GLU 14": "OE1" <-> "OE2" Residue "e GLU 66": "OE1" <-> "OE2" Residue "e GLU 102": "OE1" <-> "OE2" Residue "f PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 24": "NH1" <-> "NH2" Residue "f ARG 38": "NH1" <-> "NH2" Residue "f ARG 44": "NH1" <-> "NH2" Residue "f ARG 86": "NH1" <-> "NH2" Residue "g ARG 5": "NH1" <-> "NH2" Residue "g GLU 74": "OE1" <-> "OE2" Residue "g GLU 113": "OE1" <-> "OE2" Residue "g GLU 123": "OE1" <-> "OE2" Residue "g GLU 139": "OE1" <-> "OE2" Residue "g GLU 146": "OE1" <-> "OE2" Residue "k ARG 98": "NH1" <-> "NH2" Residue "k ARG 127": "NH1" <-> "NH2" Residue "l ARG 9": "NH1" <-> "NH2" Residue "l ARG 56": "NH1" <-> "NH2" Residue "n ARG 75": "NH1" <-> "NH2" Residue "n ARG 81": "NH1" <-> "NH2" Residue "o ARG 54": "NH1" <-> "NH2" Residue "p ARG 5": "NH1" <-> "NH2" Residue "p ARG 31": "NH1" <-> "NH2" Residue "p ARG 35": "NH1" <-> "NH2" Residue "p ARG 49": "NH1" <-> "NH2" Residue "t ARG 10": "NH1" <-> "NH2" Residue "u ARG 35": "NH1" <-> "NH2" Residue "u ARG 47": "NH1" <-> "NH2" Residue "u ARG 66": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 50569 Number of models: 1 Model: "" Number of chains: 21 Chain: "a" Number of atoms: 32595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1519, 32595 Classifications: {'RNA': 1519} Modifications used: {'5*END': 1, 'rna2p_pur': 148, 'rna2p_pyr': 106, 'rna3p_pur': 721, 'rna3p_pyr': 544} Link IDs: {'rna2p': 254, 'rna3p': 1264} Chain breaks: 4 Chain: "b" Number of atoms: 1728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1728 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 213} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "c" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1609 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 196} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "d" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1600 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 200} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "e" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1092 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 143} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "f" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 802 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 98} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "g" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1190 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 148} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "h" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 915 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 117} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "i" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 994 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "j" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 763 Classifications: {'peptide': 96} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "k" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 828 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 107} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "l" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 893 Classifications: {'peptide': 113} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 105} Chain: "m" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 847 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain breaks: 1 Chain: "n" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 776 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "o" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 686 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "p" Number of atoms: 606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 606 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 74} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "q" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 619 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "r" Number of atoms: 443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 443 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 53} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "s" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 635 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 75} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "t" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 653 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 82} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Chain: "u" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 295 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Time building chain proxies: 26.13, per 1000 atoms: 0.52 Number of scatterers: 50569 At special positions: 0 Unit cell: (235.4, 189.2, 185.9, 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 63 16.00 P 1518 15.00 O 13783 8.00 N 9455 7.00 C 25750 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS d 9 " - pdb=" SG CYS d 32 " distance=2.08 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: 26.66 Conformation dependent library (CDL) restraints added in 3.6 seconds 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4248 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 18 sheets defined 29.9% alpha, 10.7% beta 313 base pairs and 673 stacking pairs defined. Time for finding SS restraints: 22.25 Creating SS restraints... Processing helix chain 'b' and resid 5 through 12 removed outlier: 3.527A pdb=" N MET b 9 " --> pdb=" O ASN b 5 " (cutoff:3.500A) Processing helix chain 'b' and resid 45 through 59 removed outlier: 3.716A pdb=" N MET b 49 " --> pdb=" O LYS b 45 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU b 52 " --> pdb=" O PRO b 48 " (cutoff:3.500A) Processing helix chain 'b' and resid 103 through 109 removed outlier: 3.673A pdb=" N GLN b 109 " --> pdb=" O LYS b 105 " (cutoff:3.500A) Processing helix chain 'b' and resid 114 through 118 removed outlier: 3.932A pdb=" N GLU b 118 " --> pdb=" O ARG b 115 " (cutoff:3.500A) Processing helix chain 'b' and resid 131 through 140 removed outlier: 3.826A pdb=" N MET b 136 " --> pdb=" O LYS b 132 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ARG b 137 " --> pdb=" O GLU b 133 " (cutoff:3.500A) Processing helix chain 'b' and resid 140 through 148 removed outlier: 4.280A pdb=" N LEU b 144 " --> pdb=" O ASP b 140 " (cutoff:3.500A) Processing helix chain 'b' and resid 149 through 152 removed outlier: 3.838A pdb=" N LYS b 152 " --> pdb=" O GLY b 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 149 through 152' Processing helix chain 'b' and resid 169 through 180 removed outlier: 3.816A pdb=" N ILE b 173 " --> pdb=" O GLU b 169 " (cutoff:3.500A) Processing helix chain 'b' and resid 206 through 223 Processing helix chain 'c' and resid 26 through 30 removed outlier: 4.037A pdb=" N ALA c 30 " --> pdb=" O LYS c 27 " (cutoff:3.500A) Processing helix chain 'c' and resid 41 through 46 removed outlier: 3.667A pdb=" N ASP c 45 " --> pdb=" O GLU c 41 " (cutoff:3.500A) Processing helix chain 'c' and resid 72 through 77 removed outlier: 4.121A pdb=" N VAL c 76 " --> pdb=" O ARG c 72 " (cutoff:3.500A) Processing helix chain 'c' and resid 85 through 93 removed outlier: 3.683A pdb=" N GLN c 89 " --> pdb=" O GLU c 85 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU c 91 " --> pdb=" O LEU c 87 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR c 92 " --> pdb=" O ARG c 88 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS c 93 " --> pdb=" O GLN c 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 112 through 118 Processing helix chain 'c' and resid 119 through 124 removed outlier: 5.482A pdb=" N GLN c 122 " --> pdb=" O SER c 119 " (cutoff:3.500A) Processing helix chain 'c' and resid 135 through 140 Processing helix chain 'd' and resid 49 through 65 removed outlier: 3.519A pdb=" N GLN d 59 " --> pdb=" O LEU d 55 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL d 61 " --> pdb=" O GLU d 57 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG d 63 " --> pdb=" O GLN d 59 " (cutoff:3.500A) Processing helix chain 'd' and resid 68 through 81 removed outlier: 3.516A pdb=" N GLY d 74 " --> pdb=" O ARG d 70 " (cutoff:3.500A) Processing helix chain 'd' and resid 85 through 96 removed outlier: 3.776A pdb=" N LEU d 91 " --> pdb=" O GLY d 87 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 106 removed outlier: 3.545A pdb=" N TYR d 103 " --> pdb=" O ASP d 99 " (cutoff:3.500A) Processing helix chain 'd' and resid 114 through 120 removed outlier: 3.650A pdb=" N HIS d 120 " --> pdb=" O GLN d 116 " (cutoff:3.500A) Processing helix chain 'd' and resid 152 through 157 removed outlier: 4.180A pdb=" N ALA d 156 " --> pdb=" O GLN d 152 " (cutoff:3.500A) Processing helix chain 'd' and resid 160 through 165 removed outlier: 3.713A pdb=" N GLN d 164 " --> pdb=" O GLU d 160 " (cutoff:3.500A) Processing helix chain 'd' and resid 196 through 200 removed outlier: 3.875A pdb=" N ILE d 200 " --> pdb=" O GLU d 197 " (cutoff:3.500A) Processing helix chain 'e' and resid 56 through 70 removed outlier: 3.676A pdb=" N LYS e 63 " --> pdb=" O ALA e 59 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG e 70 " --> pdb=" O GLU e 66 " (cutoff:3.500A) Processing helix chain 'e' and resid 110 through 119 removed outlier: 3.626A pdb=" N ALA e 114 " --> pdb=" O GLY e 110 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL e 115 " --> pdb=" O ALA e 111 " (cutoff:3.500A) Processing helix chain 'e' and resid 133 through 147 removed outlier: 3.582A pdb=" N TYR e 139 " --> pdb=" O VAL e 135 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY e 144 " --> pdb=" O ALA e 140 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN e 147 " --> pdb=" O LYS e 143 " (cutoff:3.500A) Processing helix chain 'f' and resid 12 through 15 Processing helix chain 'f' and resid 17 through 31 removed outlier: 3.651A pdb=" N GLU f 23 " --> pdb=" O GLY f 19 " (cutoff:3.500A) Processing helix chain 'f' and resid 68 through 80 removed outlier: 4.135A pdb=" N PHE f 78 " --> pdb=" O LEU f 74 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 44 removed outlier: 4.507A pdb=" N ARG g 41 " --> pdb=" O ALA g 37 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE g 42 " --> pdb=" O VAL g 38 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR g 44 " --> pdb=" O GLU g 40 " (cutoff:3.500A) Processing helix chain 'g' and resid 46 through 51 removed outlier: 4.147A pdb=" N LYS g 51 " --> pdb=" O LEU g 47 " (cutoff:3.500A) Processing helix chain 'g' and resid 58 through 68 removed outlier: 3.629A pdb=" N THR g 61 " --> pdb=" O PRO g 58 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLU g 63 " --> pdb=" O GLU g 60 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LYS g 64 " --> pdb=" O THR g 61 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA g 65 " --> pdb=" O PHE g 62 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU g 66 " --> pdb=" O GLU g 63 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASP g 67 " --> pdb=" O LYS g 64 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA g 68 " --> pdb=" O ALA g 65 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 97 Processing helix chain 'g' and resid 101 through 107 removed outlier: 3.661A pdb=" N PHE g 107 " --> pdb=" O TRP g 103 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 122 Processing helix chain 'g' and resid 137 through 144 removed outlier: 4.103A pdb=" N HIS g 142 " --> pdb=" O ARG g 138 " (cutoff:3.500A) Processing helix chain 'h' and resid 6 through 20 Processing helix chain 'h' and resid 35 through 41 removed outlier: 3.808A pdb=" N VAL h 39 " --> pdb=" O ALA h 35 " (cutoff:3.500A) Processing helix chain 'i' and resid 35 through 39 Processing helix chain 'i' and resid 48 through 53 removed outlier: 3.605A pdb=" N LEU i 52 " --> pdb=" O VAL i 48 " (cutoff:3.500A) Processing helix chain 'i' and resid 75 through 80 removed outlier: 3.958A pdb=" N ILE i 79 " --> pdb=" O GLN i 75 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG i 80 " --> pdb=" O ALA i 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 75 through 80' Processing helix chain 'i' and resid 94 through 98 removed outlier: 4.044A pdb=" N LEU i 98 " --> pdb=" O ARG i 95 " (cutoff:3.500A) Processing helix chain 'j' and resid 22 through 31 removed outlier: 3.947A pdb=" N VAL j 26 " --> pdb=" O THR j 22 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLU j 27 " --> pdb=" O GLN j 23 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N THR j 28 " --> pdb=" O GLU j 24 " (cutoff:3.500A) Processing helix chain 'j' and resid 82 through 87 Processing helix chain 'k' and resid 59 through 75 removed outlier: 3.571A pdb=" N ALA k 63 " --> pdb=" O THR k 59 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU k 68 " --> pdb=" O GLN k 64 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG k 69 " --> pdb=" O VAL k 65 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA k 70 " --> pdb=" O ALA k 66 " (cutoff:3.500A) Processing helix chain 'l' and resid 6 through 10 Processing helix chain 'm' and resid 29 through 34 Processing helix chain 'm' and resid 49 through 53 removed outlier: 3.682A pdb=" N GLN m 52 " --> pdb=" O SER m 49 " (cutoff:3.500A) Processing helix chain 'm' and resid 65 through 72 Processing helix chain 'm' and resid 74 through 82 removed outlier: 3.544A pdb=" N LEU m 80 " --> pdb=" O ASN m 76 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASP m 82 " --> pdb=" O LYS m 78 " (cutoff:3.500A) Processing helix chain 'm' and resid 106 through 110 removed outlier: 4.495A pdb=" N ARG m 109 " --> pdb=" O ALA m 106 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LYS m 110 " --> pdb=" O ARG m 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 106 through 110' Processing helix chain 'n' and resid 6 through 11 removed outlier: 3.772A pdb=" N GLU n 10 " --> pdb=" O MET n 6 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU n 11 " --> pdb=" O LYS n 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 6 through 11' Processing helix chain 'n' and resid 12 through 17 removed outlier: 3.521A pdb=" N THR n 16 " --> pdb=" O LYS n 12 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL n 17 " --> pdb=" O ARG n 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 12 through 17' Processing helix chain 'n' and resid 22 through 27 Processing helix chain 'n' and resid 28 through 33 removed outlier: 4.903A pdb=" N ILE n 31 " --> pdb=" O LYS n 28 " (cutoff:3.500A) Processing helix chain 'n' and resid 42 through 46 Processing helix chain 'n' and resid 80 through 88 removed outlier: 4.000A pdb=" N ARG n 85 " --> pdb=" O ARG n 81 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLU n 86 " --> pdb=" O ASN n 82 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA n 88 " --> pdb=" O LEU n 84 " (cutoff:3.500A) Processing helix chain 'o' and resid 4 through 14 removed outlier: 3.583A pdb=" N VAL o 12 " --> pdb=" O LYS o 8 " (cutoff:3.500A) Processing helix chain 'o' and resid 24 through 46 removed outlier: 3.584A pdb=" N ASN o 35 " --> pdb=" O LEU o 31 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASP o 41 " --> pdb=" O ASN o 37 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N HIS o 42 " --> pdb=" O LYS o 38 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS o 44 " --> pdb=" O GLN o 40 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA o 45 " --> pdb=" O ASP o 41 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 3.661A pdb=" N ARG o 53 " --> pdb=" O ASP o 49 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLY o 55 " --> pdb=" O HIS o 51 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET o 59 " --> pdb=" O GLY o 55 " (cutoff:3.500A) Processing helix chain 'o' and resid 74 through 84 Processing helix chain 'p' and resid 55 through 64 Processing helix chain 'r' and resid 25 through 30 Processing helix chain 'r' and resid 48 through 65 removed outlier: 3.898A pdb=" N THR r 57 " --> pdb=" O ARG r 53 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LYS r 60 " --> pdb=" O ALA r 56 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 17 removed outlier: 3.705A pdb=" N LYS s 17 " --> pdb=" O LEU s 13 " (cutoff:3.500A) Processing helix chain 's' and resid 20 through 24 removed outlier: 3.527A pdb=" N VAL s 23 " --> pdb=" O GLU s 20 " (cutoff:3.500A) Processing helix chain 't' and resid 4 through 41 removed outlier: 3.539A pdb=" N GLU t 15 " --> pdb=" O ALA t 11 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS t 16 " --> pdb=" O LYS t 12 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG t 17 " --> pdb=" O GLN t 13 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER t 23 " --> pdb=" O SER t 19 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL t 28 " --> pdb=" O LEU t 24 " (cutoff:3.500A) WARNING: missing atoms! removed outlier: 3.709A pdb=" N VAL t 35 " --> pdb=" O TYR t 31 " (cutoff:3.500A) Processing helix chain 't' and resid 43 through 64 removed outlier: 3.750A pdb=" N ALA t 49 " --> pdb=" O GLU t 45 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA t 53 " --> pdb=" O ALA t 49 " (cutoff:3.500A) Proline residue: t 56 - end of helix removed outlier: 3.903A pdb=" N LYS t 64 " --> pdb=" O ARG t 60 " (cutoff:3.500A) Processing helix chain 't' and resid 68 through 83 removed outlier: 3.533A pdb=" N ALA t 73 " --> pdb=" O LYS t 69 " (cutoff:3.500A) Processing helix chain 'u' and resid 57 through 62 removed outlier: 3.994A pdb=" N ARG u 62 " --> pdb=" O LYS u 58 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'b' and resid 31 through 34 removed outlier: 5.448A pdb=" N ILE b 40 " --> pdb=" O PHE b 32 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'b' and resid 91 through 92 removed outlier: 7.877A pdb=" N VAL b 92 " --> pdb=" O ILE b 67 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N PHE b 69 " --> pdb=" O VAL b 92 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU b 68 " --> pdb=" O PHE b 162 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N LEU b 161 " --> pdb=" O ILE b 184 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N VAL b 186 " --> pdb=" O LEU b 161 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL b 163 " --> pdb=" O VAL b 186 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'c' and resid 57 through 58 Processing sheet with id=AA4, first strand: chain 'c' and resid 148 through 149 removed outlier: 3.877A pdb=" N GLY c 148 " --> pdb=" O PHE c 203 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE c 203 " --> pdb=" O GLY c 148 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'c' and resid 152 through 153 Processing sheet with id=AA6, first strand: chain 'c' and resid 187 through 190 removed outlier: 3.922A pdb=" N TYR c 187 " --> pdb=" O VAL c 198 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'd' and resid 123 through 124 removed outlier: 3.527A pdb=" N VAL d 143 " --> pdb=" O GLY d 180 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'e' and resid 15 through 25 removed outlier: 4.964A pdb=" N LEU e 16 " --> pdb=" O VAL e 39 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL e 39 " --> pdb=" O LEU e 16 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'e' and resid 86 through 90 removed outlier: 3.583A pdb=" N SER e 93 " --> pdb=" O HIS e 90 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'f' and resid 36 through 46 removed outlier: 4.762A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ARG f 44 " --> pdb=" O ALA f 57 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ALA f 57 " --> pdb=" O ARG f 44 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ARG f 86 " --> pdb=" O LEU f 9 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'h' and resid 24 through 27 Processing sheet with id=AB3, first strand: chain 'i' and resid 18 through 19 removed outlier: 3.753A pdb=" N ARG i 18 " --> pdb=" O THR i 66 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'i' and resid 29 through 30 Processing sheet with id=AB5, first strand: chain 'k' and resid 41 through 46 removed outlier: 6.696A pdb=" N ILE k 34 " --> pdb=" O LEU k 42 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N TRP k 44 " --> pdb=" O VAL k 32 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL k 32 " --> pdb=" O TRP k 44 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL k 17 " --> pdb=" O LEU k 79 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN k 81 " --> pdb=" O VAL k 17 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N THR k 111 " --> pdb=" O LEU k 82 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N VAL k 84 " --> pdb=" O THR k 111 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'l' and resid 29 through 40 removed outlier: 6.821A pdb=" N ARG l 54 " --> pdb=" O THR l 35 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N VAL l 37 " --> pdb=" O VAL l 52 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL l 52 " --> pdb=" O VAL l 37 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N THR l 39 " --> pdb=" O ARG l 50 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ARG l 50 " --> pdb=" O THR l 39 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N LYS l 51 " --> pdb=" O ILE l 67 " (cutoff:3.500A) removed outlier: 10.259A pdb=" N TYR l 95 " --> pdb=" O GLU l 62 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N SER l 64 " --> pdb=" O TYR l 95 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N THR l 97 " --> pdb=" O SER l 64 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TYR l 66 " --> pdb=" O THR l 97 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE l 82 " --> pdb=" O ARG l 30 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'p' and resid 34 through 35 removed outlier: 3.501A pdb=" N GLU p 34 " --> pdb=" O VAL p 21 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'p' and resid 9 through 11 Processing sheet with id=AB9, first strand: chain 'q' and resid 40 through 50 removed outlier: 5.738A pdb=" N THR q 23 " --> pdb=" O ASP q 18 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ASP q 18 " --> pdb=" O THR q 23 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N THR q 25 " --> pdb=" O VAL q 16 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N GLU q 29 " --> pdb=" O THR q 12 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N THR q 12 " --> pdb=" O GLU q 29 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N LEU q 61 " --> pdb=" O ILE q 81 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ILE q 81 " --> pdb=" O LEU q 61 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N THR q 63 " --> pdb=" O VAL q 79 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ALA q 75 " --> pdb=" O THR q 67 " (cutoff:3.500A) 441 hydrogen bonds defined for protein. 1233 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 762 hydrogen bonds 1174 hydrogen bond angles 0 basepair planarities 313 basepair parallelities 673 stacking parallelities Total time for adding SS restraints: 38.10 Time building geometry restraints manager: 27.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.88: 54720 1.88 - 2.60: 1 2.60 - 3.32: 0 3.32 - 4.04: 0 4.04 - 4.76: 1 Bond restraints: 54722 Sorted by residual: bond pdb=" CB ARG s 3 " pdb=" CG ARG s 3 " ideal model delta sigma weight residual 1.520 4.764 -3.244 3.00e-02 1.11e+03 1.17e+04 bond pdb=" C6 A a1313 " pdb=" N1 A a1313 " ideal model delta sigma weight residual 1.351 1.714 -0.363 2.00e-02 2.50e+03 3.30e+02 bond pdb=" N3 A a1313 " pdb=" C4 A a1313 " ideal model delta sigma weight residual 1.344 1.690 -0.346 2.00e-02 2.50e+03 3.00e+02 bond pdb=" N1 A a1313 " pdb=" C2 A a1313 " ideal model delta sigma weight residual 1.339 1.681 -0.342 2.00e-02 2.50e+03 2.92e+02 bond pdb=" C2 A a1313 " pdb=" N3 A a1313 " ideal model delta sigma weight residual 1.331 1.663 -0.332 2.00e-02 2.50e+03 2.75e+02 ... (remaining 54717 not shown) Histogram of bond angle deviations from ideal: 41.41 - 64.95: 3 64.95 - 88.50: 0 88.50 - 112.05: 35936 112.05 - 135.59: 45447 135.59 - 159.14: 19 Bond angle restraints: 81405 Sorted by residual: angle pdb=" N9 A a1219 " pdb=" C8 A a1219 " pdb=" N7 A a1219 " ideal model delta sigma weight residual 113.80 41.41 72.39 3.00e+00 1.11e-01 5.82e+02 angle pdb=" N7 A a1219 " pdb=" C5 A a1219 " pdb=" C4 A a1219 " ideal model delta sigma weight residual 110.70 42.15 68.55 3.00e+00 1.11e-01 5.22e+02 angle pdb=" C8 A a1219 " pdb=" N9 A a1219 " pdb=" C4 A a1219 " ideal model delta sigma weight residual 105.80 52.46 53.34 3.00e+00 1.11e-01 3.16e+02 angle pdb=" C1' A a1219 " pdb=" N9 A a1219 " pdb=" C8 A a1219 " ideal model delta sigma weight residual 127.70 97.72 29.98 3.00e+00 1.11e-01 9.98e+01 angle pdb=" C8 A a1219 " pdb=" N7 A a1219 " pdb=" C5 A a1219 " ideal model delta sigma weight residual 103.90 132.53 -28.63 3.00e+00 1.11e-01 9.11e+01 ... (remaining 81400 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 30085 35.90 - 71.79: 4310 71.79 - 107.69: 507 107.69 - 143.59: 35 143.59 - 179.49: 41 Dihedral angle restraints: 34978 sinusoidal: 28378 harmonic: 6600 Sorted by residual: dihedral pdb=" CA SER h 88 " pdb=" C SER h 88 " pdb=" N VAL h 89 " pdb=" CA VAL h 89 " ideal model delta harmonic sigma weight residual -180.00 -115.79 -64.21 0 5.00e+00 4.00e-02 1.65e+02 dihedral pdb=" CA LEU h 83 " pdb=" C LEU h 83 " pdb=" N ARG h 84 " pdb=" CA ARG h 84 " ideal model delta harmonic sigma weight residual -180.00 -123.29 -56.71 0 5.00e+00 4.00e-02 1.29e+02 dihedral pdb=" C5' A a 636 " pdb=" C4' A a 636 " pdb=" C3' A a 636 " pdb=" O3' A a 636 " ideal model delta sinusoidal sigma weight residual 147.00 71.69 75.31 1 8.00e+00 1.56e-02 1.12e+02 ... (remaining 34975 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.152: 9986 0.152 - 0.304: 306 0.304 - 0.456: 29 0.456 - 0.608: 8 0.608 - 0.760: 2 Chirality restraints: 10331 Sorted by residual: chirality pdb=" C1' A a 636 " pdb=" O4' A a 636 " pdb=" C2' A a 636 " pdb=" N9 A a 636 " both_signs ideal model delta sigma weight residual False 2.44 1.68 0.76 2.00e-01 2.50e+01 1.44e+01 chirality pdb=" C3' G a 356 " pdb=" C4' G a 356 " pdb=" O3' G a 356 " pdb=" C2' G a 356 " both_signs ideal model delta sigma weight residual False -2.48 -1.84 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" C1' A a1061 " pdb=" O4' A a1061 " pdb=" C2' A a1061 " pdb=" N9 A a1061 " both_signs ideal model delta sigma weight residual False 2.44 1.83 0.61 2.00e-01 2.50e+01 9.22e+00 ... (remaining 10328 not shown) Planarity restraints: 4691 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A a 60 " -0.099 2.00e-02 2.50e+03 4.20e-02 4.86e+01 pdb=" N9 A a 60 " 0.079 2.00e-02 2.50e+03 pdb=" C8 A a 60 " 0.019 2.00e-02 2.50e+03 pdb=" N7 A a 60 " 0.005 2.00e-02 2.50e+03 pdb=" C5 A a 60 " -0.004 2.00e-02 2.50e+03 pdb=" C6 A a 60 " 0.008 2.00e-02 2.50e+03 pdb=" N6 A a 60 " -0.045 2.00e-02 2.50e+03 pdb=" N1 A a 60 " -0.012 2.00e-02 2.50e+03 pdb=" C2 A a 60 " 0.012 2.00e-02 2.50e+03 pdb=" N3 A a 60 " 0.014 2.00e-02 2.50e+03 pdb=" C4 A a 60 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG h 80 " -0.093 5.00e-02 4.00e+02 1.42e-01 3.24e+01 pdb=" N PRO h 81 " 0.246 5.00e-02 4.00e+02 pdb=" CA PRO h 81 " -0.074 5.00e-02 4.00e+02 pdb=" CD PRO h 81 " -0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR l 116 " -0.060 2.00e-02 2.50e+03 3.55e-02 2.53e+01 pdb=" CG TYR l 116 " 0.074 2.00e-02 2.50e+03 pdb=" CD1 TYR l 116 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR l 116 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR l 116 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR l 116 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR l 116 " -0.019 2.00e-02 2.50e+03 pdb=" OH TYR l 116 " -0.007 2.00e-02 2.50e+03 ... (remaining 4688 not shown) Histogram of nonbonded interaction distances: 1.40 - 2.10: 26 2.10 - 2.80: 12966 2.80 - 3.50: 65414 3.50 - 4.20: 154299 4.20 - 4.90: 211025 Nonbonded interactions: 443730 Sorted by model distance: nonbonded pdb=" N7 A a1182 " pdb=" CG2 VAL c 5 " model vdw 1.399 3.540 nonbonded pdb=" N MET f 21 " pdb=" NH1 ARG f 24 " model vdw 1.427 3.200 nonbonded pdb=" NZ LYS b 73 " pdb=" OD2 ASP b 165 " model vdw 1.567 2.520 nonbonded pdb=" O2' C a1336 " pdb=" O TYR i 127 " model vdw 1.580 2.440 nonbonded pdb=" C GLY f 20 " pdb=" NH1 ARG f 24 " model vdw 1.581 3.350 ... (remaining 443725 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic 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: 3.010 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: 0.040 Extract box with map and model: 16.030 Check model and map are aligned: 0.830 Set scattering table: 0.510 Process input model: 158.110 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.500 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 193.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 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 : 0.018 3.244 54722 Z= 1.235 Angle : 1.426 72.391 81405 Z= 0.706 Chirality : 0.068 0.760 10331 Planarity : 0.008 0.142 4691 Dihedral : 25.778 179.487 30727 Min Nonbonded Distance : 1.399 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 1.50 % Allowed : 14.63 % Favored : 83.87 % Rotamer: Outliers : 9.17 % Allowed : 8.42 % Favored : 82.41 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 2.60 % Twisted General : 1.45 % 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: -5.64 (0.13), residues: 2263 helix: -4.35 (0.11), residues: 651 sheet: -2.71 (0.29), residues: 259 loop : -3.81 (0.13), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP q 76 HIS 0.039 0.004 HIS k 118 PHE 0.059 0.004 PHE h 66 TYR 0.074 0.005 TYR l 116 ARG 0.024 0.002 ARG d 115 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 415 time to evaluate : 3.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET t 27 " (corrupted residue). Skipping it. REVERT: b 6 MET cc_start: 0.4935 (mmp) cc_final: 0.4335 (tpp) REVERT: b 26 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7595 (mttt) REVERT: b 52 GLU cc_start: 0.6679 (OUTLIER) cc_final: 0.6338 (mm-30) REVERT: b 131 LYS cc_start: 0.4769 (OUTLIER) cc_final: 0.4357 (tppt) REVERT: b 154 MET cc_start: 0.6844 (OUTLIER) cc_final: 0.6189 (ttm) REVERT: c 95 MET cc_start: 0.2508 (ttt) cc_final: 0.1826 (ptt) REVERT: d 132 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8394 (mm) REVERT: e 21 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.8041 (ttp80) REVERT: e 27 LYS cc_start: 0.8176 (mtmt) cc_final: 0.7561 (mppt) REVERT: e 112 MET cc_start: 0.8361 (mtm) cc_final: 0.8156 (mtp) REVERT: e 113 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.8139 (ttm-80) REVERT: g 9 LYS cc_start: 0.2491 (OUTLIER) cc_final: 0.2191 (mmtt) REVERT: g 15 ASP cc_start: 0.4222 (OUTLIER) cc_final: 0.4007 (t0) REVERT: g 17 LYS cc_start: 0.4077 (OUTLIER) cc_final: 0.2487 (mttm) REVERT: g 25 LYS cc_start: 0.5323 (OUTLIER) cc_final: 0.4757 (ttpt) REVERT: g 52 GLU cc_start: 0.4613 (OUTLIER) cc_final: 0.3721 (tt0) REVERT: g 64 LYS cc_start: 0.0795 (OUTLIER) cc_final: -0.0172 (mptt) REVERT: g 137 LYS cc_start: 0.3970 (OUTLIER) cc_final: 0.3198 (pptt) REVERT: g 138 ARG cc_start: 0.3876 (tmt170) cc_final: 0.1637 (ttp-170) REVERT: g 149 LYS cc_start: 0.2891 (OUTLIER) cc_final: 0.1757 (ttpt) REVERT: n 89 MET cc_start: 0.4829 (mmt) cc_final: 0.4290 (mmt) REVERT: o 48 LYS cc_start: 0.8482 (mtpt) cc_final: 0.8254 (mtpt) REVERT: p 28 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.8366 (ptt90) REVERT: q 55 GLN cc_start: 0.7188 (pp30) cc_final: 0.6871 (pp30) REVERT: q 70 LEU cc_start: 0.8856 (mt) cc_final: 0.8640 (mt) REVERT: r 54 GLN cc_start: 0.8708 (tt0) cc_final: 0.8294 (tt0) REVERT: s 66 MET cc_start: -0.0213 (mtp) cc_final: -0.0643 (mmt) outliers start: 171 outliers final: 76 residues processed: 545 average time/residue: 1.9726 time to fit residues: 1303.5786 Evaluate side-chains 418 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 326 time to evaluate : 3.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 5 ASN Chi-restraints excluded: chain b residue 8 ASP Chi-restraints excluded: chain b residue 10 LEU Chi-restraints excluded: chain b residue 23 TRP Chi-restraints excluded: chain b residue 26 LYS Chi-restraints excluded: chain b residue 29 LYS Chi-restraints excluded: chain b residue 47 LEU Chi-restraints excluded: chain b residue 52 GLU Chi-restraints excluded: chain b residue 55 THR Chi-restraints excluded: chain b residue 60 LEU Chi-restraints excluded: chain b residue 66 LYS Chi-restraints excluded: chain b residue 67 ILE Chi-restraints excluded: chain b residue 74 ARG Chi-restraints excluded: chain b residue 75 SER Chi-restraints excluded: chain b residue 83 GLU Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain b residue 95 ARG Chi-restraints excluded: chain b residue 100 MET Chi-restraints excluded: chain b residue 101 LEU Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain b residue 106 THR Chi-restraints excluded: chain b residue 107 ILE Chi-restraints excluded: chain b residue 108 ARG Chi-restraints excluded: chain b residue 113 ARG Chi-restraints excluded: chain b residue 114 LEU Chi-restraints excluded: chain b residue 130 THR Chi-restraints excluded: chain b residue 131 LYS Chi-restraints excluded: chain b residue 132 LYS Chi-restraints excluded: chain b residue 141 LEU Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain b residue 154 MET Chi-restraints excluded: chain b residue 171 ILE Chi-restraints excluded: chain b residue 181 ILE Chi-restraints excluded: chain b residue 186 VAL Chi-restraints excluded: chain b residue 192 SER Chi-restraints excluded: chain b residue 205 ASP Chi-restraints excluded: chain b residue 207 ILE Chi-restraints excluded: chain b residue 210 VAL Chi-restraints excluded: chain b residue 212 LEU Chi-restraints excluded: chain b residue 214 LEU Chi-restraints excluded: chain b residue 219 GLU Chi-restraints excluded: chain b residue 222 ILE Chi-restraints excluded: chain c residue 5 VAL Chi-restraints excluded: chain c residue 6 HIS Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 110 THR Chi-restraints excluded: chain d residue 132 ILE Chi-restraints excluded: chain d residue 173 VAL Chi-restraints excluded: chain e residue 15 LYS Chi-restraints excluded: chain e residue 18 GLN Chi-restraints excluded: chain e residue 21 ARG Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 51 ARG Chi-restraints excluded: chain e residue 53 LYS Chi-restraints excluded: chain e residue 113 ARG Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain f residue 2 ARG Chi-restraints excluded: chain f residue 7 VAL Chi-restraints excluded: chain f residue 21 MET Chi-restraints excluded: chain f residue 24 ARG Chi-restraints excluded: chain f residue 86 ARG Chi-restraints excluded: chain g residue 9 LYS Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 15 ASP Chi-restraints excluded: chain g residue 17 LYS Chi-restraints excluded: chain g residue 20 SER Chi-restraints excluded: chain g residue 25 LYS Chi-restraints excluded: chain g residue 35 LYS Chi-restraints excluded: chain g residue 38 VAL Chi-restraints excluded: chain g residue 41 ARG Chi-restraints excluded: chain g residue 51 LYS Chi-restraints excluded: chain g residue 52 GLU Chi-restraints excluded: chain g residue 57 ASP Chi-restraints excluded: chain g residue 64 LYS Chi-restraints excluded: chain g residue 77 SER Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain g residue 115 SER Chi-restraints excluded: chain g residue 116 MET Chi-restraints excluded: chain g residue 125 LEU Chi-restraints excluded: chain g residue 136 LYS Chi-restraints excluded: chain g residue 137 LYS Chi-restraints excluded: chain g residue 146 GLU Chi-restraints excluded: chain g residue 149 LYS Chi-restraints excluded: chain g residue 154 TYR Chi-restraints excluded: chain h residue 7 LEU Chi-restraints excluded: chain h residue 59 LEU Chi-restraints excluded: chain h residue 106 THR Chi-restraints excluded: chain k residue 100 LEU Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 28 ARG Chi-restraints excluded: chain t residue 27 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 0.9990 chunk 281 optimal weight: 1.9990 chunk 156 optimal weight: 0.8980 chunk 96 optimal weight: 9.9990 chunk 190 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 chunk 291 optimal weight: 0.9990 chunk 112 optimal weight: 20.0000 chunk 177 optimal weight: 9.9990 chunk 217 optimal weight: 0.7980 chunk 337 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 24 ASN b 42 ASN b 65 ASN b 94 HIS b 177 ASN b 215 ASN c 6 HIS c 18 HIS ** d 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 136 GLN e 18 GLN e 20 ASN e 90 HIS e 123 ASN e 133 ASN f 55 HIS g 21 GLN g 148 ASN h 107 ASN i 6 ASN ** k 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 5 ASN l 26 ASN ** l 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 77 HIS m 40 ASN ** m 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 105 ASN n 8 ASN n 71 HIS o 42 HIS o 61 ASN q 54 ASN ** s 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 13 GLN t 68 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 1.896 54722 Z= 0.658 Angle : 0.881 70.746 81405 Z= 0.417 Chirality : 0.041 0.571 10331 Planarity : 0.006 0.108 4691 Dihedral : 26.486 179.004 26500 Min Nonbonded Distance : 1.718 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.11 % Favored : 87.54 % Rotamer: Outliers : 6.97 % Allowed : 18.55 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 1.30 % Twisted General : 0.86 % 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: -4.63 (0.14), residues: 2263 helix: -2.96 (0.16), residues: 674 sheet: -2.22 (0.29), residues: 272 loop : -3.47 (0.14), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP d 170 HIS 0.008 0.001 HIS k 118 PHE 0.030 0.002 PHE h 66 TYR 0.037 0.002 TYR b 213 ARG 0.009 0.001 ARG k 69 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 352 time to evaluate : 3.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET t 27 " (corrupted residue). Skipping it. REVERT: b 6 MET cc_start: 0.4455 (mmp) cc_final: 0.3424 (mmp) REVERT: b 111 ILE cc_start: 0.5690 (OUTLIER) cc_final: 0.5419 (mm) REVERT: b 114 LEU cc_start: 0.5073 (OUTLIER) cc_final: 0.4542 (pt) REVERT: c 114 MET cc_start: 0.2193 (OUTLIER) cc_final: 0.1991 (mtt) REVERT: d 73 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.7078 (tpt170) REVERT: e 143 LYS cc_start: 0.8253 (mtmt) cc_final: 0.7881 (mtmm) REVERT: f 25 TYR cc_start: 0.8256 (m-10) cc_final: 0.8018 (m-10) REVERT: g 41 ARG cc_start: 0.1855 (OUTLIER) cc_final: 0.1140 (mmt180) REVERT: g 138 ARG cc_start: 0.2916 (tmt170) cc_final: 0.0942 (ttp-170) REVERT: h 10 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.7992 (ttt) REVERT: k 127 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.7681 (mtm-85) REVERT: n 89 MET cc_start: 0.4721 (mmt) cc_final: 0.4327 (mmt) REVERT: o 40 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.7302 (mp10) REVERT: o 84 ARG cc_start: 0.7401 (OUTLIER) cc_final: 0.6804 (mtt180) REVERT: p 21 VAL cc_start: 0.9291 (OUTLIER) cc_final: 0.8921 (t) REVERT: p 28 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8257 (ptt90) REVERT: q 31 ARG cc_start: 0.8131 (mtp85) cc_final: 0.7765 (mtp180) REVERT: q 33 LYS cc_start: 0.8895 (tttt) cc_final: 0.8670 (tttt) REVERT: q 42 LYS cc_start: 0.8218 (mttt) cc_final: 0.8018 (mttp) REVERT: q 68 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7230 (ptm-80) REVERT: s 39 MET cc_start: 0.1923 (tpt) cc_final: 0.0902 (mpp) REVERT: s 66 MET cc_start: -0.0848 (mtp) cc_final: -0.1121 (mmt) outliers start: 130 outliers final: 49 residues processed: 445 average time/residue: 1.6791 time to fit residues: 928.0725 Evaluate side-chains 371 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 310 time to evaluate : 3.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 5 ASN Chi-restraints excluded: chain b residue 10 LEU Chi-restraints excluded: chain b residue 60 LEU Chi-restraints excluded: chain b residue 75 SER Chi-restraints excluded: chain b residue 83 GLU Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain b residue 95 ARG Chi-restraints excluded: chain b residue 107 ILE Chi-restraints excluded: chain b residue 111 ILE Chi-restraints excluded: chain b residue 113 ARG Chi-restraints excluded: chain b residue 114 LEU Chi-restraints excluded: chain b residue 130 THR Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 181 ILE Chi-restraints excluded: chain b residue 205 ASP Chi-restraints excluded: chain b residue 212 LEU Chi-restraints excluded: chain b residue 214 LEU Chi-restraints excluded: chain b residue 219 GLU Chi-restraints excluded: chain c residue 114 MET Chi-restraints excluded: chain d residue 73 ARG Chi-restraints excluded: chain d residue 110 THR Chi-restraints excluded: chain d residue 153 LEU Chi-restraints excluded: chain d residue 173 VAL Chi-restraints excluded: chain d residue 189 SER Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 131 SER Chi-restraints excluded: chain e residue 149 GLN Chi-restraints excluded: chain f residue 2 ARG Chi-restraints excluded: chain f residue 69 LYS Chi-restraints excluded: chain f residue 78 PHE Chi-restraints excluded: chain g residue 38 VAL Chi-restraints excluded: chain g residue 41 ARG Chi-restraints excluded: chain g residue 50 VAL Chi-restraints excluded: chain g residue 51 LYS Chi-restraints excluded: chain g residue 57 ASP Chi-restraints excluded: chain g residue 77 SER Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain g residue 125 LEU Chi-restraints excluded: chain g residue 136 LYS Chi-restraints excluded: chain g residue 148 ASN Chi-restraints excluded: chain g residue 149 LYS Chi-restraints excluded: chain g residue 154 TYR Chi-restraints excluded: chain h residue 7 LEU Chi-restraints excluded: chain h residue 10 MET Chi-restraints excluded: chain h residue 59 LEU Chi-restraints excluded: chain i residue 33 ARG Chi-restraints excluded: chain k residue 26 SER Chi-restraints excluded: chain k residue 100 LEU Chi-restraints excluded: chain k residue 127 ARG Chi-restraints excluded: chain o residue 40 GLN Chi-restraints excluded: chain o residue 84 ARG Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 28 ARG Chi-restraints excluded: chain p residue 50 LEU Chi-restraints excluded: chain q residue 10 THR Chi-restraints excluded: chain q residue 68 ARG Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 44 MET Chi-restraints excluded: chain t residue 27 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 187 optimal weight: 1.9990 chunk 104 optimal weight: 20.0000 chunk 281 optimal weight: 0.8980 chunk 230 optimal weight: 4.9990 chunk 93 optimal weight: 9.9990 chunk 338 optimal weight: 0.9990 chunk 365 optimal weight: 0.9990 chunk 301 optimal weight: 0.0470 chunk 335 optimal weight: 0.8980 chunk 115 optimal weight: 10.0000 chunk 271 optimal weight: 20.0000 overall best weight: 0.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 36 ASN b 177 ASN b 226 GLN c 6 HIS d 43 GLN ** d 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 136 GLN ** e 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 3 HIS ** g 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 85 ASN l 5 ASN l 26 ASN l 59 ASN ** l 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 14 HIS ** m 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 71 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 1.884 54722 Z= 0.644 Angle : 0.813 70.882 81405 Z= 0.376 Chirality : 0.038 0.457 10331 Planarity : 0.005 0.105 4691 Dihedral : 26.169 179.408 26354 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.58 % Favored : 88.11 % Rotamer: Outliers : 6.43 % Allowed : 21.07 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 1.30 % Twisted General : 0.45 % 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: -3.80 (0.16), residues: 2263 helix: -2.07 (0.19), residues: 658 sheet: -1.83 (0.31), residues: 264 loop : -3.05 (0.15), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP d 170 HIS 0.005 0.001 HIS k 118 PHE 0.028 0.002 PHE h 66 TYR 0.028 0.002 TYR b 213 ARG 0.010 0.001 ARG i 99 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 321 time to evaluate : 3.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET t 27 " (corrupted residue). Skipping it. REVERT: c 134 MET cc_start: 0.3360 (tpt) cc_final: 0.2317 (ptp) REVERT: e 19 VAL cc_start: 0.8879 (OUTLIER) cc_final: 0.8662 (t) REVERT: e 39 VAL cc_start: 0.8719 (OUTLIER) cc_final: 0.8498 (m) REVERT: e 49 PHE cc_start: 0.8767 (p90) cc_final: 0.8561 (p90) REVERT: e 143 LYS cc_start: 0.8131 (mtmt) cc_final: 0.7895 (mtmm) REVERT: g 64 LYS cc_start: 0.0899 (OUTLIER) cc_final: 0.0043 (mptt) REVERT: g 77 SER cc_start: 0.5225 (OUTLIER) cc_final: 0.4996 (t) REVERT: g 138 ARG cc_start: 0.2553 (tmt170) cc_final: 0.0765 (ttp-170) REVERT: h 74 GLU cc_start: 0.5562 (pp20) cc_final: 0.5205 (pp20) REVERT: n 6 MET cc_start: -0.1175 (ttt) cc_final: -0.1494 (mmt) REVERT: n 84 LEU cc_start: 0.1076 (OUTLIER) cc_final: 0.0689 (tt) REVERT: n 89 MET cc_start: 0.5163 (mmt) cc_final: 0.4876 (mmt) REVERT: o 40 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.7518 (mp10) REVERT: o 84 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.6808 (mtm180) REVERT: p 21 VAL cc_start: 0.9224 (OUTLIER) cc_final: 0.8826 (t) REVERT: p 28 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.8282 (tmm160) REVERT: q 31 ARG cc_start: 0.8023 (mtp85) cc_final: 0.7783 (mtp180) REVERT: q 55 GLN cc_start: 0.7425 (OUTLIER) cc_final: 0.6957 (pp30) REVERT: q 78 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7847 (mp) outliers start: 120 outliers final: 41 residues processed: 407 average time/residue: 1.6363 time to fit residues: 837.0856 Evaluate side-chains 344 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 292 time to evaluate : 3.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 5 ASN Chi-restraints excluded: chain b residue 60 LEU Chi-restraints excluded: chain b residue 83 GLU Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain b residue 95 ARG Chi-restraints excluded: chain b residue 113 ARG Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 181 ILE Chi-restraints excluded: chain b residue 212 LEU Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 73 ARG Chi-restraints excluded: chain d residue 110 THR Chi-restraints excluded: chain d residue 173 VAL Chi-restraints excluded: chain e residue 19 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 124 VAL Chi-restraints excluded: chain e residue 149 GLN Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain g residue 15 ASP Chi-restraints excluded: chain g residue 38 VAL Chi-restraints excluded: chain g residue 41 ARG Chi-restraints excluded: chain g residue 50 VAL Chi-restraints excluded: chain g residue 57 ASP Chi-restraints excluded: chain g residue 64 LYS Chi-restraints excluded: chain g residue 77 SER Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain g residue 136 LYS Chi-restraints excluded: chain g residue 154 TYR Chi-restraints excluded: chain h residue 55 VAL Chi-restraints excluded: chain h residue 121 VAL Chi-restraints excluded: chain h residue 129 VAL Chi-restraints excluded: chain i residue 33 ARG Chi-restraints excluded: chain k residue 26 SER Chi-restraints excluded: chain k residue 50 SER Chi-restraints excluded: chain k residue 100 LEU Chi-restraints excluded: chain l residue 77 HIS Chi-restraints excluded: chain n residue 84 LEU Chi-restraints excluded: chain o residue 40 GLN Chi-restraints excluded: chain o residue 73 LYS Chi-restraints excluded: chain o residue 84 ARG Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 28 ARG Chi-restraints excluded: chain q residue 10 THR Chi-restraints excluded: chain q residue 55 GLN Chi-restraints excluded: chain q residue 77 THR Chi-restraints excluded: chain q residue 78 LEU Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 52 HIS Chi-restraints excluded: chain s residue 55 ARG Chi-restraints excluded: chain t residue 6 SER Chi-restraints excluded: chain t residue 33 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 334 optimal weight: 3.9990 chunk 254 optimal weight: 0.6980 chunk 175 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 227 optimal weight: 1.9990 chunk 339 optimal weight: 2.9990 chunk 359 optimal weight: 6.9990 chunk 177 optimal weight: 5.9990 chunk 321 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 18 HIS b 36 ASN b 177 ASN c 69 HIS ** d 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 89 ASN ** d 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 136 GLN e 90 HIS ** e 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 21 GLN g 148 ASN ** h 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 5 ASN ** l 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 77 HIS m 14 HIS m 91 HIS n 33 ASN q 34 HIS r 74 HIS ** s 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.883 54722 Z= 0.732 Angle : 0.935 70.814 81405 Z= 0.440 Chirality : 0.046 0.562 10331 Planarity : 0.006 0.110 4691 Dihedral : 26.229 179.591 26317 Min Nonbonded Distance : 1.716 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.90 % Favored : 86.74 % Rotamer: Outliers : 7.51 % Allowed : 20.97 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 1.30 % Twisted General : 0.54 % 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: -3.75 (0.16), residues: 2263 helix: -1.90 (0.19), residues: 663 sheet: -1.82 (0.30), residues: 278 loop : -3.09 (0.15), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP b 23 HIS 0.009 0.001 HIS k 118 PHE 0.030 0.002 PHE h 66 TYR 0.035 0.002 TYR l 116 ARG 0.008 0.001 ARG d 115 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 294 time to evaluate : 3.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET t 27 " (corrupted residue). Skipping it. REVERT: b 26 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.7847 (mtpt) REVERT: b 188 ASP cc_start: 0.7603 (t0) cc_final: 0.7262 (t70) REVERT: d 69 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7134 (tm-30) REVERT: d 77 GLN cc_start: 0.7289 (OUTLIER) cc_final: 0.6953 (mp10) REVERT: e 18 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7939 (tt0) REVERT: e 39 VAL cc_start: 0.8862 (OUTLIER) cc_final: 0.8584 (m) REVERT: e 55 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.7139 (ttm110) REVERT: e 143 LYS cc_start: 0.8149 (mtmt) cc_final: 0.7888 (mtmm) REVERT: g 64 LYS cc_start: 0.1154 (OUTLIER) cc_final: 0.0189 (mptt) REVERT: g 138 ARG cc_start: 0.3158 (tmt170) cc_final: 0.1016 (ttp-170) REVERT: h 38 LYS cc_start: 0.8143 (tttt) cc_final: 0.7939 (ptmm) REVERT: h 49 PHE cc_start: 0.6209 (OUTLIER) cc_final: 0.5696 (t80) REVERT: k 20 ILE cc_start: 0.7526 (OUTLIER) cc_final: 0.7131 (mp) REVERT: k 127 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.8027 (mtm-85) REVERT: n 89 MET cc_start: 0.5366 (mmt) cc_final: 0.4721 (mmt) REVERT: o 3 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8123 (tt) REVERT: o 40 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.7448 (mp10) REVERT: o 84 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.7364 (mtt180) REVERT: q 55 GLN cc_start: 0.7799 (OUTLIER) cc_final: 0.7461 (pp30) REVERT: s 39 MET cc_start: 0.2007 (mmm) cc_final: 0.1796 (mmm) outliers start: 140 outliers final: 67 residues processed: 384 average time/residue: 1.6627 time to fit residues: 802.8606 Evaluate side-chains 379 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 298 time to evaluate : 3.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 5 ASN Chi-restraints excluded: chain b residue 10 LEU Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 26 LYS Chi-restraints excluded: chain b residue 31 ILE Chi-restraints excluded: chain b residue 60 LEU Chi-restraints excluded: chain b residue 83 GLU Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain b residue 95 ARG Chi-restraints excluded: chain b residue 105 LYS Chi-restraints excluded: chain b residue 113 ARG Chi-restraints excluded: chain b residue 139 ARG Chi-restraints excluded: chain b residue 181 ILE Chi-restraints excluded: chain b residue 192 SER Chi-restraints excluded: chain b residue 205 ASP Chi-restraints excluded: chain b residue 219 GLU Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 69 GLU Chi-restraints excluded: chain d residue 73 ARG Chi-restraints excluded: chain d residue 77 GLN Chi-restraints excluded: chain d residue 168 VAL Chi-restraints excluded: chain d residue 173 VAL Chi-restraints excluded: chain d residue 189 SER Chi-restraints excluded: chain e residue 18 GLN Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 55 ARG Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 124 VAL Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain e residue 131 SER Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 36 ILE Chi-restraints excluded: chain f residue 78 PHE Chi-restraints excluded: chain g residue 5 ARG Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 38 VAL Chi-restraints excluded: chain g residue 50 VAL Chi-restraints excluded: chain g residue 64 LYS Chi-restraints excluded: chain g residue 101 MET Chi-restraints excluded: chain g residue 125 LEU Chi-restraints excluded: chain g residue 136 LYS Chi-restraints excluded: chain g residue 154 TYR Chi-restraints excluded: chain h residue 10 MET Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 49 PHE Chi-restraints excluded: chain h residue 55 VAL Chi-restraints excluded: chain h residue 59 LEU Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 91 GLN Chi-restraints excluded: chain h residue 121 VAL Chi-restraints excluded: chain h residue 129 VAL Chi-restraints excluded: chain i residue 33 ARG Chi-restraints excluded: chain i residue 111 VAL Chi-restraints excluded: chain k residue 20 ILE Chi-restraints excluded: chain k residue 26 SER Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 50 SER Chi-restraints excluded: chain k residue 83 ASP Chi-restraints excluded: chain k residue 100 LEU Chi-restraints excluded: chain k residue 127 ARG Chi-restraints excluded: chain l residue 25 GLN Chi-restraints excluded: chain l residue 58 THR Chi-restraints excluded: chain l residue 77 HIS Chi-restraints excluded: chain l residue 82 ILE Chi-restraints excluded: chain l residue 107 VAL Chi-restraints excluded: chain n residue 60 LEU Chi-restraints excluded: chain n residue 84 LEU Chi-restraints excluded: chain o residue 3 LEU Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 40 GLN Chi-restraints excluded: chain o residue 41 ASP Chi-restraints excluded: chain o residue 73 LYS Chi-restraints excluded: chain o residue 84 ARG Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 51 SER Chi-restraints excluded: chain q residue 10 THR Chi-restraints excluded: chain q residue 33 LYS Chi-restraints excluded: chain q residue 55 GLN Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 52 HIS Chi-restraints excluded: chain t residue 6 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 299 optimal weight: 7.9990 chunk 204 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 267 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 306 optimal weight: 0.9980 chunk 248 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 183 optimal weight: 0.0270 chunk 322 optimal weight: 20.0000 chunk 90 optimal weight: 2.9990 overall best weight: 0.9842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 36 ASN b 177 ASN ** d 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 148 ASN ** h 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 28 ASN l 5 ASN ** l 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 14 HIS ** n 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 1.880 54722 Z= 0.647 Angle : 0.812 70.987 81405 Z= 0.375 Chirality : 0.038 0.460 10331 Planarity : 0.005 0.105 4691 Dihedral : 26.086 178.528 26302 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.36 % Favored : 88.38 % Rotamer: Outliers : 6.27 % Allowed : 22.90 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.41 % 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: -3.30 (0.16), residues: 2263 helix: -1.42 (0.20), residues: 661 sheet: -1.70 (0.31), residues: 278 loop : -2.84 (0.16), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP d 170 HIS 0.021 0.001 HIS l 77 PHE 0.025 0.002 PHE h 66 TYR 0.024 0.001 TYR l 116 ARG 0.011 0.000 ARG b 146 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 307 time to evaluate : 3.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET t 27 " (corrupted residue). Skipping it. REVERT: b 95 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.8099 (tpt-90) REVERT: d 69 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7022 (tm-30) REVERT: d 77 GLN cc_start: 0.7266 (OUTLIER) cc_final: 0.6905 (mp10) REVERT: e 143 LYS cc_start: 0.8173 (mtmt) cc_final: 0.7899 (mtmm) REVERT: g 138 ARG cc_start: 0.3072 (tmt170) cc_final: 0.1249 (mmm160) REVERT: h 38 LYS cc_start: 0.8051 (tttt) cc_final: 0.7663 (tmmt) REVERT: h 74 GLU cc_start: 0.5629 (pp20) cc_final: 0.5346 (pp20) REVERT: k 20 ILE cc_start: 0.7501 (OUTLIER) cc_final: 0.7158 (mp) REVERT: k 127 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.7938 (mtm-85) REVERT: n 89 MET cc_start: 0.5370 (mmt) cc_final: 0.4739 (mmt) REVERT: o 40 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8118 (mp10) REVERT: o 84 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.6840 (mtt180) REVERT: q 31 ARG cc_start: 0.7937 (mtp85) cc_final: 0.7580 (mtp180) REVERT: q 42 LYS cc_start: 0.8194 (mttt) cc_final: 0.7990 (mttt) REVERT: q 55 GLN cc_start: 0.7476 (OUTLIER) cc_final: 0.7135 (pp30) outliers start: 117 outliers final: 59 residues processed: 383 average time/residue: 1.8314 time to fit residues: 883.6216 Evaluate side-chains 362 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 295 time to evaluate : 3.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 5 ASN Chi-restraints excluded: chain b residue 10 LEU Chi-restraints excluded: chain b residue 31 ILE Chi-restraints excluded: chain b residue 83 GLU Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain b residue 95 ARG Chi-restraints excluded: chain b residue 113 ARG Chi-restraints excluded: chain b residue 139 ARG Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 181 ILE Chi-restraints excluded: chain b residue 219 GLU Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 69 GLU Chi-restraints excluded: chain d residue 73 ARG Chi-restraints excluded: chain d residue 77 GLN Chi-restraints excluded: chain d residue 110 THR Chi-restraints excluded: chain d residue 168 VAL Chi-restraints excluded: chain d residue 173 VAL Chi-restraints excluded: chain d residue 189 SER Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 124 VAL Chi-restraints excluded: chain e residue 131 SER Chi-restraints excluded: chain e residue 149 GLN Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 78 PHE Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 38 VAL Chi-restraints excluded: chain g residue 61 THR Chi-restraints excluded: chain g residue 77 SER Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 101 MET Chi-restraints excluded: chain g residue 123 GLU Chi-restraints excluded: chain g residue 125 LEU Chi-restraints excluded: chain g residue 136 LYS Chi-restraints excluded: chain h residue 10 MET Chi-restraints excluded: chain h residue 55 VAL Chi-restraints excluded: chain h residue 59 LEU Chi-restraints excluded: chain h residue 107 ASN Chi-restraints excluded: chain h residue 121 VAL Chi-restraints excluded: chain h residue 129 VAL Chi-restraints excluded: chain i residue 33 ARG Chi-restraints excluded: chain i residue 111 VAL Chi-restraints excluded: chain k residue 20 ILE Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 50 SER Chi-restraints excluded: chain k residue 83 ASP Chi-restraints excluded: chain k residue 100 LEU Chi-restraints excluded: chain k residue 110 ILE Chi-restraints excluded: chain k residue 127 ARG Chi-restraints excluded: chain l residue 25 GLN Chi-restraints excluded: chain l residue 58 THR Chi-restraints excluded: chain l residue 59 ASN Chi-restraints excluded: chain n residue 84 LEU Chi-restraints excluded: chain o residue 40 GLN Chi-restraints excluded: chain o residue 73 LYS Chi-restraints excluded: chain o residue 84 ARG Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 51 SER Chi-restraints excluded: chain p residue 69 GLU Chi-restraints excluded: chain q residue 10 THR Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 33 LYS Chi-restraints excluded: chain q residue 55 GLN Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 52 HIS Chi-restraints excluded: chain t residue 6 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 120 optimal weight: 20.0000 chunk 323 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 chunk 211 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 359 optimal weight: 4.9990 chunk 298 optimal weight: 0.7980 chunk 166 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 119 optimal weight: 9.9990 chunk 188 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 36 ASN b 94 HIS b 177 ASN ** d 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 148 ASN ** k 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 5 ASN ** l 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 77 HIS ** n 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 13 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.885 54722 Z= 0.744 Angle : 0.957 70.812 81405 Z= 0.451 Chirality : 0.047 0.570 10331 Planarity : 0.006 0.132 4691 Dihedral : 26.200 179.787 26297 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.31 % Allowed : 14.14 % Favored : 85.55 % Rotamer: Outliers : 6.81 % Allowed : 24.24 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.63 % 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: -3.43 (0.16), residues: 2263 helix: -1.63 (0.19), residues: 681 sheet: -1.66 (0.31), residues: 281 loop : -2.89 (0.16), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP b 23 HIS 0.008 0.001 HIS k 118 PHE 0.030 0.002 PHE h 66 TYR 0.035 0.002 TYR l 116 ARG 0.009 0.001 ARG g 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 291 time to evaluate : 2.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET t 27 " (corrupted residue). Skipping it. REVERT: b 26 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.7927 (mtpt) REVERT: b 59 ARG cc_start: 0.6972 (ttp80) cc_final: 0.6768 (ttp80) REVERT: d 37 VAL cc_start: 0.0836 (OUTLIER) cc_final: 0.0509 (m) REVERT: d 69 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7147 (tm-30) REVERT: d 77 GLN cc_start: 0.7263 (OUTLIER) cc_final: 0.6924 (mp10) REVERT: e 18 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.7949 (tt0) REVERT: e 143 LYS cc_start: 0.8133 (mtmt) cc_final: 0.7869 (mtmm) REVERT: g 5 ARG cc_start: 0.3331 (OUTLIER) cc_final: 0.2354 (ptp-170) REVERT: g 64 LYS cc_start: 0.0918 (OUTLIER) cc_final: -0.0011 (mptt) REVERT: g 125 LEU cc_start: 0.3857 (OUTLIER) cc_final: 0.3372 (mt) REVERT: g 138 ARG cc_start: 0.3290 (tmt170) cc_final: 0.1045 (ttp-170) REVERT: h 38 LYS cc_start: 0.8238 (tttt) cc_final: 0.7819 (tmmt) REVERT: h 49 PHE cc_start: 0.6433 (OUTLIER) cc_final: 0.5809 (t80) REVERT: h 74 GLU cc_start: 0.6785 (pp20) cc_final: 0.6543 (pp20) REVERT: j 16 ARG cc_start: 0.2376 (OUTLIER) cc_final: 0.1978 (pmm-80) REVERT: k 20 ILE cc_start: 0.7618 (OUTLIER) cc_final: 0.7302 (pt) REVERT: k 127 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.8047 (mtm-85) REVERT: l 14 ARG cc_start: 0.7274 (OUTLIER) cc_final: 0.6707 (tpp-160) REVERT: n 89 MET cc_start: 0.5332 (mmt) cc_final: 0.4333 (mmt) REVERT: o 40 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.7527 (mp10) REVERT: o 84 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7432 (mtt180) REVERT: p 28 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.8211 (ptt90) REVERT: q 19 LYS cc_start: 0.7832 (OUTLIER) cc_final: 0.7507 (mtmt) REVERT: q 55 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7565 (pp30) REVERT: t 61 MET cc_start: 0.8756 (mmt) cc_final: 0.8475 (mmt) outliers start: 127 outliers final: 71 residues processed: 375 average time/residue: 1.7212 time to fit residues: 801.8089 Evaluate side-chains 372 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 283 time to evaluate : 3.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 5 ASN Chi-restraints excluded: chain b residue 10 LEU Chi-restraints excluded: chain b residue 26 LYS Chi-restraints excluded: chain b residue 31 ILE Chi-restraints excluded: chain b residue 83 GLU Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain b residue 95 ARG Chi-restraints excluded: chain b residue 113 ARG Chi-restraints excluded: chain b residue 139 ARG Chi-restraints excluded: chain b residue 181 ILE Chi-restraints excluded: chain b residue 192 SER Chi-restraints excluded: chain b residue 205 ASP Chi-restraints excluded: chain b residue 219 GLU Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 37 VAL Chi-restraints excluded: chain d residue 69 GLU Chi-restraints excluded: chain d residue 73 ARG Chi-restraints excluded: chain d residue 77 GLN Chi-restraints excluded: chain d residue 110 THR Chi-restraints excluded: chain d residue 168 VAL Chi-restraints excluded: chain d residue 173 VAL Chi-restraints excluded: chain d residue 189 SER Chi-restraints excluded: chain e residue 18 GLN Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 121 VAL Chi-restraints excluded: chain e residue 125 LEU Chi-restraints excluded: chain e residue 131 SER Chi-restraints excluded: chain e residue 148 MET Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 36 ILE Chi-restraints excluded: chain f residue 69 LYS Chi-restraints excluded: chain f residue 78 PHE Chi-restraints excluded: chain g residue 5 ARG Chi-restraints excluded: chain g residue 13 LEU Chi-restraints excluded: chain g residue 38 VAL Chi-restraints excluded: chain g residue 61 THR Chi-restraints excluded: chain g residue 64 LYS Chi-restraints excluded: chain g residue 77 SER Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain g residue 101 MET Chi-restraints excluded: chain g residue 123 GLU Chi-restraints excluded: chain g residue 125 LEU Chi-restraints excluded: chain g residue 136 LYS Chi-restraints excluded: chain g residue 148 ASN Chi-restraints excluded: chain g residue 154 TYR Chi-restraints excluded: chain h residue 12 THR Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 49 PHE Chi-restraints excluded: chain h residue 55 VAL Chi-restraints excluded: chain h residue 59 LEU Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 107 ASN Chi-restraints excluded: chain h residue 121 VAL Chi-restraints excluded: chain h residue 129 VAL Chi-restraints excluded: chain i residue 33 ARG Chi-restraints excluded: chain i residue 111 VAL Chi-restraints excluded: chain j residue 16 ARG Chi-restraints excluded: chain k residue 20 ILE Chi-restraints excluded: chain k residue 26 SER Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 50 SER Chi-restraints excluded: chain k residue 83 ASP Chi-restraints excluded: chain k residue 100 LEU Chi-restraints excluded: chain k residue 127 ARG Chi-restraints excluded: chain l residue 14 ARG Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 58 THR Chi-restraints excluded: chain l residue 59 ASN Chi-restraints excluded: chain l residue 77 HIS Chi-restraints excluded: chain n residue 60 LEU Chi-restraints excluded: chain n residue 84 LEU Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 40 GLN Chi-restraints excluded: chain o residue 41 ASP Chi-restraints excluded: chain o residue 73 LYS Chi-restraints excluded: chain o residue 84 ARG Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 28 ARG Chi-restraints excluded: chain q residue 10 THR Chi-restraints excluded: chain q residue 19 LYS Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 33 LYS Chi-restraints excluded: chain q residue 55 GLN Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 44 MET Chi-restraints excluded: chain s residue 52 HIS Chi-restraints excluded: chain t residue 6 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 347 optimal weight: 0.9990 chunk 40 optimal weight: 10.0000 chunk 205 optimal weight: 0.2980 chunk 262 optimal weight: 0.9980 chunk 203 optimal weight: 5.9990 chunk 302 optimal weight: 2.9990 chunk 200 optimal weight: 0.9980 chunk 358 optimal weight: 6.9990 chunk 224 optimal weight: 0.9980 chunk 218 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 36 ASN ** d 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 148 ASN h 4 GLN ** h 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 59 ASN ** l 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 8 ASN ** s 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 52 HIS t 13 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 1.879 54722 Z= 0.642 Angle : 0.804 71.169 81405 Z= 0.371 Chirality : 0.037 0.428 10331 Planarity : 0.005 0.110 4691 Dihedral : 26.028 179.539 26297 Min Nonbonded Distance : 1.721 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.09 % Favored : 88.73 % Rotamer: Outliers : 4.77 % Allowed : 26.49 % Favored : 68.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -3.06 (0.17), residues: 2263 helix: -1.13 (0.20), residues: 663 sheet: -1.67 (0.30), residues: 280 loop : -2.72 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP d 170 HIS 0.019 0.001 HIS l 77 PHE 0.023 0.002 PHE h 66 TYR 0.021 0.001 TYR b 213 ARG 0.008 0.000 ARG d 104 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 292 time to evaluate : 3.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET t 27 " (corrupted residue). Skipping it. REVERT: b 74 ARG cc_start: 0.6169 (OUTLIER) cc_final: 0.5585 (tpt-90) REVERT: b 219 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.7011 (pp20) REVERT: e 21 ARG cc_start: 0.8279 (tmm-80) cc_final: 0.8068 (ttp80) REVERT: e 143 LYS cc_start: 0.8171 (mtmt) cc_final: 0.7892 (mtmm) REVERT: g 125 LEU cc_start: 0.3729 (OUTLIER) cc_final: 0.3255 (mt) REVERT: g 138 ARG cc_start: 0.3024 (tmt170) cc_final: 0.1176 (mmm160) REVERT: h 38 LYS cc_start: 0.8042 (tttt) cc_final: 0.7618 (tmmt) REVERT: h 74 GLU cc_start: 0.6164 (pp20) cc_final: 0.5850 (pp20) REVERT: k 20 ILE cc_start: 0.7541 (OUTLIER) cc_final: 0.7206 (mp) REVERT: k 127 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.7905 (mtm-85) REVERT: l 14 ARG cc_start: 0.7223 (OUTLIER) cc_final: 0.6674 (tpp-160) REVERT: l 77 HIS cc_start: 0.6987 (OUTLIER) cc_final: 0.6035 (t-170) REVERT: l 94 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7340 (mtt180) REVERT: n 89 MET cc_start: 0.5244 (mmt) cc_final: 0.4420 (mmt) REVERT: o 40 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8107 (mp10) REVERT: o 84 ARG cc_start: 0.7341 (OUTLIER) cc_final: 0.6783 (mtt180) REVERT: p 28 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.8175 (ptt90) REVERT: q 31 ARG cc_start: 0.7826 (mtp85) cc_final: 0.7612 (mtp85) REVERT: q 55 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.7243 (pp30) REVERT: s 39 MET cc_start: 0.1950 (mmm) cc_final: 0.1132 (tpp) outliers start: 89 outliers final: 44 residues processed: 351 average time/residue: 1.7760 time to fit residues: 773.3347 Evaluate side-chains 337 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 281 time to evaluate : 2.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 5 ASN Chi-restraints excluded: chain b residue 31 ILE Chi-restraints excluded: chain b residue 74 ARG Chi-restraints excluded: chain b residue 83 GLU Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain b residue 113 ARG Chi-restraints excluded: chain b residue 139 ARG Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 181 ILE Chi-restraints excluded: chain b residue 219 GLU Chi-restraints excluded: chain d residue 37 VAL Chi-restraints excluded: chain d residue 73 ARG Chi-restraints excluded: chain d residue 110 THR Chi-restraints excluded: chain d residue 168 VAL Chi-restraints excluded: chain d residue 173 VAL Chi-restraints excluded: chain d residue 189 SER Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 121 VAL Chi-restraints excluded: chain e residue 131 SER Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 69 LYS Chi-restraints excluded: chain f residue 78 PHE Chi-restraints excluded: chain g residue 38 VAL Chi-restraints excluded: chain g residue 61 THR Chi-restraints excluded: chain g residue 77 SER Chi-restraints excluded: chain g residue 125 LEU Chi-restraints excluded: chain g residue 136 LYS Chi-restraints excluded: chain h residue 10 MET Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 55 VAL Chi-restraints excluded: chain h residue 59 LEU Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 107 ASN Chi-restraints excluded: chain h residue 121 VAL Chi-restraints excluded: chain h residue 129 VAL Chi-restraints excluded: chain i residue 111 VAL Chi-restraints excluded: chain k residue 20 ILE Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 50 SER Chi-restraints excluded: chain k residue 83 ASP Chi-restraints excluded: chain k residue 100 LEU Chi-restraints excluded: chain k residue 127 ARG Chi-restraints excluded: chain l residue 14 ARG Chi-restraints excluded: chain l residue 25 GLN Chi-restraints excluded: chain l residue 77 HIS Chi-restraints excluded: chain l residue 94 ARG Chi-restraints excluded: chain o residue 40 GLN Chi-restraints excluded: chain o residue 73 LYS Chi-restraints excluded: chain o residue 84 ARG Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 28 ARG Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 55 GLN Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 52 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 221 optimal weight: 1.9990 chunk 143 optimal weight: 6.9990 chunk 214 optimal weight: 0.1980 chunk 108 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 227 optimal weight: 0.8980 chunk 244 optimal weight: 2.9990 chunk 177 optimal weight: 0.3980 chunk 33 optimal weight: 3.9990 chunk 281 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 36 ASN d 59 GLN ** e 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 148 ASN l 59 ASN ** l 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 77 HIS ** s 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 1.880 54722 Z= 0.643 Angle : 0.793 71.033 81405 Z= 0.365 Chirality : 0.036 0.413 10331 Planarity : 0.005 0.106 4691 Dihedral : 25.914 179.700 26293 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.93 % Favored : 87.89 % Rotamer: Outliers : 4.40 % Allowed : 27.13 % Favored : 68.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.17), residues: 2263 helix: -0.96 (0.20), residues: 661 sheet: -1.53 (0.32), residues: 264 loop : -2.63 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP d 170 HIS 0.023 0.001 HIS s 52 PHE 0.025 0.001 PHE h 66 TYR 0.021 0.001 TYR b 213 ARG 0.013 0.001 ARG b 146 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 297 time to evaluate : 3.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET t 27 " (corrupted residue). Skipping it. REVERT: b 26 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.7888 (mtpt) REVERT: b 219 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.6957 (pp20) REVERT: c 134 MET cc_start: 0.4397 (tpt) cc_final: 0.4197 (tpt) REVERT: d 69 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.6977 (tm-30) REVERT: d 70 ARG cc_start: 0.7246 (tpp80) cc_final: 0.6980 (tpp80) REVERT: e 21 ARG cc_start: 0.8275 (tmm-80) cc_final: 0.7983 (ttp80) REVERT: e 143 LYS cc_start: 0.8167 (mtmt) cc_final: 0.7838 (mtmm) REVERT: g 125 LEU cc_start: 0.3612 (OUTLIER) cc_final: 0.3175 (mt) REVERT: g 138 ARG cc_start: 0.2998 (tmt170) cc_final: 0.1153 (mmm160) REVERT: h 38 LYS cc_start: 0.8096 (tttt) cc_final: 0.7847 (tmmt) REVERT: h 74 GLU cc_start: 0.6127 (pp20) cc_final: 0.5885 (pp20) REVERT: i 33 ARG cc_start: 0.1441 (OUTLIER) cc_final: 0.0989 (pmt170) REVERT: i 85 ARG cc_start: 0.2842 (ttm-80) cc_final: 0.2512 (tmm160) REVERT: k 20 ILE cc_start: 0.7492 (OUTLIER) cc_final: 0.7248 (mp) REVERT: l 94 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7349 (mtt180) REVERT: n 89 MET cc_start: 0.5208 (mmt) cc_final: 0.4374 (mmt) REVERT: o 40 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.7595 (mp10) REVERT: o 84 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.6801 (mtm180) REVERT: q 31 ARG cc_start: 0.7797 (mtp85) cc_final: 0.7449 (mtp180) REVERT: s 39 MET cc_start: 0.1842 (mmm) cc_final: 0.1573 (tpt) REVERT: s 66 MET cc_start: -0.0628 (mpp) cc_final: -0.0848 (mpp) outliers start: 82 outliers final: 46 residues processed: 354 average time/residue: 1.7519 time to fit residues: 773.0363 Evaluate side-chains 339 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 284 time to evaluate : 3.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 5 ASN Chi-restraints excluded: chain b residue 26 LYS Chi-restraints excluded: chain b residue 83 GLU Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain b residue 113 ARG Chi-restraints excluded: chain b residue 139 ARG Chi-restraints excluded: chain b residue 181 ILE Chi-restraints excluded: chain b residue 219 GLU Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 69 GLU Chi-restraints excluded: chain d residue 73 ARG Chi-restraints excluded: chain d residue 110 THR Chi-restraints excluded: chain d residue 168 VAL Chi-restraints excluded: chain d residue 173 VAL Chi-restraints excluded: chain d residue 189 SER Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 121 VAL Chi-restraints excluded: chain e residue 131 SER Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 69 LYS Chi-restraints excluded: chain f residue 78 PHE Chi-restraints excluded: chain g residue 5 ARG Chi-restraints excluded: chain g residue 38 VAL Chi-restraints excluded: chain g residue 61 THR Chi-restraints excluded: chain g residue 77 SER Chi-restraints excluded: chain g residue 123 GLU Chi-restraints excluded: chain g residue 125 LEU Chi-restraints excluded: chain g residue 136 LYS Chi-restraints excluded: chain g residue 154 TYR Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 55 VAL Chi-restraints excluded: chain h residue 59 LEU Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 107 ASN Chi-restraints excluded: chain h residue 121 VAL Chi-restraints excluded: chain h residue 129 VAL Chi-restraints excluded: chain i residue 33 ARG Chi-restraints excluded: chain i residue 111 VAL Chi-restraints excluded: chain k residue 20 ILE Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 50 SER Chi-restraints excluded: chain k residue 100 LEU Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 77 HIS Chi-restraints excluded: chain l residue 94 ARG Chi-restraints excluded: chain l residue 102 LEU Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 40 GLN Chi-restraints excluded: chain o residue 73 LYS Chi-restraints excluded: chain o residue 84 ARG Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain t residue 6 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 326 optimal weight: 1.9990 chunk 343 optimal weight: 1.9990 chunk 313 optimal weight: 5.9990 chunk 334 optimal weight: 0.6980 chunk 201 optimal weight: 9.9990 chunk 145 optimal weight: 5.9990 chunk 262 optimal weight: 0.5980 chunk 102 optimal weight: 40.0000 chunk 301 optimal weight: 1.9990 chunk 316 optimal weight: 5.9990 chunk 332 optimal weight: 0.5980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 36 ASN b 94 HIS b 177 ASN d 157 GLN ** e 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 148 ASN l 59 ASN ** l 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 77 HIS ** s 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 1.879 54722 Z= 0.654 Angle : 0.811 71.075 81405 Z= 0.373 Chirality : 0.037 0.427 10331 Planarity : 0.005 0.105 4691 Dihedral : 25.880 179.271 26293 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.40 % Favored : 88.42 % Rotamer: Outliers : 4.08 % Allowed : 27.83 % Favored : 68.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.17), residues: 2263 helix: -0.87 (0.20), residues: 661 sheet: -1.42 (0.31), residues: 282 loop : -2.63 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP d 170 HIS 0.023 0.001 HIS l 77 PHE 0.027 0.002 PHE h 66 TYR 0.020 0.001 TYR b 213 ARG 0.013 0.001 ARG k 69 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 280 time to evaluate : 2.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET t 27 " (corrupted residue). Skipping it. REVERT: b 26 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.7877 (mtpt) REVERT: b 74 ARG cc_start: 0.6176 (OUTLIER) cc_final: 0.5685 (tpt170) REVERT: c 95 MET cc_start: 0.2371 (ttp) cc_final: 0.2096 (ttt) REVERT: d 69 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.6969 (tm-30) REVERT: d 70 ARG cc_start: 0.7272 (tpp80) cc_final: 0.7022 (tpp80) REVERT: e 55 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.7080 (ttm110) REVERT: e 143 LYS cc_start: 0.8172 (mtmt) cc_final: 0.7878 (mtmm) REVERT: g 125 LEU cc_start: 0.3621 (OUTLIER) cc_final: 0.3178 (mt) REVERT: g 138 ARG cc_start: 0.3133 (tmt170) cc_final: 0.1213 (mmm160) REVERT: h 38 LYS cc_start: 0.8153 (tttt) cc_final: 0.7917 (tmmt) REVERT: h 74 GLU cc_start: 0.6410 (pp20) cc_final: 0.6193 (pp20) REVERT: i 33 ARG cc_start: 0.1633 (OUTLIER) cc_final: 0.1183 (pmt170) REVERT: i 85 ARG cc_start: 0.2980 (ttm-80) cc_final: 0.2583 (tmm160) REVERT: k 20 ILE cc_start: 0.7580 (OUTLIER) cc_final: 0.7272 (mp) REVERT: l 94 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7415 (mtt180) REVERT: n 89 MET cc_start: 0.5127 (mmt) cc_final: 0.4278 (mmt) REVERT: o 40 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.7580 (mp10) REVERT: o 84 ARG cc_start: 0.7456 (OUTLIER) cc_final: 0.6833 (mtt180) REVERT: q 31 ARG cc_start: 0.7787 (mtp85) cc_final: 0.7530 (mtp85) REVERT: s 39 MET cc_start: 0.1707 (mmm) cc_final: 0.1420 (tpt) outliers start: 76 outliers final: 48 residues processed: 332 average time/residue: 1.7299 time to fit residues: 714.2087 Evaluate side-chains 332 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 274 time to evaluate : 2.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 26 LYS Chi-restraints excluded: chain b residue 74 ARG Chi-restraints excluded: chain b residue 83 GLU Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain b residue 113 ARG Chi-restraints excluded: chain b residue 139 ARG Chi-restraints excluded: chain b residue 181 ILE Chi-restraints excluded: chain b residue 192 SER Chi-restraints excluded: chain b residue 219 GLU Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 37 VAL Chi-restraints excluded: chain d residue 69 GLU Chi-restraints excluded: chain d residue 73 ARG Chi-restraints excluded: chain d residue 110 THR Chi-restraints excluded: chain d residue 168 VAL Chi-restraints excluded: chain d residue 173 VAL Chi-restraints excluded: chain d residue 189 SER Chi-restraints excluded: chain e residue 55 ARG Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 121 VAL Chi-restraints excluded: chain e residue 131 SER Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 69 LYS Chi-restraints excluded: chain f residue 78 PHE Chi-restraints excluded: chain g residue 38 VAL Chi-restraints excluded: chain g residue 61 THR Chi-restraints excluded: chain g residue 77 SER Chi-restraints excluded: chain g residue 123 GLU Chi-restraints excluded: chain g residue 125 LEU Chi-restraints excluded: chain g residue 148 ASN Chi-restraints excluded: chain g residue 154 TYR Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 55 VAL Chi-restraints excluded: chain h residue 59 LEU Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 107 ASN Chi-restraints excluded: chain h residue 121 VAL Chi-restraints excluded: chain h residue 129 VAL Chi-restraints excluded: chain i residue 33 ARG Chi-restraints excluded: chain i residue 111 VAL Chi-restraints excluded: chain k residue 20 ILE Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 50 SER Chi-restraints excluded: chain k residue 100 LEU Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 94 ARG Chi-restraints excluded: chain l residue 102 LEU Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 40 GLN Chi-restraints excluded: chain o residue 73 LYS Chi-restraints excluded: chain o residue 84 ARG Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain r residue 21 ILE Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 44 MET Chi-restraints excluded: chain t residue 6 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 219 optimal weight: 1.9990 chunk 353 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 167 optimal weight: 2.9990 chunk 245 optimal weight: 20.0000 chunk 370 optimal weight: 0.9990 chunk 341 optimal weight: 0.9980 chunk 295 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 227 optimal weight: 0.5980 chunk 180 optimal weight: 40.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 36 ASN ** e 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 97 ASN g 148 ASN l 59 ASN ** l 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 1.881 54722 Z= 0.650 Angle : 0.803 71.115 81405 Z= 0.367 Chirality : 0.037 0.406 10331 Planarity : 0.005 0.132 4691 Dihedral : 25.837 179.226 26287 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.67 % Favored : 88.16 % Rotamer: Outliers : 3.43 % Allowed : 28.85 % Favored : 67.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.17), residues: 2263 helix: -0.83 (0.20), residues: 664 sheet: -1.44 (0.30), residues: 298 loop : -2.60 (0.16), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP d 170 HIS 0.006 0.001 HIS t 20 PHE 0.022 0.002 PHE h 49 TYR 0.019 0.001 TYR b 213 ARG 0.012 0.001 ARG k 69 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4526 Ramachandran restraints generated. 2263 Oldfield, 0 Emsley, 2263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 280 time to evaluate : 3.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET t 27 " (corrupted residue). Skipping it. REVERT: b 26 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.7908 (mtpt) REVERT: b 64 LYS cc_start: 0.6400 (tppt) cc_final: 0.5545 (tttt) REVERT: b 74 ARG cc_start: 0.6183 (OUTLIER) cc_final: 0.5692 (tpt170) REVERT: c 95 MET cc_start: 0.2338 (ttp) cc_final: 0.2016 (ttt) REVERT: d 69 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.6990 (tm-30) REVERT: d 70 ARG cc_start: 0.7243 (tpp80) cc_final: 0.7026 (tpp80) REVERT: e 55 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.7055 (ttm110) REVERT: e 143 LYS cc_start: 0.8172 (mtmt) cc_final: 0.7880 (mtmm) REVERT: g 5 ARG cc_start: 0.3237 (OUTLIER) cc_final: 0.2074 (ptp-170) REVERT: g 31 MET cc_start: 0.2336 (ppp) cc_final: 0.2095 (pmm) REVERT: g 125 LEU cc_start: 0.3605 (OUTLIER) cc_final: 0.3164 (mt) REVERT: g 138 ARG cc_start: 0.3021 (tmt170) cc_final: 0.1165 (mmm160) REVERT: h 38 LYS cc_start: 0.8128 (tttt) cc_final: 0.7904 (tmmt) REVERT: h 74 GLU cc_start: 0.6103 (pp20) cc_final: 0.5811 (pp20) REVERT: k 20 ILE cc_start: 0.7575 (OUTLIER) cc_final: 0.7264 (mp) REVERT: l 94 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7415 (mtt180) REVERT: n 89 MET cc_start: 0.5056 (mmt) cc_final: 0.4262 (mmt) REVERT: o 40 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.7565 (mp10) REVERT: o 84 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.6818 (mtt180) REVERT: q 31 ARG cc_start: 0.7780 (mtp85) cc_final: 0.7534 (mtp85) REVERT: s 39 MET cc_start: 0.1580 (mmm) cc_final: 0.1299 (tpt) outliers start: 64 outliers final: 46 residues processed: 323 average time/residue: 1.8672 time to fit residues: 743.0009 Evaluate side-chains 328 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 272 time to evaluate : 3.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 26 LYS Chi-restraints excluded: chain b residue 74 ARG Chi-restraints excluded: chain b residue 83 GLU Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain b residue 113 ARG Chi-restraints excluded: chain b residue 139 ARG Chi-restraints excluded: chain b residue 181 ILE Chi-restraints excluded: chain b residue 192 SER Chi-restraints excluded: chain b residue 219 GLU Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 37 VAL Chi-restraints excluded: chain d residue 69 GLU Chi-restraints excluded: chain d residue 73 ARG Chi-restraints excluded: chain d residue 110 THR Chi-restraints excluded: chain d residue 168 VAL Chi-restraints excluded: chain d residue 173 VAL Chi-restraints excluded: chain d residue 189 SER Chi-restraints excluded: chain e residue 55 ARG Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain e residue 104 THR Chi-restraints excluded: chain e residue 121 VAL Chi-restraints excluded: chain e residue 131 SER Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 69 LYS Chi-restraints excluded: chain f residue 78 PHE Chi-restraints excluded: chain g residue 5 ARG Chi-restraints excluded: chain g residue 38 VAL Chi-restraints excluded: chain g residue 61 THR Chi-restraints excluded: chain g residue 77 SER Chi-restraints excluded: chain g residue 125 LEU Chi-restraints excluded: chain g residue 154 TYR Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 55 VAL Chi-restraints excluded: chain h residue 59 LEU Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 107 ASN Chi-restraints excluded: chain h residue 121 VAL Chi-restraints excluded: chain h residue 129 VAL Chi-restraints excluded: chain i residue 33 ARG Chi-restraints excluded: chain i residue 111 VAL Chi-restraints excluded: chain k residue 20 ILE Chi-restraints excluded: chain k residue 26 SER Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 50 SER Chi-restraints excluded: chain k residue 100 LEU Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 94 ARG Chi-restraints excluded: chain l residue 102 LEU Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 40 GLN Chi-restraints excluded: chain o residue 41 ASP Chi-restraints excluded: chain o residue 73 LYS Chi-restraints excluded: chain o residue 84 ARG Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain t residue 6 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 234 optimal weight: 2.9990 chunk 314 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 272 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 295 optimal weight: 0.1980 chunk 123 optimal weight: 20.0000 chunk 303 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 36 ASN b 177 ASN d 41 HIS ** e 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 148 ASN ** k 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 59 ASN ** l 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 77 HIS ** s 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 13 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.214471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.185123 restraints weight = 63359.581| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 0.48 r_work: 0.3771 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3589 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.884 54722 Z= 0.709 Angle : 0.901 71.072 81405 Z= 0.420 Chirality : 0.043 0.477 10331 Planarity : 0.006 0.142 4691 Dihedral : 25.959 179.865 26287 Min Nonbonded Distance : 1.717 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.22 % Allowed : 12.95 % Favored : 86.83 % Rotamer: Outliers : 4.29 % Allowed : 28.15 % Favored : 67.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.17), residues: 2263 helix: -1.11 (0.20), residues: 677 sheet: -1.52 (0.29), residues: 307 loop : -2.68 (0.16), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP b 23 HIS 0.009 0.001 HIS t 20 PHE 0.029 0.002 PHE h 66 TYR 0.018 0.002 TYR b 213 ARG 0.012 0.001 ARG b 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14108.99 seconds wall clock time: 254 minutes 33.39 seconds (15273.39 seconds total)