Starting phenix.real_space_refine on Thu Feb 22 02:48:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzp_8937/02_2024/6dzp_8937.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzp_8937/02_2024/6dzp_8937.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzp_8937/02_2024/6dzp_8937.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzp_8937/02_2024/6dzp_8937.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzp_8937/02_2024/6dzp_8937.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzp_8937/02_2024/6dzp_8937.pdb" } resolution = 3.42 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= 0.007 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 3237 5.49 5 S 49 5.16 5 C 48776 2.51 5 N 18331 2.21 5 O 27704 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 3": "NH1" <-> "NH2" Residue "T TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 2": "NH1" <-> "NH2" Residue "c ARG 6": "NH1" <-> "NH2" Residue "c ARG 12": "NH1" <-> "NH2" Residue "c ARG 24": "NH1" <-> "NH2" Residue "c ARG 37": "NH1" <-> "NH2" Residue "c ARG 44": "NH1" <-> "NH2" Residue "c ARG 45": "NH1" <-> "NH2" Residue "d ARG 17": "NH1" <-> "NH2" Residue "y ARG 26": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 98097 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 66981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3119, 66981 Classifications: {'RNA': 3119} Modifications used: {'rna2p_pur': 301, 'rna2p_pyr': 150, 'rna3p_pur': 1482, 'rna3p_pyr': 1186} Link IDs: {'rna2p': 451, 'rna3p': 2667} Chain: "B" Number of atoms: 2522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2522 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 8, 'rna3p_pur': 57, 'rna3p_pyr': 46} Link IDs: {'rna2p': 15, 'rna3p': 102} Chain: "C" Number of atoms: 2110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2110 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 19, 'TRANS': 255} Chain: "D" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1587 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 205} Chain: "E" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1569 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1445 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain: "G" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1348 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 11, 'TRANS': 164} Chain: "H" Number of atoms: 1119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1119 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 3, 'TRANS': 147} Chain: "I" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 918 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain: "J" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 990 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 8, 'TRANS': 124} Chain: "K" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1130 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 10, 'TRANS': 135} Chain: "L" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "M" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1078 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain: "N" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1092 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 9, 'TRANS': 126} Chain: "O" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain: "P" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 956 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "Q" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 907 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "R" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 988 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "S" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 754 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "T" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 873 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 8, 'TRANS': 105} Chain: "U" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 756 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "V" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 732 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "W" Number of atoms: 1428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1428 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 9, 'TRANS': 182} Chain: "X" Number of atoms: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 586 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "Z" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 531 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "a" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 474 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "b" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 423 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "c" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 456 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 3, 'TRANS': 49} Chain: "d" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "e" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 502 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "f" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 299 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "g" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 494 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 8, 'TRANS': 55} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "y" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 617 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 4, 'TRANS': 72} Chain: "3" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 189 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Time building chain proxies: 39.66, per 1000 atoms: 0.40 Number of scatterers: 98097 At special positions: 0 Unit cell: (224.7, 208.65, 237.54, 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 49 16.00 P 3237 15.00 O 27704 8.00 N 18331 7.00 C 48776 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 41.97 Conformation dependent library (CDL) restraints added in 4.7 seconds 7298 Ramachandran restraints generated. 3649 Oldfield, 0 Emsley, 3649 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6734 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 0 sheets defined 32.3% alpha, 0.0% beta 915 base pairs and 1683 stacking pairs defined. Time for finding SS restraints: 35.92 Creating SS restraints... Processing helix chain 'C' and resid 132 through 137 removed outlier: 3.842A pdb=" N ILE C 136 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Proline residue: C 137 - end of helix No H-bonds generated for 'chain 'C' and resid 132 through 137' Processing helix chain 'C' and resid 208 through 216 removed outlier: 4.202A pdb=" N MET C 212 " --> pdb=" O LYS C 208 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS C 215 " --> pdb=" O ARG C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 227 removed outlier: 4.771A pdb=" N MET C 226 " --> pdb=" O ARG C 222 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ASN C 227 " --> pdb=" O GLY C 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 222 through 227' Processing helix chain 'C' and resid 262 through 269 removed outlier: 4.758A pdb=" N LYS C 266 " --> pdb=" O LYS C 262 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU C 267 " --> pdb=" O PRO C 263 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N VAL C 269 " --> pdb=" O ASP C 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 46 removed outlier: 3.726A pdb=" N GLY D 46 " --> pdb=" O THR D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 74 removed outlier: 4.009A pdb=" N ALA D 73 " --> pdb=" O GLN D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 95 removed outlier: 4.288A pdb=" N GLU D 94 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N TYR D 95 " --> pdb=" O ALA D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 130 Processing helix chain 'E' and resid 21 through 26 removed outlier: 4.391A pdb=" N PHE E 25 " --> pdb=" O PRO E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 47 removed outlier: 5.136A pdb=" N GLN E 47 " --> pdb=" O ALA E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 122 removed outlier: 3.912A pdb=" N ASN E 121 " --> pdb=" O ASP E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 149 removed outlier: 3.657A pdb=" N ALA E 141 " --> pdb=" O SER E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 170 removed outlier: 3.981A pdb=" N ALA E 166 " --> pdb=" O ASP E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 192 removed outlier: 4.268A pdb=" N VAL E 188 " --> pdb=" O ASN E 184 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA E 191 " --> pdb=" O ASP E 187 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ASP E 192 " --> pdb=" O VAL E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 210 removed outlier: 4.836A pdb=" N LYS E 210 " --> pdb=" O SER E 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 28 removed outlier: 3.647A pdb=" N ILE F 19 " --> pdb=" O TYR F 15 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ARG F 20 " --> pdb=" O ARG F 16 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLU F 21 " --> pdb=" O GLU F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 69 removed outlier: 7.806A pdb=" N ALA F 51 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ARG F 52 " --> pdb=" O GLY F 48 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA F 54 " --> pdb=" O ALA F 50 " (cutoff:3.500A) removed outlier: 9.080A pdb=" N LYS F 55 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N LEU F 56 " --> pdb=" O ARG F 52 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ILE F 57 " --> pdb=" O ASP F 53 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ASN F 58 " --> pdb=" O ALA F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 118 removed outlier: 3.557A pdb=" N ALA F 114 " --> pdb=" O LEU F 110 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N LEU F 115 " --> pdb=" O ILE F 111 " (cutoff:3.500A) Proline residue: F 116 - end of helix Processing helix chain 'F' and resid 169 through 181 Processing helix chain 'G' and resid 2 through 7 removed outlier: 4.369A pdb=" N GLN G 7 " --> pdb=" O ARG G 3 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 82 removed outlier: 4.421A pdb=" N GLY G 67 " --> pdb=" O ARG G 63 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU G 68 " --> pdb=" O SER G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 153 removed outlier: 3.724A pdb=" N LEU G 152 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ARG G 153 " --> pdb=" O ILE G 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 29 Processing helix chain 'H' and resid 42 through 60 removed outlier: 4.454A pdb=" N ARG H 60 " --> pdb=" O SER H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 74 removed outlier: 3.940A pdb=" N ALA H 71 " --> pdb=" O GLU H 67 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N GLY H 74 " --> pdb=" O THR H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 108 removed outlier: 3.936A pdb=" N VAL H 100 " --> pdb=" O THR H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 118 removed outlier: 4.084A pdb=" N VAL H 117 " --> pdb=" O ASP H 113 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N GLN H 118 " --> pdb=" O LYS H 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 113 through 118' Processing helix chain 'I' and resid 2 through 21 removed outlier: 3.715A pdb=" N ALA I 19 " --> pdb=" O GLU I 15 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N THR I 21 " --> pdb=" O PHE I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 32 through 43 Processing helix chain 'I' and resid 53 through 65 removed outlier: 4.050A pdb=" N ARG I 59 " --> pdb=" O THR I 55 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N SER I 62 " --> pdb=" O LYS I 58 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N GLU I 63 " --> pdb=" O ARG I 59 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA I 64 " --> pdb=" O ALA I 60 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N GLY I 65 " --> pdb=" O ALA I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 101 removed outlier: 4.560A pdb=" N ALA I 89 " --> pdb=" O GLU I 85 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ALA I 90 " --> pdb=" O ALA I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 126 Processing helix chain 'J' and resid 24 through 32 Proline residue: J 28 - end of helix removed outlier: 4.644A pdb=" N GLN J 32 " --> pdb=" O PRO J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 52 removed outlier: 4.480A pdb=" N PHE J 40 " --> pdb=" O ASN J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 85 Processing helix chain 'J' and resid 103 through 118 Processing helix chain 'J' and resid 122 through 138 Processing helix chain 'K' and resid 24 through 38 Processing helix chain 'K' and resid 67 through 72 removed outlier: 3.769A pdb=" N LYS K 72 " --> pdb=" O LYS K 68 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 110 removed outlier: 3.905A pdb=" N LEU K 92 " --> pdb=" O THR K 88 " (cutoff:3.500A) Proline residue: K 97 - end of helix removed outlier: 4.740A pdb=" N VAL K 100 " --> pdb=" O HIS K 96 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL K 101 " --> pdb=" O PRO K 97 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET K 108 " --> pdb=" O ALA K 104 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU K 109 " --> pdb=" O ILE K 105 " (cutoff:3.500A) Proline residue: K 110 - end of helix Processing helix chain 'K' and resid 112 through 123 removed outlier: 3.792A pdb=" N LYS K 120 " --> pdb=" O ARG K 116 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LYS K 121 " --> pdb=" O GLN K 117 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU K 122 " --> pdb=" O ILE K 118 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LYS K 123 " --> pdb=" O GLN K 119 " (cutoff:3.500A) Processing helix chain 'L' and resid 103 through 118 removed outlier: 4.989A pdb=" N ARG L 107 " --> pdb=" O GLY L 103 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU L 108 " --> pdb=" O ARG L 104 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N PHE L 111 " --> pdb=" O ARG L 107 " (cutoff:3.500A) removed outlier: 8.626A pdb=" N MET L 112 " --> pdb=" O GLU L 108 " (cutoff:3.500A) removed outlier: 9.506A pdb=" N LYS L 113 " --> pdb=" O LYS L 109 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ILE L 114 " --> pdb=" O LYS L 110 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL L 115 " --> pdb=" O PHE L 111 " (cutoff:3.500A) Processing helix chain 'M' and resid 39 through 44 removed outlier: 3.540A pdb=" N LYS M 44 " --> pdb=" O THR M 40 " (cutoff:3.500A) Processing helix chain 'M' and resid 56 through 61 Processing helix chain 'M' and resid 79 through 87 removed outlier: 3.577A pdb=" N ILE M 83 " --> pdb=" O ASN M 79 " (cutoff:3.500A) Processing helix chain 'M' and resid 94 through 102 removed outlier: 3.620A pdb=" N LYS M 101 " --> pdb=" O GLU M 97 " (cutoff:3.500A) Processing helix chain 'M' and resid 130 through 141 Processing helix chain 'N' and resid 43 through 59 removed outlier: 3.787A pdb=" N ILE N 47 " --> pdb=" O THR N 43 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS N 57 " --> pdb=" O ALA N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 126 removed outlier: 3.914A pdb=" N LYS N 124 " --> pdb=" O ARG N 120 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU N 125 " --> pdb=" O ALA N 121 " (cutoff:3.500A) Proline residue: N 126 - end of helix Processing helix chain 'O' and resid 13 through 32 Processing helix chain 'O' and resid 38 through 89 Proline residue: O 46 - end of helix removed outlier: 3.832A pdb=" N GLY O 58 " --> pdb=" O HIS O 54 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N ALA O 59 " --> pdb=" O ALA O 55 " (cutoff:3.500A) removed outlier: 9.771A pdb=" N LEU O 60 " --> pdb=" O LYS O 56 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N HIS O 61 " --> pdb=" O LYS O 57 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ASN O 62 " --> pdb=" O GLY O 58 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N LYS O 69 " --> pdb=" O GLU O 65 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE O 70 " --> pdb=" O VAL O 66 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ARG O 71 " --> pdb=" O MET O 67 " (cutoff:3.500A) removed outlier: 9.117A pdb=" N ASP O 72 " --> pdb=" O LYS O 68 " (cutoff:3.500A) removed outlier: 9.541A pdb=" N LYS O 73 " --> pdb=" O LYS O 69 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ASP O 74 " --> pdb=" O ILE O 70 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N VAL O 75 " --> pdb=" O ARG O 71 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N GLY O 84 " --> pdb=" O PHE O 80 " (cutoff:3.500A) Proline residue: O 85 - end of helix removed outlier: 3.597A pdb=" N ALA O 88 " --> pdb=" O GLY O 84 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ASP O 89 " --> pdb=" O PRO O 85 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 30 removed outlier: 4.496A pdb=" N LYS P 27 " --> pdb=" O ALA P 23 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N LYS P 28 " --> pdb=" O ARG P 24 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL P 29 " --> pdb=" O LEU P 25 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ALA P 30 " --> pdb=" O ARG P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 67 through 74 removed outlier: 4.732A pdb=" N ILE P 73 " --> pdb=" O ASP P 69 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ASP P 74 " --> pdb=" O VAL P 70 " (cutoff:3.500A) Processing helix chain 'P' and resid 76 through 96 Processing helix chain 'P' and resid 111 through 124 Processing helix chain 'Q' and resid 4 through 12 removed outlier: 4.977A pdb=" N ALA Q 10 " --> pdb=" O PHE Q 6 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N SER Q 11 " --> pdb=" O VAL Q 7 " (cutoff:3.500A) Processing helix chain 'Q' and resid 96 through 109 removed outlier: 5.202A pdb=" N ARG Q 100 " --> pdb=" O LEU Q 96 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N GLU Q 101 " --> pdb=" O TYR Q 97 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LEU Q 102 " --> pdb=" O TYR Q 98 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ARG Q 103 " --> pdb=" O LEU Q 99 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N GLY Q 104 " --> pdb=" O ARG Q 100 " (cutoff:3.500A) removed outlier: 10.168A pdb=" N LYS Q 105 " --> pdb=" O GLU Q 101 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LYS Q 106 " --> pdb=" O LEU Q 102 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA Q 107 " --> pdb=" O ARG Q 103 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LYS Q 108 " --> pdb=" O GLY Q 104 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE Q 109 " --> pdb=" O LYS Q 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 96 through 109' Processing helix chain 'R' and resid 8 through 22 removed outlier: 5.112A pdb=" N LYS R 13 " --> pdb=" O ASN R 9 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LYS R 22 " --> pdb=" O LEU R 18 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 31 removed outlier: 4.062A pdb=" N ARG R 30 " --> pdb=" O GLY R 26 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU R 31 " --> pdb=" O GLN R 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 26 through 31' Processing helix chain 'R' and resid 36 through 72 removed outlier: 4.844A pdb=" N LYS R 54 " --> pdb=" O ARG R 50 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY R 55 " --> pdb=" O ARG R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 87 Processing helix chain 'R' and resid 91 through 117 Proline residue: R 103 - end of helix removed outlier: 3.673A pdb=" N PHE R 106 " --> pdb=" O ASP R 102 " (cutoff:3.500A) Processing helix chain 'S' and resid 51 through 59 removed outlier: 4.876A pdb=" N ALA S 59 " --> pdb=" O LEU S 55 " (cutoff:3.500A) Processing helix chain 'T' and resid 20 through 32 removed outlier: 4.316A pdb=" N VAL T 27 " --> pdb=" O LYS T 23 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N LEU T 30 " --> pdb=" O ARG T 26 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL T 31 " --> pdb=" O VAL T 27 " (cutoff:3.500A) Processing helix chain 'T' and resid 35 through 46 Processing helix chain 'T' and resid 50 through 68 removed outlier: 4.066A pdb=" N VAL T 54 " --> pdb=" O ALA T 50 " (cutoff:3.500A) Processing helix chain 'U' and resid 6 through 12 removed outlier: 4.682A pdb=" N ILE U 10 " --> pdb=" O ASP U 6 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE U 11 " --> pdb=" O PRO U 7 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LEU U 12 " --> pdb=" O ARG U 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 6 through 12' Processing helix chain 'U' and resid 17 through 27 removed outlier: 3.963A pdb=" N ASP U 26 " --> pdb=" O GLY U 22 " (cutoff:3.500A) Processing helix chain 'U' and resid 38 through 51 removed outlier: 4.101A pdb=" N ASP U 51 " --> pdb=" O GLU U 47 " (cutoff:3.500A) Processing helix chain 'W' and resid 20 through 31 Processing helix chain 'W' and resid 50 through 62 Processing helix chain 'W' and resid 186 through 193 removed outlier: 4.258A pdb=" N GLU W 191 " --> pdb=" O ALA W 187 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU W 192 " --> pdb=" O GLU W 188 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU W 193 " --> pdb=" O ALA W 189 " (cutoff:3.500A) Processing helix chain 'Z' and resid 6 through 39 removed outlier: 3.708A pdb=" N GLU Z 12 " --> pdb=" O GLY Z 8 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU Z 13 " --> pdb=" O GLU Z 9 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N THR Z 14 " --> pdb=" O LEU Z 10 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ASP Z 15 " --> pdb=" O ARG Z 11 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N ASP Z 16 " --> pdb=" O GLU Z 12 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLU Z 17 " --> pdb=" O LEU Z 13 " (cutoff:3.500A) Processing helix chain 'Z' and resid 43 through 67 removed outlier: 4.955A pdb=" N LEU Z 47 " --> pdb=" O ASN Z 43 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ARG Z 48 " --> pdb=" O ASN Z 44 " (cutoff:3.500A) Processing helix chain 'a' and resid 16 through 27 Processing helix chain 'a' and resid 40 through 51 Processing helix chain 'b' and resid 9 through 21 removed outlier: 3.908A pdb=" N GLN b 19 " --> pdb=" O SER b 15 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TRP b 20 " --> pdb=" O ARG b 16 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LYS b 21 " --> pdb=" O ARG b 17 " (cutoff:3.500A) Processing helix chain 'b' and resid 40 through 50 removed outlier: 3.999A pdb=" N LEU b 44 " --> pdb=" O PRO b 40 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N LYS b 45 " --> pdb=" O ARG b 41 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ALA b 46 " --> pdb=" O ARG b 42 " (cutoff:3.500A) Processing helix chain 'd' and resid 11 through 28 removed outlier: 4.033A pdb=" N ARG d 15 " --> pdb=" O ASN d 11 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N PHE d 21 " --> pdb=" O ARG d 17 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ARG d 22 " --> pdb=" O VAL d 18 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU d 23 " --> pdb=" O HIS d 19 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N THR d 27 " --> pdb=" O LEU d 23 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ARG d 28 " --> pdb=" O ARG d 24 " (cutoff:3.500A) Processing helix chain 'e' and resid 7 through 14 Processing helix chain 'e' and resid 32 through 46 removed outlier: 4.727A pdb=" N LYS e 36 " --> pdb=" O LEU e 32 " (cutoff:3.500A) Proline residue: e 37 - end of helix removed outlier: 6.168A pdb=" N ARG e 40 " --> pdb=" O LYS e 36 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU e 44 " --> pdb=" O ARG e 40 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASP e 45 " --> pdb=" O THR e 41 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N GLY e 46 " --> pdb=" O ARG e 42 " (cutoff:3.500A) Processing helix chain 'e' and resid 51 through 64 removed outlier: 3.769A pdb=" N ASN e 55 " --> pdb=" O SER e 51 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N SER e 56 " --> pdb=" O ALA e 52 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ARG e 57 " --> pdb=" O ALA e 53 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY e 64 " --> pdb=" O LYS e 60 " (cutoff:3.500A) Processing helix chain 'g' and resid 54 through 59 Proline residue: g 59 - end of helix Processing helix chain 'y' and resid 51 through 74 removed outlier: 7.861A pdb=" N ILE y 63 " --> pdb=" O ASP y 59 " (cutoff:3.500A) removed outlier: 10.617A pdb=" N GLU y 64 " --> pdb=" O ARG y 60 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ALA y 65 " --> pdb=" O ASP y 61 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL y 66 " --> pdb=" O GLY y 62 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG y 73 " --> pdb=" O ARG y 69 " (cutoff:3.500A) Processing helix chain '3' and resid 2 through 14 removed outlier: 4.668A pdb=" N HIS 3 13 " --> pdb=" O ARG 3 9 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N SER 3 14 " --> pdb=" O ASP 3 10 " (cutoff:3.500A) 668 hydrogen bonds defined for protein. 2004 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2334 hydrogen bonds 3934 hydrogen bond angles 0 basepair planarities 915 basepair parallelities 1683 stacking parallelities Total time for adding SS restraints: 154.68 Time building geometry restraints manager: 44.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.39: 40545 1.39 - 1.58: 60326 1.58 - 1.78: 5891 1.78 - 1.97: 71 1.97 - 2.16: 1 Bond restraints: 106834 Sorted by residual: bond pdb=" C VAL V 47 " pdb=" N SER V 56 " ideal model delta sigma weight residual 1.332 2.163 -0.831 1.31e-02 5.83e+03 4.03e+03 bond pdb=" CA GLN Q 50 " pdb=" CB GLN Q 50 " ideal model delta sigma weight residual 1.527 1.349 0.178 1.75e-02 3.27e+03 1.03e+02 bond pdb=" CA ALA C 45 " pdb=" C ALA C 45 " ideal model delta sigma weight residual 1.523 1.445 0.078 1.41e-02 5.03e+03 3.07e+01 bond pdb=" C GLN d 9 " pdb=" N PRO d 10 " ideal model delta sigma weight residual 1.329 1.386 -0.057 1.25e-02 6.40e+03 2.05e+01 bond pdb=" C ARG c 6 " pdb=" N PRO c 7 " ideal model delta sigma weight residual 1.335 1.392 -0.057 1.30e-02 5.92e+03 1.93e+01 ... (remaining 106829 not shown) Histogram of bond angle deviations from ideal: 84.25 - 95.34: 2 95.34 - 106.43: 20227 106.43 - 117.53: 79711 117.53 - 128.62: 55449 128.62 - 139.71: 5086 Bond angle restraints: 160475 Sorted by residual: angle pdb=" CA VAL V 47 " pdb=" C VAL V 47 " pdb=" N SER V 56 " ideal model delta sigma weight residual 116.60 84.25 32.35 1.45e+00 4.76e-01 4.98e+02 angle pdb=" O VAL V 47 " pdb=" C VAL V 47 " pdb=" N SER V 56 " ideal model delta sigma weight residual 122.57 102.47 20.10 1.25e+00 6.40e-01 2.59e+02 angle pdb=" C ARG Q 93 " pdb=" N ALA Q 94 " pdb=" CA ALA Q 94 " ideal model delta sigma weight residual 122.46 138.16 -15.70 1.80e+00 3.09e-01 7.60e+01 angle pdb=" C VAL C 221 " pdb=" N ARG C 222 " pdb=" CA ARG C 222 " ideal model delta sigma weight residual 121.06 137.42 -16.36 1.88e+00 2.83e-01 7.57e+01 angle pdb=" C VAL V 47 " pdb=" N SER V 56 " pdb=" CA SER V 56 " ideal model delta sigma weight residual 122.08 135.07 -12.99 1.50e+00 4.44e-01 7.50e+01 ... (remaining 160470 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 60241 35.92 - 71.85: 7567 71.85 - 107.77: 855 107.77 - 143.70: 38 143.70 - 179.62: 28 Dihedral angle restraints: 68729 sinusoidal: 58240 harmonic: 10489 Sorted by residual: dihedral pdb=" CA VAL V 47 " pdb=" C VAL V 47 " pdb=" N SER V 56 " pdb=" CA SER V 56 " ideal model delta harmonic sigma weight residual 180.00 103.52 76.48 0 5.00e+00 4.00e-02 2.34e+02 dihedral pdb=" C5' U A 316 " pdb=" C4' U A 316 " pdb=" C3' U A 316 " pdb=" O3' U A 316 " ideal model delta sinusoidal sigma weight residual 147.00 77.13 69.87 1 8.00e+00 1.56e-02 9.84e+01 dihedral pdb=" C4' U A 316 " pdb=" C3' U A 316 " pdb=" C2' U A 316 " pdb=" C1' U A 316 " ideal model delta sinusoidal sigma weight residual -35.00 34.50 -69.50 1 8.00e+00 1.56e-02 9.75e+01 ... (remaining 68726 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.267: 20559 0.267 - 0.534: 30 0.534 - 0.801: 8 0.801 - 1.068: 2 1.068 - 1.335: 1 Chirality restraints: 20600 Sorted by residual: chirality pdb=" CB THR C 220 " pdb=" CA THR C 220 " pdb=" OG1 THR C 220 " pdb=" CG2 THR C 220 " both_signs ideal model delta sigma weight residual False 2.55 1.22 1.33 2.00e-01 2.50e+01 4.45e+01 chirality pdb=" C2' A A2510 " pdb=" C3' A A2510 " pdb=" O2' A A2510 " pdb=" C1' A A2510 " both_signs ideal model delta sigma weight residual False -2.52 -1.61 -0.91 2.00e-01 2.50e+01 2.08e+01 chirality pdb=" C4' A A2003 " pdb=" C5' A A2003 " pdb=" O4' A A2003 " pdb=" C3' A A2003 " both_signs ideal model delta sigma weight residual False -2.50 -1.67 -0.83 2.00e-01 2.50e+01 1.73e+01 ... (remaining 20597 not shown) Planarity restraints: 8340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL V 47 " -0.156 2.00e-02 2.50e+03 2.57e-01 6.61e+02 pdb=" C VAL V 47 " 0.430 2.00e-02 2.50e+03 pdb=" O VAL V 47 " -0.231 2.00e-02 2.50e+03 pdb=" N SER V 56 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A1747 " 0.059 2.00e-02 2.50e+03 3.14e-02 2.22e+01 pdb=" N1 C A1747 " -0.061 2.00e-02 2.50e+03 pdb=" C2 C A1747 " 0.021 2.00e-02 2.50e+03 pdb=" O2 C A1747 " -0.022 2.00e-02 2.50e+03 pdb=" N3 C A1747 " -0.001 2.00e-02 2.50e+03 pdb=" C4 C A1747 " 0.004 2.00e-02 2.50e+03 pdb=" N4 C A1747 " 0.023 2.00e-02 2.50e+03 pdb=" C5 C A1747 " -0.006 2.00e-02 2.50e+03 pdb=" C6 C A1747 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY y 10 " 0.067 5.00e-02 4.00e+02 1.03e-01 1.70e+01 pdb=" N PRO y 11 " -0.178 5.00e-02 4.00e+02 pdb=" CA PRO y 11 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO y 11 " 0.055 5.00e-02 4.00e+02 ... (remaining 8337 not shown) Histogram of nonbonded interaction distances: 1.03 - 1.80: 10 1.80 - 2.58: 1929 2.58 - 3.35: 111583 3.35 - 4.13: 296934 4.13 - 4.90: 455828 Nonbonded interactions: 866284 Sorted by model distance: nonbonded pdb=" OP1 G A1379 " pdb=" NH2 ARG b 16 " model vdw 1.028 2.520 nonbonded pdb=" NZ LYS H 57 " pdb=" NH2 ARG H 60 " model vdw 1.281 3.200 nonbonded pdb=" O HIS y 19 " pdb=" OG SER y 20 " model vdw 1.482 2.440 nonbonded pdb=" CZ PHE g 60 " pdb=" OG1 THR g 62 " model vdw 1.489 3.340 nonbonded pdb=" O VAL c 35 " pdb=" NH1 ARG c 37 " model vdw 1.551 2.520 ... (remaining 866279 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: 6.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.090 Extract box with map and model: 22.020 Check model and map are aligned: 1.210 Set scattering table: 0.740 Process input model: 344.730 Find NCS groups from input model: 1.740 Set up NCS constraints: 0.240 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: 0.020 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 379.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 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 : 0.012 0.831 106834 Z= 0.765 Angle : 1.078 32.353 160475 Z= 0.545 Chirality : 0.063 1.335 20600 Planarity : 0.008 0.257 8340 Dihedral : 23.741 179.624 61995 Min Nonbonded Distance : 1.028 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.99 % Allowed : 9.81 % Favored : 89.20 % Rotamer: Outliers : 0.60 % Allowed : 2.61 % Favored : 96.79 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.03 % 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: -4.67 (0.11), residues: 3649 helix: -2.38 (0.13), residues: 998 sheet: -3.01 (0.16), residues: 730 loop : -3.62 (0.11), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP N 93 HIS 0.025 0.003 HIS O 16 PHE 0.039 0.004 PHE d 8 TYR 0.048 0.004 TYR N 41 ARG 0.018 0.002 ARG R 15 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7298 Ramachandran restraints generated. 3649 Oldfield, 0 Emsley, 3649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7298 Ramachandran restraints generated. 3649 Oldfield, 0 Emsley, 3649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 887 residues out of total 2993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 869 time to evaluate : 4.283 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 g 1 " (corrupted residue). Skipping it. REVERT: C 112 LYS cc_start: 0.7817 (pttt) cc_final: 0.6942 (mmtp) REVERT: C 240 THR cc_start: 0.8271 (t) cc_final: 0.7926 (p) REVERT: E 63 LYS cc_start: 0.8274 (tmtp) cc_final: 0.7923 (pttm) REVERT: F 27 PHE cc_start: 0.6171 (m-80) cc_final: 0.5794 (m-80) REVERT: F 29 TYR cc_start: 0.7757 (m-80) cc_final: 0.7501 (m-80) REVERT: F 73 GLU cc_start: 0.7465 (tt0) cc_final: 0.6999 (tm-30) REVERT: F 108 ASP cc_start: 0.8279 (t70) cc_final: 0.8074 (t0) REVERT: F 127 LYS cc_start: 0.7909 (mmtt) cc_final: 0.7382 (mtmt) REVERT: F 147 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7967 (mp0) REVERT: F 149 ASP cc_start: 0.8205 (m-30) cc_final: 0.7643 (t70) REVERT: G 130 THR cc_start: 0.8361 (p) cc_final: 0.7920 (t) REVERT: H 2 LYS cc_start: 0.7371 (mtmt) cc_final: 0.6987 (mmtp) REVERT: J 38 MET cc_start: 0.5345 (ptm) cc_final: 0.4946 (ptm) REVERT: J 42 LYS cc_start: 0.6511 (mmtm) cc_final: 0.5964 (ptpt) REVERT: K 89 ILE cc_start: 0.9038 (mm) cc_final: 0.8761 (mt) REVERT: K 108 MET cc_start: 0.8519 (mtt) cc_final: 0.8311 (mtt) REVERT: L 120 GLU cc_start: 0.7896 (tt0) cc_final: 0.7041 (tt0) REVERT: M 43 ARG cc_start: 0.8329 (mmt-90) cc_final: 0.8024 (mpp-170) REVERT: N 27 VAL cc_start: 0.8570 (t) cc_final: 0.8365 (p) REVERT: N 92 TRP cc_start: 0.8176 (p90) cc_final: 0.7854 (p90) REVERT: N 98 LYS cc_start: 0.8977 (mttt) cc_final: 0.8739 (mttm) REVERT: N 128 LYS cc_start: 0.8142 (mmmt) cc_final: 0.7930 (ttmt) REVERT: O 107 ASN cc_start: 0.9006 (t0) cc_final: 0.8785 (t0) REVERT: P 43 SER cc_start: 0.8307 (t) cc_final: 0.8083 (t) REVERT: P 107 TYR cc_start: 0.8730 (m-80) cc_final: 0.8017 (m-80) REVERT: P 108 THR cc_start: 0.8929 (m) cc_final: 0.8680 (t) REVERT: Q 23 ASP cc_start: 0.8355 (m-30) cc_final: 0.8143 (m-30) REVERT: U 34 HIS cc_start: 0.8388 (t-90) cc_final: 0.8103 (t-170) REVERT: U 78 SER cc_start: 0.9066 (m) cc_final: 0.8802 (t) REVERT: V 34 LEU cc_start: 0.8645 (tt) cc_final: 0.8413 (tt) REVERT: V 93 LYS cc_start: 0.7914 (mttt) cc_final: 0.7600 (mmtt) REVERT: W 86 HIS cc_start: 0.7573 (t-90) cc_final: 0.7290 (t-90) REVERT: W 90 ARG cc_start: 0.8262 (mtt-85) cc_final: 0.7945 (mtm110) REVERT: X 25 ARG cc_start: 0.8733 (mmt-90) cc_final: 0.8528 (mmt-90) REVERT: X 35 GLU cc_start: 0.6818 (tt0) cc_final: 0.6564 (tt0) REVERT: Z 20 ASP cc_start: 0.8167 (m-30) cc_final: 0.7511 (m-30) REVERT: Z 22 LEU cc_start: 0.8284 (tp) cc_final: 0.7957 (tp) REVERT: c 24 ARG cc_start: 0.5402 (ttt180) cc_final: 0.5095 (mtp180) REVERT: c 33 ARG cc_start: 0.2484 (OUTLIER) cc_final: 0.2213 (mmm-85) REVERT: e 22 ILE cc_start: 0.9112 (mm) cc_final: 0.8856 (mt) REVERT: y 31 ASN cc_start: 0.9105 (t0) cc_final: 0.8884 (t0) outliers start: 18 outliers final: 4 residues processed: 883 average time/residue: 1.1597 time to fit residues: 1650.9730 Evaluate side-chains 624 residues out of total 2993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 619 time to evaluate : 4.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 104 ARG Chi-restraints excluded: chain c residue 8 ILE Chi-restraints excluded: chain c residue 33 ARG Chi-restraints excluded: chain g residue 53 VAL Chi-restraints excluded: chain y residue 53 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 572 optimal weight: 0.9990 chunk 513 optimal weight: 6.9990 chunk 285 optimal weight: 3.9990 chunk 175 optimal weight: 10.0000 chunk 346 optimal weight: 2.9990 chunk 274 optimal weight: 0.6980 chunk 531 optimal weight: 0.6980 chunk 205 optimal weight: 2.9990 chunk 323 optimal weight: 3.9990 chunk 395 optimal weight: 5.9990 chunk 615 optimal weight: 5.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 ASN C 87 ASN C 143 HIS C 205 ASN D 69 GLN D 183 HIS D 189 ASN E 121 ASN E 176 HIS H 11 HIS H 118 GLN ** H 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 GLN ** N 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 67 ASN V 31 ASN V 70 ASN W 9 ASN W 64 ASN W 76 GLN X 29 GLN b 12 ASN ** c 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 46 HIS g 58 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 106834 Z= 0.211 Angle : 0.667 10.288 160475 Z= 0.332 Chirality : 0.036 0.301 20600 Planarity : 0.005 0.090 8340 Dihedral : 24.409 179.062 54943 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.08 % Favored : 93.70 % Rotamer: Outliers : 2.21 % Allowed : 9.66 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.10 (0.12), residues: 3651 helix: -0.58 (0.15), residues: 1013 sheet: -2.36 (0.17), residues: 744 loop : -2.83 (0.12), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP g 61 HIS 0.015 0.001 HIS H 11 PHE 0.022 0.002 PHE g 60 TYR 0.022 0.002 TYR c 39 ARG 0.014 0.001 ARG c 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 808 residues out of total 2993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 742 time to evaluate : 4.277 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 g 1 " (corrupted residue). Skipping it. REVERT: C 112 LYS cc_start: 0.7761 (pttt) cc_final: 0.7127 (tptm) REVERT: C 187 VAL cc_start: 0.8992 (m) cc_final: 0.8686 (t) REVERT: D 172 ASN cc_start: 0.8690 (t0) cc_final: 0.8228 (t0) REVERT: F 40 LYS cc_start: 0.8810 (ptmt) cc_final: 0.8540 (ptmt) REVERT: F 73 GLU cc_start: 0.7401 (tt0) cc_final: 0.6811 (tt0) REVERT: F 122 ARG cc_start: 0.7502 (mtt-85) cc_final: 0.7278 (mtt-85) REVERT: F 147 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7880 (mp0) REVERT: F 149 ASP cc_start: 0.8335 (m-30) cc_final: 0.7754 (t0) REVERT: H 2 LYS cc_start: 0.7422 (mtmt) cc_final: 0.7048 (mmtp) REVERT: H 57 LYS cc_start: 0.3949 (OUTLIER) cc_final: 0.2815 (ttmm) REVERT: I 1 MET cc_start: 0.1699 (tmm) cc_final: 0.0721 (tpt) REVERT: J 38 MET cc_start: 0.5471 (ptm) cc_final: 0.5019 (ptm) REVERT: J 42 LYS cc_start: 0.6261 (mmtm) cc_final: 0.5897 (ptpt) REVERT: K 34 THR cc_start: 0.8769 (m) cc_final: 0.8447 (p) REVERT: K 89 ILE cc_start: 0.8993 (mm) cc_final: 0.8613 (mt) REVERT: K 108 MET cc_start: 0.8859 (mtt) cc_final: 0.8615 (mtt) REVERT: L 1 MET cc_start: 0.7054 (mtp) cc_final: 0.6787 (ttm) REVERT: M 26 GLU cc_start: 0.6741 (tp30) cc_final: 0.6343 (mm-30) REVERT: N 105 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7257 (mt-10) REVERT: P 64 SER cc_start: 0.8436 (p) cc_final: 0.6789 (p) REVERT: Q 20 SER cc_start: 0.8638 (t) cc_final: 0.8155 (m) REVERT: Q 111 GLU cc_start: 0.7462 (tm-30) cc_final: 0.6861 (tm-30) REVERT: V 93 LYS cc_start: 0.7854 (mttt) cc_final: 0.7559 (mmtt) REVERT: W 45 GLN cc_start: 0.8543 (mm-40) cc_final: 0.8284 (mm-40) REVERT: W 90 ARG cc_start: 0.8109 (mtt-85) cc_final: 0.7735 (mtm110) REVERT: W 129 ASN cc_start: 0.7491 (p0) cc_final: 0.7144 (p0) REVERT: X 25 ARG cc_start: 0.8725 (mmt-90) cc_final: 0.8496 (mmt-90) REVERT: X 68 GLU cc_start: 0.7617 (tm-30) cc_final: 0.7232 (tm-30) REVERT: Z 27 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8036 (mp0) REVERT: a 21 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7743 (mm-30) REVERT: a 34 SER cc_start: 0.8260 (OUTLIER) cc_final: 0.8019 (m) REVERT: a 57 GLU cc_start: 0.7453 (tm-30) cc_final: 0.7177 (tm-30) REVERT: c 28 ARG cc_start: 0.6024 (tpt170) cc_final: 0.5258 (tpp-160) REVERT: e 5 LYS cc_start: 0.9188 (mttt) cc_final: 0.8745 (mttt) REVERT: e 22 ILE cc_start: 0.9141 (mm) cc_final: 0.8888 (mt) REVERT: f 18 ARG cc_start: 0.8505 (mtp-110) cc_final: 0.8155 (mtp-110) outliers start: 66 outliers final: 37 residues processed: 769 average time/residue: 1.0250 time to fit residues: 1302.4481 Evaluate side-chains 674 residues out of total 2993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 635 time to evaluate : 4.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain K residue 11 THR Chi-restraints excluded: chain K residue 96 HIS Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 121 LYS Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain S residue 54 ASP Chi-restraints excluded: chain T residue 29 ASP Chi-restraints excluded: chain T residue 107 THR Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 77 LYS Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain V residue 63 GLU Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 119 THR Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain Z residue 24 GLU Chi-restraints excluded: chain Z residue 44 ASN Chi-restraints excluded: chain a residue 34 SER Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain g residue 53 VAL Chi-restraints excluded: chain y residue 46 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 342 optimal weight: 2.9990 chunk 191 optimal weight: 7.9990 chunk 512 optimal weight: 1.9990 chunk 419 optimal weight: 2.9990 chunk 169 optimal weight: 8.9990 chunk 616 optimal weight: 10.0000 chunk 666 optimal weight: 9.9990 chunk 549 optimal weight: 9.9990 chunk 611 optimal weight: 5.9990 chunk 210 optimal weight: 10.0000 chunk 494 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 80 HIS D 130 HIS ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 HIS G 86 GLN H 147 ASN J 33 HIS K 130 HIS L 4 GLN ** M 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 50 GLN ** R 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 88 GLN T 67 ASN U 34 HIS U 58 ASN W 9 ASN X 29 GLN Z 40 GLN Z 44 ASN a 42 GLN ** c 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 36 GLN y 21 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 106834 Z= 0.313 Angle : 0.665 10.298 160475 Z= 0.335 Chirality : 0.038 0.300 20600 Planarity : 0.006 0.076 8340 Dihedral : 24.257 179.261 54929 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.53 % Favored : 92.36 % Rotamer: Outliers : 3.44 % Allowed : 12.53 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.34 (0.13), residues: 3651 helix: 0.03 (0.16), residues: 1006 sheet: -1.86 (0.18), residues: 707 loop : -2.36 (0.13), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP N 92 HIS 0.011 0.001 HIS G 66 PHE 0.027 0.002 PHE g 60 TYR 0.015 0.002 TYR C 84 ARG 0.018 0.001 ARG U 81 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 853 residues out of total 2993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 750 time to evaluate : 4.411 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 g 1 " (corrupted residue). Skipping it. REVERT: C 6 TYR cc_start: 0.9111 (m-80) cc_final: 0.8905 (m-10) REVERT: C 112 LYS cc_start: 0.8004 (pttt) cc_final: 0.6952 (mmtp) REVERT: C 186 ASP cc_start: 0.7814 (OUTLIER) cc_final: 0.7572 (t0) REVERT: C 217 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8705 (mtpt) REVERT: C 220 THR cc_start: 0.9024 (m) cc_final: 0.8676 (p) REVERT: D 60 ARG cc_start: 0.8078 (ttp80) cc_final: 0.7813 (ttp80) REVERT: D 172 ASN cc_start: 0.8904 (t0) cc_final: 0.8537 (t0) REVERT: F 71 LYS cc_start: 0.7913 (ttpt) cc_final: 0.7482 (tppt) REVERT: F 73 GLU cc_start: 0.7327 (tt0) cc_final: 0.6740 (tm-30) REVERT: F 108 ASP cc_start: 0.8425 (t70) cc_final: 0.8104 (t0) REVERT: F 147 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7783 (mp0) REVERT: F 172 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7039 (mm-30) REVERT: G 170 ILE cc_start: 0.6944 (OUTLIER) cc_final: 0.6734 (pp) REVERT: H 2 LYS cc_start: 0.7478 (mtmt) cc_final: 0.7123 (mmtp) REVERT: J 38 MET cc_start: 0.5490 (ptm) cc_final: 0.4968 (ptm) REVERT: J 42 LYS cc_start: 0.6022 (mmtm) cc_final: 0.5739 (ptpt) REVERT: K 89 ILE cc_start: 0.9102 (mm) cc_final: 0.8760 (mt) REVERT: K 108 MET cc_start: 0.8926 (mtt) cc_final: 0.8636 (mtt) REVERT: K 120 LYS cc_start: 0.8946 (mmmt) cc_final: 0.8374 (mmtt) REVERT: L 1 MET cc_start: 0.7689 (mtp) cc_final: 0.7265 (ttm) REVERT: L 2 ILE cc_start: 0.8662 (mm) cc_final: 0.8431 (tp) REVERT: L 9 LYS cc_start: 0.8217 (mmtt) cc_final: 0.8009 (mmtt) REVERT: L 113 LYS cc_start: 0.8529 (mmmm) cc_final: 0.8242 (mmmm) REVERT: M 10 LYS cc_start: 0.8356 (mttt) cc_final: 0.8137 (mttp) REVERT: M 26 GLU cc_start: 0.6780 (tp30) cc_final: 0.5933 (tp30) REVERT: N 132 VAL cc_start: 0.8949 (t) cc_final: 0.8677 (m) REVERT: P 12 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7428 (tm-30) REVERT: P 86 GLN cc_start: 0.8405 (mp10) cc_final: 0.7974 (mp-120) REVERT: P 118 ASP cc_start: 0.8093 (m-30) cc_final: 0.7883 (m-30) REVERT: Q 26 ASN cc_start: 0.7345 (p0) cc_final: 0.7092 (p0) REVERT: Q 93 ARG cc_start: 0.8641 (mtp85) cc_final: 0.7113 (mtp85) REVERT: R 42 SER cc_start: 0.9191 (t) cc_final: 0.8878 (p) REVERT: T 108 SER cc_start: 0.9515 (p) cc_final: 0.9238 (p) REVERT: U 23 LEU cc_start: 0.9049 (mp) cc_final: 0.8817 (mp) REVERT: V 40 ARG cc_start: 0.7244 (mmm160) cc_final: 0.6536 (mmm160) REVERT: W 45 GLN cc_start: 0.8669 (mm-40) cc_final: 0.8436 (mm-40) REVERT: W 86 HIS cc_start: 0.7686 (t-90) cc_final: 0.7389 (t-90) REVERT: W 90 ARG cc_start: 0.8264 (mtt-85) cc_final: 0.7902 (mtm110) REVERT: W 129 ASN cc_start: 0.7942 (p0) cc_final: 0.7522 (p0) REVERT: X 68 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7311 (tm-30) REVERT: a 57 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7268 (tm-30) REVERT: b 7 ARG cc_start: 0.8602 (ttp80) cc_final: 0.8311 (ttp80) REVERT: b 41 ARG cc_start: 0.8211 (ttt180) cc_final: 0.7971 (ttt180) REVERT: c 28 ARG cc_start: 0.6582 (tpt170) cc_final: 0.6221 (tpm170) REVERT: y 57 VAL cc_start: 0.8999 (t) cc_final: 0.8787 (t) REVERT: 3 6 ARG cc_start: 0.8395 (mtm-85) cc_final: 0.8100 (mtm180) outliers start: 103 outliers final: 59 residues processed: 803 average time/residue: 0.9715 time to fit residues: 1311.0903 Evaluate side-chains 730 residues out of total 2993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 668 time to evaluate : 4.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 217 LYS Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 154 CYS Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 11 THR Chi-restraints excluded: chain K residue 96 HIS Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain N residue 31 ASP Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain T residue 67 ASN Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 37 SER Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain U residue 77 LYS Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain V residue 63 GLU Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 119 THR Chi-restraints excluded: chain W residue 182 VAL Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain Z residue 38 THR Chi-restraints excluded: chain Z residue 44 ASN Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 29 THR Chi-restraints excluded: chain g residue 46 TYR Chi-restraints excluded: chain g residue 53 VAL Chi-restraints excluded: chain y residue 21 HIS Chi-restraints excluded: chain y residue 46 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 609 optimal weight: 2.9990 chunk 463 optimal weight: 5.9990 chunk 320 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 294 optimal weight: 4.9990 chunk 414 optimal weight: 8.9990 chunk 619 optimal weight: 7.9990 chunk 655 optimal weight: 0.9980 chunk 323 optimal weight: 4.9990 chunk 586 optimal weight: 0.0470 chunk 176 optimal weight: 7.9990 overall best weight: 2.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 66 ASN K 103 ASN ** M 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 16 HIS S 13 GLN W 9 ASN ** W 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 12 ASN X 44 HIS Z 35 GLN Z 44 ASN a 42 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 106834 Z= 0.287 Angle : 0.623 10.083 160475 Z= 0.315 Chirality : 0.037 0.296 20600 Planarity : 0.005 0.065 8340 Dihedral : 24.187 179.937 54929 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.82 % Favored : 93.07 % Rotamer: Outliers : 4.31 % Allowed : 14.81 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.13), residues: 3651 helix: 0.37 (0.16), residues: 1005 sheet: -1.61 (0.19), residues: 713 loop : -2.13 (0.13), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP g 37 HIS 0.012 0.001 HIS y 21 PHE 0.026 0.002 PHE M 87 TYR 0.014 0.002 TYR U 29 ARG 0.009 0.001 ARG b 16 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 831 residues out of total 2993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 702 time to evaluate : 4.388 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 g 1 " (corrupted residue). Skipping it. REVERT: C 112 LYS cc_start: 0.7990 (pttt) cc_final: 0.6865 (mmtp) REVERT: C 220 THR cc_start: 0.9038 (m) cc_final: 0.8722 (p) REVERT: D 60 ARG cc_start: 0.8131 (ttp80) cc_final: 0.7895 (ttp80) REVERT: D 172 ASN cc_start: 0.8946 (t0) cc_final: 0.8565 (t0) REVERT: E 112 ARG cc_start: 0.8230 (mmt90) cc_final: 0.8006 (mmt90) REVERT: F 71 LYS cc_start: 0.7819 (ttpt) cc_final: 0.7397 (tppt) REVERT: F 73 GLU cc_start: 0.7332 (tt0) cc_final: 0.6600 (tt0) REVERT: F 141 GLU cc_start: 0.5875 (tt0) cc_final: 0.5614 (tt0) REVERT: F 147 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7636 (mp0) REVERT: G 116 ILE cc_start: 0.8088 (mt) cc_final: 0.7855 (mm) REVERT: H 2 LYS cc_start: 0.7553 (mtmt) cc_final: 0.7121 (mmtp) REVERT: J 38 MET cc_start: 0.5591 (ptm) cc_final: 0.5076 (ptm) REVERT: K 89 ILE cc_start: 0.9129 (mm) cc_final: 0.8780 (mt) REVERT: K 108 MET cc_start: 0.8872 (mtt) cc_final: 0.8583 (mtt) REVERT: L 1 MET cc_start: 0.7616 (mtp) cc_final: 0.7221 (ttm) REVERT: L 2 ILE cc_start: 0.8690 (mm) cc_final: 0.8481 (tp) REVERT: L 9 LYS cc_start: 0.8222 (mmtt) cc_final: 0.7999 (mmtt) REVERT: M 10 LYS cc_start: 0.8550 (mttt) cc_final: 0.8324 (mttm) REVERT: M 26 GLU cc_start: 0.6790 (tp30) cc_final: 0.5983 (tp30) REVERT: N 132 VAL cc_start: 0.9049 (t) cc_final: 0.8780 (m) REVERT: P 12 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7404 (tm-30) REVERT: P 58 THR cc_start: 0.8773 (OUTLIER) cc_final: 0.8517 (p) REVERT: P 86 GLN cc_start: 0.8523 (mp10) cc_final: 0.7755 (mp10) REVERT: P 107 TYR cc_start: 0.8993 (m-80) cc_final: 0.8788 (m-80) REVERT: P 118 ASP cc_start: 0.8093 (m-30) cc_final: 0.7857 (m-30) REVERT: Q 111 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7243 (tm-30) REVERT: R 111 ASP cc_start: 0.7884 (m-30) cc_final: 0.7657 (m-30) REVERT: T 41 ASP cc_start: 0.7406 (m-30) cc_final: 0.7141 (m-30) REVERT: T 108 SER cc_start: 0.9513 (p) cc_final: 0.9232 (p) REVERT: T 113 ILE cc_start: 0.8896 (mp) cc_final: 0.8637 (pt) REVERT: U 23 LEU cc_start: 0.9041 (mp) cc_final: 0.8722 (mp) REVERT: V 40 ARG cc_start: 0.7226 (mmm160) cc_final: 0.6566 (mmm160) REVERT: W 45 GLN cc_start: 0.8690 (mm-40) cc_final: 0.7785 (mt0) REVERT: W 86 HIS cc_start: 0.7745 (t-90) cc_final: 0.7470 (t-90) REVERT: W 90 ARG cc_start: 0.8232 (mtt-85) cc_final: 0.7946 (mtm110) REVERT: W 129 ASN cc_start: 0.8014 (p0) cc_final: 0.7594 (p0) REVERT: W 188 GLU cc_start: 0.8037 (pp20) cc_final: 0.7625 (pp20) REVERT: X 68 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7344 (tm-30) REVERT: X 76 LYS cc_start: 0.8555 (mtmm) cc_final: 0.8326 (mtmm) REVERT: a 57 GLU cc_start: 0.7553 (tm-30) cc_final: 0.7240 (tm-30) REVERT: b 7 ARG cc_start: 0.8623 (ttp80) cc_final: 0.8385 (ttp80) REVERT: b 41 ARG cc_start: 0.8134 (ttt180) cc_final: 0.7886 (ttt180) REVERT: c 28 ARG cc_start: 0.6666 (OUTLIER) cc_final: 0.6295 (tpm170) REVERT: f 18 ARG cc_start: 0.8656 (mtp-110) cc_final: 0.8230 (mtp-110) REVERT: g 49 ILE cc_start: 0.7507 (mp) cc_final: 0.6975 (mm) REVERT: 3 6 ARG cc_start: 0.8348 (mtm-85) cc_final: 0.8059 (mtm180) outliers start: 129 outliers final: 88 residues processed: 763 average time/residue: 0.9667 time to fit residues: 1242.2856 Evaluate side-chains 763 residues out of total 2993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 672 time to evaluate : 4.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 49 ASP Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 11 THR Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 96 HIS Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 44 ASN Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain N residue 77 LYS Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain O residue 113 ILE Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 73 ILE Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 81 ASP Chi-restraints excluded: chain Q residue 111 GLU Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain R residue 89 GLU Chi-restraints excluded: chain S residue 94 LEU Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 107 THR Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 37 SER Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain V residue 63 GLU Chi-restraints excluded: chain V residue 87 ILE Chi-restraints excluded: chain W residue 14 ASN Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 119 THR Chi-restraints excluded: chain W residue 182 VAL Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain Z residue 22 LEU Chi-restraints excluded: chain Z residue 38 THR Chi-restraints excluded: chain Z residue 44 ASN Chi-restraints excluded: chain a residue 47 ILE Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 29 THR Chi-restraints excluded: chain c residue 28 ARG Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 59 ASN Chi-restraints excluded: chain g residue 46 TYR Chi-restraints excluded: chain g residue 53 VAL Chi-restraints excluded: chain y residue 46 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 545 optimal weight: 1.9990 chunk 372 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 487 optimal weight: 6.9990 chunk 270 optimal weight: 7.9990 chunk 559 optimal weight: 0.8980 chunk 453 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 334 optimal weight: 7.9990 chunk 588 optimal weight: 6.9990 chunk 165 optimal weight: 6.9990 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 26 ASN ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 94 ASN T 67 ASN ** W 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 12 ASN e 63 ASN ** y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 106834 Z= 0.349 Angle : 0.668 10.111 160475 Z= 0.337 Chirality : 0.039 0.317 20600 Planarity : 0.005 0.063 8340 Dihedral : 24.205 179.999 54929 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.78 % Favored : 92.11 % Rotamer: Outliers : 4.95 % Allowed : 16.28 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.13), residues: 3651 helix: 0.38 (0.16), residues: 1002 sheet: -1.58 (0.19), residues: 724 loop : -2.01 (0.13), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP g 37 HIS 0.011 0.001 HIS G 66 PHE 0.025 0.002 PHE G 91 TYR 0.020 0.002 TYR U 29 ARG 0.010 0.001 ARG e 47 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 861 residues out of total 2993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 713 time to evaluate : 4.572 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 g 1 " (corrupted residue). Skipping it. REVERT: C 112 LYS cc_start: 0.8024 (pttt) cc_final: 0.7124 (tptm) REVERT: C 146 GLU cc_start: 0.7229 (mt-10) cc_final: 0.6920 (mt-10) REVERT: C 186 ASP cc_start: 0.7813 (OUTLIER) cc_final: 0.7589 (t0) REVERT: C 220 THR cc_start: 0.9072 (m) cc_final: 0.8828 (p) REVERT: D 172 ASN cc_start: 0.8966 (t0) cc_final: 0.8590 (t0) REVERT: E 112 ARG cc_start: 0.8179 (mmt90) cc_final: 0.7911 (mmt90) REVERT: F 71 LYS cc_start: 0.7778 (ttpt) cc_final: 0.7436 (tppt) REVERT: F 73 GLU cc_start: 0.7363 (tt0) cc_final: 0.7078 (tm-30) REVERT: F 147 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7588 (mp0) REVERT: G 120 GLU cc_start: 0.7007 (pm20) cc_final: 0.6728 (pm20) REVERT: H 2 LYS cc_start: 0.7591 (mtmt) cc_final: 0.7171 (mmtp) REVERT: K 89 ILE cc_start: 0.9188 (mm) cc_final: 0.8890 (mt) REVERT: K 108 MET cc_start: 0.8955 (mtt) cc_final: 0.8734 (mtt) REVERT: L 9 LYS cc_start: 0.8317 (mmtt) cc_final: 0.8037 (mmtt) REVERT: M 10 LYS cc_start: 0.8579 (mttt) cc_final: 0.8326 (mttp) REVERT: M 26 GLU cc_start: 0.6952 (tp30) cc_final: 0.6360 (tp30) REVERT: N 132 VAL cc_start: 0.9099 (t) cc_final: 0.8881 (m) REVERT: P 12 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7432 (tm-30) REVERT: P 86 GLN cc_start: 0.8472 (mp10) cc_final: 0.8242 (mm-40) REVERT: P 107 TYR cc_start: 0.9086 (m-80) cc_final: 0.8700 (m-80) REVERT: P 118 ASP cc_start: 0.8126 (m-30) cc_final: 0.7910 (m-30) REVERT: Q 93 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.7621 (mtp85) REVERT: Q 111 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7458 (tm-30) REVERT: R 42 SER cc_start: 0.9183 (t) cc_final: 0.8920 (p) REVERT: R 47 TYR cc_start: 0.9025 (t80) cc_final: 0.8809 (t80) REVERT: R 111 ASP cc_start: 0.7929 (m-30) cc_final: 0.7697 (m-30) REVERT: T 108 SER cc_start: 0.9495 (p) cc_final: 0.9222 (p) REVERT: U 23 LEU cc_start: 0.9064 (mp) cc_final: 0.8781 (mp) REVERT: V 40 ARG cc_start: 0.7344 (mmm160) cc_final: 0.6647 (mmm160) REVERT: W 45 GLN cc_start: 0.8683 (mm-40) cc_final: 0.7754 (mt0) REVERT: W 86 HIS cc_start: 0.7778 (t-90) cc_final: 0.7493 (t-90) REVERT: W 129 ASN cc_start: 0.8146 (p0) cc_final: 0.7700 (p0) REVERT: X 68 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7347 (tm-30) REVERT: Z 9 GLU cc_start: 0.7748 (tt0) cc_final: 0.7190 (pt0) REVERT: Z 26 LYS cc_start: 0.9189 (mttp) cc_final: 0.8974 (ttmm) REVERT: a 57 GLU cc_start: 0.7633 (tm-30) cc_final: 0.7354 (tm-30) REVERT: b 41 ARG cc_start: 0.8270 (ttt180) cc_final: 0.7997 (ttt180) REVERT: c 52 GLU cc_start: 0.7308 (tp30) cc_final: 0.6795 (tp30) REVERT: f 18 ARG cc_start: 0.8746 (mtp-110) cc_final: 0.8320 (mtp-110) REVERT: g 49 ILE cc_start: 0.7676 (mp) cc_final: 0.7187 (mm) REVERT: 3 6 ARG cc_start: 0.8384 (mtm-85) cc_final: 0.8046 (mtm180) outliers start: 148 outliers final: 106 residues processed: 789 average time/residue: 0.9475 time to fit residues: 1264.3148 Evaluate side-chains 783 residues out of total 2993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 674 time to evaluate : 4.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 11 THR Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 96 HIS Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 121 LYS Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 31 ASP Chi-restraints excluded: chain N residue 44 ASN Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain N residue 77 LYS Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 113 ILE Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain P residue 73 ILE Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 81 ASP Chi-restraints excluded: chain Q residue 82 HIS Chi-restraints excluded: chain Q residue 91 VAL Chi-restraints excluded: chain Q residue 93 ARG Chi-restraints excluded: chain Q residue 111 GLU Chi-restraints excluded: chain R residue 6 ARG Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain R residue 75 THR Chi-restraints excluded: chain S residue 94 LEU Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 31 VAL Chi-restraints excluded: chain T residue 67 ASN Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 107 THR Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 37 SER Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain V residue 63 GLU Chi-restraints excluded: chain W residue 14 ASN Chi-restraints excluded: chain W residue 33 VAL Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 119 THR Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 29 THR Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 36 LYS Chi-restraints excluded: chain e residue 59 ASN Chi-restraints excluded: chain g residue 46 TYR Chi-restraints excluded: chain g residue 53 VAL Chi-restraints excluded: chain y residue 46 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 220 optimal weight: 5.9990 chunk 590 optimal weight: 6.9990 chunk 129 optimal weight: 8.9990 chunk 384 optimal weight: 4.9990 chunk 161 optimal weight: 30.0000 chunk 655 optimal weight: 1.9990 chunk 544 optimal weight: 7.9990 chunk 303 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 216 optimal weight: 7.9990 chunk 344 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 GLN ** M 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 79 ASN ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 94 ASN T 67 ASN V 101 ASN ** W 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 12 ASN a 42 GLN e 63 ASN f 36 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.096 106834 Z= 0.470 Angle : 0.764 10.680 160475 Z= 0.383 Chirality : 0.043 0.353 20600 Planarity : 0.006 0.067 8340 Dihedral : 24.309 179.384 54929 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.79 % Favored : 91.10 % Rotamer: Outliers : 5.41 % Allowed : 17.81 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.13), residues: 3651 helix: 0.15 (0.16), residues: 1007 sheet: -1.77 (0.19), residues: 715 loop : -2.15 (0.13), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP g 37 HIS 0.015 0.002 HIS G 66 PHE 0.023 0.002 PHE H 92 TYR 0.034 0.002 TYR U 29 ARG 0.010 0.001 ARG a 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 856 residues out of total 2993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 694 time to evaluate : 4.549 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 g 1 " (corrupted residue). Skipping it. REVERT: C 177 MET cc_start: 0.8394 (mmt) cc_final: 0.7910 (mmt) REVERT: C 186 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7597 (t0) REVERT: D 172 ASN cc_start: 0.9014 (t0) cc_final: 0.8677 (t0) REVERT: F 43 VAL cc_start: 0.8987 (OUTLIER) cc_final: 0.8693 (m) REVERT: F 73 GLU cc_start: 0.7370 (tt0) cc_final: 0.7143 (tm-30) REVERT: F 147 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7405 (mp0) REVERT: G 89 GLU cc_start: 0.8498 (tt0) cc_final: 0.8263 (tt0) REVERT: H 2 LYS cc_start: 0.7635 (mtmt) cc_final: 0.7279 (mmtp) REVERT: J 11 ILE cc_start: 0.1981 (OUTLIER) cc_final: 0.1659 (pt) REVERT: K 89 ILE cc_start: 0.9214 (mm) cc_final: 0.8970 (mt) REVERT: L 9 LYS cc_start: 0.8468 (mmtt) cc_final: 0.8225 (mmtt) REVERT: M 10 LYS cc_start: 0.8566 (mttt) cc_final: 0.8345 (mttp) REVERT: M 26 GLU cc_start: 0.6826 (tp30) cc_final: 0.6319 (tp30) REVERT: O 80 PHE cc_start: 0.8913 (m-80) cc_final: 0.8482 (m-80) REVERT: P 12 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7495 (tm-30) REVERT: P 86 GLN cc_start: 0.8530 (mp10) cc_final: 0.8284 (mm-40) REVERT: P 107 TYR cc_start: 0.9180 (m-80) cc_final: 0.8823 (m-80) REVERT: Q 93 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.7641 (mtp85) REVERT: Q 111 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7478 (tm-30) REVERT: R 42 SER cc_start: 0.9239 (t) cc_final: 0.8982 (p) REVERT: T 26 ARG cc_start: 0.9222 (OUTLIER) cc_final: 0.8859 (ttp-110) REVERT: T 108 SER cc_start: 0.9499 (p) cc_final: 0.9197 (p) REVERT: T 113 ILE cc_start: 0.9068 (mp) cc_final: 0.8727 (pt) REVERT: U 23 LEU cc_start: 0.9085 (mp) cc_final: 0.8807 (mp) REVERT: V 40 ARG cc_start: 0.7358 (mmm160) cc_final: 0.6640 (mmm160) REVERT: V 72 MET cc_start: 0.7644 (tpt) cc_final: 0.7355 (tpt) REVERT: W 45 GLN cc_start: 0.8673 (mm-40) cc_final: 0.7693 (mt0) REVERT: W 84 ASP cc_start: 0.7381 (t70) cc_final: 0.7160 (t0) REVERT: W 86 HIS cc_start: 0.7886 (t-90) cc_final: 0.7620 (t-90) REVERT: W 90 ARG cc_start: 0.8107 (mtt-85) cc_final: 0.7808 (mmt180) REVERT: W 129 ASN cc_start: 0.8188 (p0) cc_final: 0.7706 (p0) REVERT: X 68 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7113 (tm-30) REVERT: Z 9 GLU cc_start: 0.7931 (tt0) cc_final: 0.7213 (pt0) REVERT: Z 62 ARG cc_start: 0.8735 (tpp80) cc_final: 0.8425 (tpp80) REVERT: Z 65 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7986 (tm-30) REVERT: a 57 GLU cc_start: 0.7535 (tm-30) cc_final: 0.7323 (tm-30) REVERT: b 41 ARG cc_start: 0.8424 (ttt180) cc_final: 0.8174 (ttt180) REVERT: e 60 LYS cc_start: 0.8102 (mttt) cc_final: 0.7839 (mmtt) REVERT: f 18 ARG cc_start: 0.8738 (mtp-110) cc_final: 0.8352 (mtp-110) REVERT: 3 6 ARG cc_start: 0.8403 (mtm-85) cc_final: 0.8059 (mtm180) outliers start: 162 outliers final: 118 residues processed: 782 average time/residue: 1.0740 time to fit residues: 1437.8191 Evaluate side-chains 803 residues out of total 2993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 679 time to evaluate : 4.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain J residue 11 ILE Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 91 GLU Chi-restraints excluded: chain K residue 96 HIS Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 121 LYS Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain M residue 137 ILE Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 31 ASP Chi-restraints excluded: chain N residue 44 ASN Chi-restraints excluded: chain N residue 45 ARG Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain O residue 95 THR Chi-restraints excluded: chain O residue 113 ILE Chi-restraints excluded: chain P residue 40 VAL Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 81 ASP Chi-restraints excluded: chain Q residue 91 VAL Chi-restraints excluded: chain Q residue 93 ARG Chi-restraints excluded: chain Q residue 111 GLU Chi-restraints excluded: chain R residue 6 ARG Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain R residue 27 GLN Chi-restraints excluded: chain R residue 89 GLU Chi-restraints excluded: chain S residue 94 LEU Chi-restraints excluded: chain T residue 26 ARG Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 67 ASN Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 92 ILE Chi-restraints excluded: chain T residue 107 THR Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain V residue 63 GLU Chi-restraints excluded: chain W residue 7 ILE Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 119 THR Chi-restraints excluded: chain W residue 182 VAL Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain Z residue 38 THR Chi-restraints excluded: chain a residue 25 THR Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 29 THR Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 36 LYS Chi-restraints excluded: chain e residue 59 ASN Chi-restraints excluded: chain g residue 46 TYR Chi-restraints excluded: chain g residue 53 VAL Chi-restraints excluded: chain y residue 46 ILE Chi-restraints excluded: chain 3 residue 12 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 632 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 373 optimal weight: 4.9990 chunk 479 optimal weight: 1.9990 chunk 371 optimal weight: 10.0000 chunk 552 optimal weight: 1.9990 chunk 366 optimal weight: 2.9990 chunk 653 optimal weight: 0.0870 chunk 408 optimal weight: 6.9990 chunk 398 optimal weight: 4.9990 chunk 301 optimal weight: 10.0000 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 203 ASN D 20 ASN ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 22 GLN ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 GLN ** Q 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 50 GLN R 72 ASN ** W 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 12 ASN Z 35 GLN e 63 ASN f 36 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 106834 Z= 0.199 Angle : 0.582 10.021 160475 Z= 0.298 Chirality : 0.035 0.300 20600 Planarity : 0.005 0.064 8340 Dihedral : 24.189 179.650 54929 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.27 % Favored : 93.65 % Rotamer: Outliers : 3.88 % Allowed : 20.25 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.14), residues: 3651 helix: 0.60 (0.17), residues: 1000 sheet: -1.52 (0.20), residues: 679 loop : -1.88 (0.13), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP N 92 HIS 0.012 0.001 HIS G 66 PHE 0.021 0.001 PHE g 60 TYR 0.029 0.001 TYR U 29 ARG 0.008 0.001 ARG a 44 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 2993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 718 time to evaluate : 4.307 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 g 1 " (corrupted residue). Skipping it. REVERT: C 14 ARG cc_start: 0.8400 (mtp85) cc_final: 0.7988 (mmm160) REVERT: C 186 ASP cc_start: 0.7705 (OUTLIER) cc_final: 0.7500 (t0) REVERT: D 172 ASN cc_start: 0.8974 (t0) cc_final: 0.8610 (t0) REVERT: E 112 ARG cc_start: 0.8114 (mmt90) cc_final: 0.7814 (mmt90) REVERT: F 71 LYS cc_start: 0.7670 (ttpt) cc_final: 0.7350 (tppt) REVERT: F 73 GLU cc_start: 0.7461 (tt0) cc_final: 0.6858 (tt0) REVERT: F 147 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7440 (mp0) REVERT: G 120 GLU cc_start: 0.6789 (pm20) cc_final: 0.6565 (pm20) REVERT: H 2 LYS cc_start: 0.7613 (mtmt) cc_final: 0.7148 (mmtp) REVERT: K 52 ASP cc_start: 0.8099 (m-30) cc_final: 0.7756 (m-30) REVERT: K 89 ILE cc_start: 0.9166 (mm) cc_final: 0.8836 (mt) REVERT: K 108 MET cc_start: 0.8873 (mtt) cc_final: 0.8633 (mtt) REVERT: L 9 LYS cc_start: 0.8338 (mmtt) cc_final: 0.8069 (mmtt) REVERT: M 10 LYS cc_start: 0.8599 (mttt) cc_final: 0.8347 (mttp) REVERT: M 26 GLU cc_start: 0.6771 (tp30) cc_final: 0.6253 (tp30) REVERT: N 105 GLU cc_start: 0.7448 (mt-10) cc_final: 0.7202 (tt0) REVERT: O 80 PHE cc_start: 0.8796 (m-80) cc_final: 0.8345 (m-80) REVERT: P 12 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7417 (tm-30) REVERT: P 86 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.8295 (mm-40) REVERT: P 107 TYR cc_start: 0.9104 (m-80) cc_final: 0.8740 (m-80) REVERT: P 118 ASP cc_start: 0.8094 (m-30) cc_final: 0.7887 (m-30) REVERT: Q 30 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.7971 (mtmm) REVERT: Q 93 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.7295 (mtp85) REVERT: Q 111 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7437 (tm-30) REVERT: R 111 ASP cc_start: 0.7894 (m-30) cc_final: 0.7660 (m-30) REVERT: S 68 THR cc_start: 0.8073 (m) cc_final: 0.7719 (p) REVERT: T 108 SER cc_start: 0.9475 (p) cc_final: 0.9191 (p) REVERT: U 23 LEU cc_start: 0.9075 (mp) cc_final: 0.8784 (mp) REVERT: V 40 ARG cc_start: 0.7275 (mmm160) cc_final: 0.6558 (mmm160) REVERT: V 62 GLN cc_start: 0.7516 (mm-40) cc_final: 0.7098 (tp-100) REVERT: W 45 GLN cc_start: 0.8543 (mm-40) cc_final: 0.7524 (mt0) REVERT: W 84 ASP cc_start: 0.7530 (t70) cc_final: 0.7327 (t0) REVERT: W 86 HIS cc_start: 0.7835 (t-90) cc_final: 0.7576 (t-90) REVERT: W 129 ASN cc_start: 0.8172 (p0) cc_final: 0.7692 (p0) REVERT: X 68 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7157 (tm-30) REVERT: Z 9 GLU cc_start: 0.7864 (tt0) cc_final: 0.7410 (pt0) REVERT: Z 26 LYS cc_start: 0.9197 (mttp) cc_final: 0.8961 (ttmm) REVERT: b 41 ARG cc_start: 0.8116 (ttt180) cc_final: 0.7856 (ttt180) REVERT: f 36 GLN cc_start: 0.8631 (tt0) cc_final: 0.8314 (tt0) REVERT: g 49 ILE cc_start: 0.7719 (mp) cc_final: 0.7286 (mm) REVERT: y 26 ARG cc_start: 0.8327 (ptm-80) cc_final: 0.8056 (ttp80) REVERT: 3 6 ARG cc_start: 0.8326 (mtm-85) cc_final: 0.8018 (mtm180) outliers start: 116 outliers final: 85 residues processed: 779 average time/residue: 0.9529 time to fit residues: 1261.4441 Evaluate side-chains 765 residues out of total 2993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 675 time to evaluate : 4.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 96 HIS Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 44 ASN Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 86 GLN Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 26 ASN Chi-restraints excluded: chain Q residue 30 LYS Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 82 HIS Chi-restraints excluded: chain Q residue 93 ARG Chi-restraints excluded: chain Q residue 111 GLU Chi-restraints excluded: chain R residue 6 ARG Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain R residue 27 GLN Chi-restraints excluded: chain R residue 29 SER Chi-restraints excluded: chain S residue 94 LEU Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 107 THR Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain U residue 83 ILE Chi-restraints excluded: chain U residue 84 VAL Chi-restraints excluded: chain V residue 63 GLU Chi-restraints excluded: chain W residue 33 VAL Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 119 THR Chi-restraints excluded: chain W residue 158 THR Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 29 THR Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 59 ASN Chi-restraints excluded: chain g residue 46 TYR Chi-restraints excluded: chain g residue 53 VAL Chi-restraints excluded: chain y residue 46 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 404 optimal weight: 5.9990 chunk 260 optimal weight: 8.9990 chunk 390 optimal weight: 2.9990 chunk 196 optimal weight: 7.9990 chunk 128 optimal weight: 7.9990 chunk 126 optimal weight: 7.9990 chunk 415 optimal weight: 4.9990 chunk 445 optimal weight: 0.0030 chunk 323 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 513 optimal weight: 8.9990 overall best weight: 4.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 67 ASN ** W 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 35 GLN Z 40 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 106834 Z= 0.419 Angle : 0.708 10.191 160475 Z= 0.355 Chirality : 0.041 0.341 20600 Planarity : 0.006 0.065 8340 Dihedral : 24.237 179.432 54929 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.46 % Favored : 91.45 % Rotamer: Outliers : 4.81 % Allowed : 20.42 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.13), residues: 3651 helix: 0.27 (0.16), residues: 1011 sheet: -1.58 (0.20), residues: 664 loop : -1.99 (0.13), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP N 92 HIS 0.013 0.001 HIS G 66 PHE 0.022 0.002 PHE g 60 TYR 0.039 0.002 TYR U 29 ARG 0.009 0.001 ARG a 44 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 826 residues out of total 2993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 682 time to evaluate : 4.474 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 g 1 " (corrupted residue). Skipping it. REVERT: C 14 ARG cc_start: 0.8502 (mtp85) cc_final: 0.8125 (mmm160) REVERT: C 186 ASP cc_start: 0.7814 (OUTLIER) cc_final: 0.7581 (t0) REVERT: D 172 ASN cc_start: 0.8987 (t0) cc_final: 0.8631 (t0) REVERT: E 28 GLU cc_start: 0.7600 (tp30) cc_final: 0.7260 (tp30) REVERT: E 112 ARG cc_start: 0.8208 (mmt90) cc_final: 0.7895 (mmt90) REVERT: F 71 LYS cc_start: 0.7705 (ttpt) cc_final: 0.7344 (tppt) REVERT: F 73 GLU cc_start: 0.7419 (tt0) cc_final: 0.7185 (tm-30) REVERT: F 147 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7451 (mp0) REVERT: G 120 GLU cc_start: 0.6722 (pm20) cc_final: 0.6436 (pm20) REVERT: H 2 LYS cc_start: 0.7668 (mtmt) cc_final: 0.7157 (mmtp) REVERT: K 52 ASP cc_start: 0.8086 (m-30) cc_final: 0.7710 (m-30) REVERT: K 89 ILE cc_start: 0.9218 (mm) cc_final: 0.8940 (mt) REVERT: L 9 LYS cc_start: 0.8424 (mmtt) cc_final: 0.8158 (mmtt) REVERT: M 10 LYS cc_start: 0.8561 (mttt) cc_final: 0.8342 (mttp) REVERT: M 26 GLU cc_start: 0.6804 (tp30) cc_final: 0.6316 (tp30) REVERT: N 105 GLU cc_start: 0.7417 (mt-10) cc_final: 0.7169 (tt0) REVERT: P 12 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7469 (tm-30) REVERT: P 86 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.8287 (mm-40) REVERT: P 107 TYR cc_start: 0.9152 (m-80) cc_final: 0.8721 (m-80) REVERT: Q 48 ARG cc_start: 0.8440 (ptt180) cc_final: 0.8095 (ptt180) REVERT: Q 93 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.7528 (mtp85) REVERT: Q 111 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7531 (tm-30) REVERT: R 42 SER cc_start: 0.9221 (t) cc_final: 0.8968 (p) REVERT: S 68 THR cc_start: 0.8101 (m) cc_final: 0.7757 (p) REVERT: T 108 SER cc_start: 0.9491 (p) cc_final: 0.9210 (p) REVERT: T 113 ILE cc_start: 0.9096 (mp) cc_final: 0.8737 (pt) REVERT: U 23 LEU cc_start: 0.9089 (mp) cc_final: 0.8805 (mp) REVERT: V 40 ARG cc_start: 0.7386 (mmm160) cc_final: 0.6668 (mmm160) REVERT: V 62 GLN cc_start: 0.7502 (mm-40) cc_final: 0.7005 (tp-100) REVERT: W 45 GLN cc_start: 0.8642 (mm-40) cc_final: 0.7645 (mt0) REVERT: W 81 LYS cc_start: 0.8252 (tptt) cc_final: 0.8050 (tptt) REVERT: W 84 ASP cc_start: 0.7553 (t70) cc_final: 0.7334 (t0) REVERT: W 86 HIS cc_start: 0.7981 (t-90) cc_final: 0.7686 (t-90) REVERT: W 129 ASN cc_start: 0.8116 (p0) cc_final: 0.7666 (p0) REVERT: X 68 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7076 (tm-30) REVERT: Z 9 GLU cc_start: 0.7848 (tt0) cc_final: 0.7068 (pt0) REVERT: b 41 ARG cc_start: 0.8336 (ttt180) cc_final: 0.8079 (ttt180) REVERT: c 33 ARG cc_start: 0.3527 (OUTLIER) cc_final: 0.0514 (mmm-85) REVERT: f 18 ARG cc_start: 0.8923 (mtp-110) cc_final: 0.8440 (mtp-110) REVERT: y 26 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8159 (ptm-80) REVERT: 3 6 ARG cc_start: 0.8443 (mtm-85) cc_final: 0.8071 (mtm180) outliers start: 144 outliers final: 119 residues processed: 757 average time/residue: 0.9827 time to fit residues: 1260.8985 Evaluate side-chains 798 residues out of total 2993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 673 time to evaluate : 4.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain I residue 66 ILE Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 67 ASP Chi-restraints excluded: chain K residue 96 HIS Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain L residue 13 ASN Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain M residue 137 ILE Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 31 ASP Chi-restraints excluded: chain N residue 44 ASN Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain O residue 113 ILE Chi-restraints excluded: chain P residue 40 VAL Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 86 GLN Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 26 ASN Chi-restraints excluded: chain Q residue 36 LYS Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 57 THR Chi-restraints excluded: chain Q residue 81 ASP Chi-restraints excluded: chain Q residue 91 VAL Chi-restraints excluded: chain Q residue 93 ARG Chi-restraints excluded: chain Q residue 111 GLU Chi-restraints excluded: chain R residue 6 ARG Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain R residue 27 GLN Chi-restraints excluded: chain R residue 29 SER Chi-restraints excluded: chain S residue 54 ASP Chi-restraints excluded: chain S residue 94 LEU Chi-restraints excluded: chain T residue 67 ASN Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 107 THR Chi-restraints excluded: chain U residue 5 THR Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain U residue 84 VAL Chi-restraints excluded: chain V residue 76 SER Chi-restraints excluded: chain V residue 87 ILE Chi-restraints excluded: chain V residue 101 ASN Chi-restraints excluded: chain W residue 33 VAL Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 119 THR Chi-restraints excluded: chain W residue 158 THR Chi-restraints excluded: chain W residue 182 VAL Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain Z residue 16 ASP Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 29 THR Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain c residue 6 ARG Chi-restraints excluded: chain c residue 23 THR Chi-restraints excluded: chain c residue 33 ARG Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain e residue 36 LYS Chi-restraints excluded: chain e residue 59 ASN Chi-restraints excluded: chain f residue 13 LYS Chi-restraints excluded: chain g residue 46 TYR Chi-restraints excluded: chain g residue 53 VAL Chi-restraints excluded: chain y residue 21 HIS Chi-restraints excluded: chain y residue 26 ARG Chi-restraints excluded: chain y residue 46 ILE Chi-restraints excluded: chain 3 residue 12 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 594 optimal weight: 7.9990 chunk 626 optimal weight: 0.9980 chunk 571 optimal weight: 0.9980 chunk 608 optimal weight: 0.9990 chunk 625 optimal weight: 0.9980 chunk 366 optimal weight: 0.4980 chunk 265 optimal weight: 4.9990 chunk 478 optimal weight: 2.9990 chunk 186 optimal weight: 3.9990 chunk 550 optimal weight: 0.6980 chunk 575 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 147 GLN M 79 ASN ** M 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 72 ASN R 94 ASN W 9 ASN ** W 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 35 GLN f 36 GLN g 15 GLN ** y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.084 106834 Z= 0.142 Angle : 0.548 10.858 160475 Z= 0.280 Chirality : 0.033 0.285 20600 Planarity : 0.004 0.062 8340 Dihedral : 24.122 179.693 54929 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.12 % Favored : 94.80 % Rotamer: Outliers : 3.11 % Allowed : 22.29 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.14), residues: 3651 helix: 0.71 (0.17), residues: 1005 sheet: -1.39 (0.20), residues: 687 loop : -1.72 (0.13), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP N 92 HIS 0.009 0.001 HIS G 66 PHE 0.021 0.001 PHE g 60 TYR 0.020 0.001 TYR U 29 ARG 0.010 0.001 ARG T 117 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 824 residues out of total 2993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 731 time to evaluate : 4.416 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 g 1 " (corrupted residue). Skipping it. REVERT: D 172 ASN cc_start: 0.8929 (t0) cc_final: 0.8576 (t0) REVERT: E 28 GLU cc_start: 0.7728 (tp30) cc_final: 0.7400 (tp30) REVERT: E 112 ARG cc_start: 0.8046 (mmt90) cc_final: 0.7742 (mmt90) REVERT: F 71 LYS cc_start: 0.7666 (ttpt) cc_final: 0.7405 (tppt) REVERT: F 73 GLU cc_start: 0.7486 (tt0) cc_final: 0.6865 (tt0) REVERT: F 147 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7228 (mp0) REVERT: F 172 GLU cc_start: 0.7603 (mt-10) cc_final: 0.6920 (mm-30) REVERT: G 120 GLU cc_start: 0.6762 (pm20) cc_final: 0.6544 (pm20) REVERT: H 2 LYS cc_start: 0.7584 (mtmt) cc_final: 0.6998 (mmtp) REVERT: K 52 ASP cc_start: 0.8028 (m-30) cc_final: 0.7701 (m-30) REVERT: K 89 ILE cc_start: 0.9108 (mm) cc_final: 0.8733 (mt) REVERT: L 2 ILE cc_start: 0.8687 (mm) cc_final: 0.8482 (tp) REVERT: M 10 LYS cc_start: 0.8572 (mttt) cc_final: 0.8297 (mttp) REVERT: M 26 GLU cc_start: 0.6794 (tp30) cc_final: 0.6313 (tp30) REVERT: N 105 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7194 (tt0) REVERT: P 12 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7401 (tm-30) REVERT: P 86 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.8241 (mm-40) REVERT: P 107 TYR cc_start: 0.9025 (m-80) cc_final: 0.8641 (m-80) REVERT: Q 93 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.7126 (mtp85) REVERT: Q 111 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7437 (tm-30) REVERT: S 68 THR cc_start: 0.8066 (m) cc_final: 0.7537 (p) REVERT: T 108 SER cc_start: 0.9492 (p) cc_final: 0.9244 (p) REVERT: U 23 LEU cc_start: 0.9040 (mp) cc_final: 0.8751 (mp) REVERT: W 45 GLN cc_start: 0.8570 (mm-40) cc_final: 0.7607 (mt0) REVERT: W 86 HIS cc_start: 0.7925 (t-90) cc_final: 0.7677 (t-90) REVERT: W 129 ASN cc_start: 0.8072 (p0) cc_final: 0.7612 (p0) REVERT: W 188 GLU cc_start: 0.8176 (pp20) cc_final: 0.7796 (pp20) REVERT: X 68 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7002 (tm-30) REVERT: Z 9 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7060 (pt0) REVERT: b 41 ARG cc_start: 0.7951 (ttt180) cc_final: 0.7662 (ttt180) REVERT: e 57 ARG cc_start: 0.8290 (mmm-85) cc_final: 0.8004 (mtp85) REVERT: g 58 HIS cc_start: 0.4465 (t-170) cc_final: 0.4252 (t-170) REVERT: y 26 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7867 (ttp80) REVERT: 3 6 ARG cc_start: 0.8351 (mtm-85) cc_final: 0.8048 (mtm180) outliers start: 93 outliers final: 65 residues processed: 767 average time/residue: 0.9749 time to fit residues: 1265.2102 Evaluate side-chains 758 residues out of total 2993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 688 time to evaluate : 4.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 91 PHE Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain K residue 67 ASP Chi-restraints excluded: chain K residue 96 HIS Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain M residue 137 ILE Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain O residue 113 ILE Chi-restraints excluded: chain P residue 40 VAL Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 86 GLN Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 81 ASP Chi-restraints excluded: chain Q residue 91 VAL Chi-restraints excluded: chain Q residue 93 ARG Chi-restraints excluded: chain Q residue 111 GLU Chi-restraints excluded: chain R residue 6 ARG Chi-restraints excluded: chain R residue 27 GLN Chi-restraints excluded: chain R residue 89 GLU Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 107 THR Chi-restraints excluded: chain U residue 84 VAL Chi-restraints excluded: chain V residue 76 SER Chi-restraints excluded: chain V residue 101 ASN Chi-restraints excluded: chain W residue 33 VAL Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 158 THR Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain Z residue 9 GLU Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain c residue 6 ARG Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain e residue 59 ASN Chi-restraints excluded: chain g residue 46 TYR Chi-restraints excluded: chain g residue 53 VAL Chi-restraints excluded: chain y residue 26 ARG Chi-restraints excluded: chain y residue 46 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 606 optimal weight: 7.9990 chunk 399 optimal weight: 0.9990 chunk 643 optimal weight: 0.6980 chunk 393 optimal weight: 2.9990 chunk 305 optimal weight: 7.9990 chunk 447 optimal weight: 0.4980 chunk 675 optimal weight: 2.9990 chunk 621 optimal weight: 0.0070 chunk 537 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 415 optimal weight: 3.9990 overall best weight: 1.0402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 135 ASN ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 GLN ** F 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 ASN ** M 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 107 ASN ** Q 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 68 ASN W 9 ASN ** W 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 35 GLN ** f 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.4489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 106834 Z= 0.151 Angle : 0.527 10.101 160475 Z= 0.267 Chirality : 0.031 0.286 20600 Planarity : 0.005 0.174 8340 Dihedral : 24.030 179.602 54929 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.75 % Favored : 94.22 % Rotamer: Outliers : 2.67 % Allowed : 22.59 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.14), residues: 3651 helix: 0.88 (0.17), residues: 1005 sheet: -1.23 (0.20), residues: 661 loop : -1.57 (0.13), residues: 1985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP g 37 HIS 0.014 0.001 HIS F 146 PHE 0.026 0.001 PHE g 60 TYR 0.020 0.001 TYR U 29 ARG 0.009 0.001 ARG b 37 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7302 Ramachandran restraints generated. 3651 Oldfield, 0 Emsley, 3651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 2993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 709 time to evaluate : 4.519 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 g 1 " (corrupted residue). Skipping it. REVERT: D 6 ILE cc_start: 0.8994 (tt) cc_final: 0.8745 (tp) REVERT: D 172 ASN cc_start: 0.8928 (t0) cc_final: 0.8544 (t0) REVERT: E 28 GLU cc_start: 0.7751 (tp30) cc_final: 0.7428 (tp30) REVERT: E 34 MET cc_start: 0.7713 (mmm) cc_final: 0.7459 (mmt) REVERT: E 76 GLN cc_start: 0.8960 (mm-40) cc_final: 0.8686 (mm-40) REVERT: E 112 ARG cc_start: 0.8073 (mmt90) cc_final: 0.7794 (mmt90) REVERT: F 21 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7670 (mp0) REVERT: F 33 MET cc_start: 0.8140 (ttm) cc_final: 0.7715 (ttm) REVERT: F 71 LYS cc_start: 0.7695 (ttpt) cc_final: 0.7428 (tppt) REVERT: F 73 GLU cc_start: 0.7511 (tt0) cc_final: 0.6899 (tt0) REVERT: F 147 GLU cc_start: 0.7485 (mt-10) cc_final: 0.6845 (mp0) REVERT: H 2 LYS cc_start: 0.7582 (mtmt) cc_final: 0.7090 (mmtp) REVERT: K 52 ASP cc_start: 0.7991 (m-30) cc_final: 0.7664 (m-30) REVERT: K 89 ILE cc_start: 0.9150 (mm) cc_final: 0.8795 (mt) REVERT: L 2 ILE cc_start: 0.8634 (mm) cc_final: 0.8394 (tp) REVERT: M 10 LYS cc_start: 0.8550 (mttt) cc_final: 0.8271 (mttp) REVERT: N 105 GLU cc_start: 0.7415 (mt-10) cc_final: 0.7146 (tt0) REVERT: P 12 GLU cc_start: 0.7751 (tm-30) cc_final: 0.7336 (tm-30) REVERT: P 86 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.8230 (mm-40) REVERT: P 107 TYR cc_start: 0.8998 (m-80) cc_final: 0.8700 (m-80) REVERT: Q 1 MET cc_start: 0.6675 (mmm) cc_final: 0.5255 (tmm) REVERT: Q 93 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7057 (mtp85) REVERT: Q 111 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7430 (tm-30) REVERT: S 68 THR cc_start: 0.8049 (OUTLIER) cc_final: 0.7495 (p) REVERT: T 108 SER cc_start: 0.9498 (p) cc_final: 0.9248 (p) REVERT: U 23 LEU cc_start: 0.9027 (mp) cc_final: 0.8744 (mp) REVERT: W 45 GLN cc_start: 0.8567 (mm-40) cc_final: 0.7660 (mt0) REVERT: W 72 GLU cc_start: 0.6485 (tt0) cc_final: 0.5645 (mm-30) REVERT: W 86 HIS cc_start: 0.7924 (t-90) cc_final: 0.7658 (t-90) REVERT: W 129 ASN cc_start: 0.8083 (p0) cc_final: 0.7579 (p0) REVERT: W 188 GLU cc_start: 0.8202 (pp20) cc_final: 0.7836 (pp20) REVERT: X 68 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7067 (tm-30) REVERT: Z 9 GLU cc_start: 0.7537 (tt0) cc_final: 0.7024 (pt0) REVERT: a 58 GLU cc_start: 0.8089 (mp0) cc_final: 0.7873 (mp0) REVERT: b 41 ARG cc_start: 0.7874 (ttt180) cc_final: 0.7552 (ttt180) REVERT: f 18 ARG cc_start: 0.8952 (mtp-110) cc_final: 0.8339 (mtp-110) REVERT: g 49 ILE cc_start: 0.7403 (mp) cc_final: 0.6976 (mm) REVERT: g 58 HIS cc_start: 0.4698 (t-170) cc_final: 0.4468 (t-170) REVERT: y 26 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7871 (ttp80) REVERT: 3 6 ARG cc_start: 0.8372 (mtm-85) cc_final: 0.8071 (mtm180) outliers start: 80 outliers final: 60 residues processed: 743 average time/residue: 0.9587 time to fit residues: 1208.4317 Evaluate side-chains 762 residues out of total 2993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 697 time to evaluate : 4.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 91 PHE Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain K residue 96 HIS Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 52 VAL Chi-restraints excluded: chain L residue 65 THR Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain M residue 137 ILE Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 68 ILE Chi-restraints excluded: chain N residue 133 THR Chi-restraints excluded: chain O residue 113 ILE Chi-restraints excluded: chain P residue 10 ILE Chi-restraints excluded: chain P residue 40 VAL Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 86 GLN Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 81 ASP Chi-restraints excluded: chain Q residue 91 VAL Chi-restraints excluded: chain Q residue 93 ARG Chi-restraints excluded: chain Q residue 111 GLU Chi-restraints excluded: chain R residue 6 ARG Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 107 THR Chi-restraints excluded: chain U residue 84 VAL Chi-restraints excluded: chain V residue 87 ILE Chi-restraints excluded: chain W residue 33 VAL Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain Z residue 5 THR Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain c residue 9 VAL Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain g residue 46 TYR Chi-restraints excluded: chain g residue 53 VAL Chi-restraints excluded: chain y residue 26 ARG Chi-restraints excluded: chain y residue 46 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 329 optimal weight: 8.9990 chunk 427 optimal weight: 3.9990 chunk 572 optimal weight: 2.9990 chunk 164 optimal weight: 7.9990 chunk 495 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 chunk 538 optimal weight: 0.0970 chunk 225 optimal weight: 5.9990 chunk 553 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 GLN ** F 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 ASN ** M 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 9 ASN ** W 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 31 ASN Z 35 GLN ** f 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 15 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.126587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.097689 restraints weight = 205797.273| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.14 r_work: 0.3097 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 106834 Z= 0.260 Angle : 0.583 9.897 160475 Z= 0.294 Chirality : 0.034 0.283 20600 Planarity : 0.005 0.060 8340 Dihedral : 24.039 179.757 54929 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.27 % Favored : 93.70 % Rotamer: Outliers : 2.77 % Allowed : 22.66 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.14), residues: 3651 helix: 0.75 (0.17), residues: 1010 sheet: -1.25 (0.20), residues: 654 loop : -1.59 (0.13), residues: 1987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP g 37 HIS 0.010 0.001 HIS G 66 PHE 0.020 0.002 PHE I 81 TYR 0.025 0.002 TYR U 29 ARG 0.010 0.001 ARG F 117 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21751.04 seconds wall clock time: 385 minutes 1.52 seconds (23101.52 seconds total)