Starting phenix.real_space_refine (version: dev) on Sat Dec 17 10:31:15 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzp_8937/12_2022/6dzp_8937.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzp_8937/12_2022/6dzp_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_8937/12_2022/6dzp_8937.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzp_8937/12_2022/6dzp_8937.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzp_8937/12_2022/6dzp_8937.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzp_8937/12_2022/6dzp_8937.pdb" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 41.30, per 1000 atoms: 0.42 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: 40.17 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: 30.96 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: 164.16 Time building geometry restraints manager: 43.54 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: 54328 35.92 - 71.85: 2177 71.85 - 107.77: 184 107.77 - 143.70: 38 143.70 - 179.62: 28 Dihedral angle restraints: 56755 sinusoidal: 46266 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 56752 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 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. 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: 5.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 23.910 Check model and map are aligned: 1.120 Convert atoms to be neutral: 0.660 Process input model: 346.250 Find NCS groups from input model: 1.780 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 382.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 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 : 15.974 179.624 50021 Min Nonbonded Distance : 1.028 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.99 % Allowed : 9.81 % Favored : 89.20 % Rotamer Outliers : 0.60 % 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 *********************** 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 : 4.324 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. outliers start: 18 outliers final: 4 residues processed: 883 average time/residue: 1.0531 time to fit residues: 1491.2557 Evaluate side-chains 608 residues out of total 2993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 604 time to evaluate : 4.161 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 1.0508 time to fit residues: 11.0164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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** R 94 ASN T 67 ASN V 31 ASN W 64 ASN W 76 GLN X 29 GLN a 42 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: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.076 106834 Z= 0.208 Angle : 0.660 10.679 160475 Z= 0.329 Chirality : 0.036 0.303 20600 Planarity : 0.005 0.091 8340 Dihedral : 15.881 178.962 42954 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.14 % Favored : 93.67 % Rotamer Outliers : 2.21 % 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: -3.02 (0.13), residues: 3651 helix: -0.48 (0.15), residues: 1013 sheet: -2.36 (0.17), residues: 754 loop : -2.78 (0.12), residues: 1884 *********************** 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 800 residues out of total 2993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 734 time to evaluate : 4.201 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. outliers start: 66 outliers final: 36 residues processed: 761 average time/residue: 0.9836 time to fit residues: 1239.8557 Evaluate side-chains 656 residues out of total 2993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 620 time to evaluate : 4.180 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.7047 time to fit residues: 52.4354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 419 optimal weight: 8.9990 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: 6.9990 chunk 210 optimal weight: 10.0000 chunk 494 optimal weight: 0.2980 overall best weight: 4.2588 ------------------------------------------------------------------------------- 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 176 HIS G 86 GLN H 66 ASN H 147 ASN J 33 HIS K 103 ASN K 130 HIS ** M 84 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** ** Q 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 88 GLN T 67 ASN U 58 ASN V 70 ASN W 61 HIS ** W 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 29 GLN Z 40 GLN Z 44 ASN a 8 GLN c 26 ASN f 36 GLN y 21 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.091 106834 Z= 0.425 Angle : 0.757 10.256 160475 Z= 0.378 Chirality : 0.042 0.315 20600 Planarity : 0.006 0.071 8340 Dihedral : 16.119 178.695 42954 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.35 % Favored : 91.51 % Rotamer Outliers : 3.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.00 % Twisted Proline : 0.59 % 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: -2.56 (0.13), residues: 3651 helix: -0.22 (0.16), residues: 1018 sheet: -2.02 (0.18), residues: 709 loop : -2.45 (0.13), residues: 1924 *********************** 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 810 residues out of total 2993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 718 time to evaluate : 4.262 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. outliers start: 92 outliers final: 54 residues processed: 767 average time/residue: 0.9817 time to fit residues: 1269.1675 Evaluate side-chains 710 residues out of total 2993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 656 time to evaluate : 4.277 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 0 residues processed: 54 average time/residue: 0.7518 time to fit residues: 80.3038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 609 optimal weight: 5.9990 chunk 463 optimal weight: 5.9990 chunk 320 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 294 optimal weight: 2.9990 chunk 414 optimal weight: 1.9990 chunk 619 optimal weight: 0.9980 chunk 655 optimal weight: 0.5980 chunk 323 optimal weight: 1.9990 chunk 586 optimal weight: 3.9990 chunk 176 optimal weight: 7.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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** ** N 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 16 HIS Q 26 ASN W 9 ASN W 64 ASN X 12 ASN Z 35 GLN a 42 GLN y 15 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 106834 Z= 0.196 Angle : 0.572 9.837 160475 Z= 0.292 Chirality : 0.034 0.293 20600 Planarity : 0.005 0.060 8340 Dihedral : 15.746 179.406 42954 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.72 % Favored : 94.17 % Rotamer Outliers : 2.17 % 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: -1.89 (0.13), residues: 3651 helix: 0.41 (0.16), residues: 1008 sheet: -1.56 (0.19), residues: 708 loop : -2.10 (0.13), residues: 1935 *********************** 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 798 residues out of total 2993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 733 time to evaluate : 4.319 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. outliers start: 65 outliers final: 34 residues processed: 759 average time/residue: 0.9505 time to fit residues: 1212.6076 Evaluate side-chains 693 residues out of total 2993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 659 time to evaluate : 4.227 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.6748 time to fit residues: 48.7400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 545 optimal weight: 3.9990 chunk 372 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 487 optimal weight: 5.9990 chunk 270 optimal weight: 7.9990 chunk 559 optimal weight: 0.9990 chunk 453 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 334 optimal weight: 0.0060 chunk 588 optimal weight: 2.9990 chunk 165 optimal weight: 6.9990 overall best weight: 2.2004 ------------------------------------------------------------------------------- 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** ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 50 GLN ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 13 GLN W 9 ASN X 44 HIS Z 35 GLN e 63 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 106834 Z= 0.236 Angle : 0.580 10.007 160475 Z= 0.294 Chirality : 0.034 0.281 20600 Planarity : 0.005 0.061 8340 Dihedral : 15.672 179.901 42954 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.77 % Favored : 93.15 % Rotamer Outliers : 2.01 % 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: -1.62 (0.14), residues: 3651 helix: 0.64 (0.17), residues: 1009 sheet: -1.35 (0.19), residues: 690 loop : -1.96 (0.13), residues: 1952 *********************** 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 751 residues out of total 2993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 691 time to evaluate : 4.434 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. outliers start: 60 outliers final: 37 residues processed: 724 average time/residue: 0.9274 time to fit residues: 1134.1503 Evaluate side-chains 700 residues out of total 2993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 663 time to evaluate : 4.209 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.7245 time to fit residues: 54.6124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 384 optimal weight: 5.9990 chunk 161 optimal weight: 20.0000 chunk 655 optimal weight: 5.9990 chunk 544 optimal weight: 0.2980 chunk 303 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 216 optimal weight: 7.9990 chunk 344 optimal weight: 0.3980 overall best weight: 3.7386 ------------------------------------------------------------------------------- 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** F 58 ASN ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 94 ASN T 67 ASN W 9 ASN ** W 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 40 GLN ** 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: 0.8341 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.083 106834 Z= 0.372 Angle : 0.674 9.992 160475 Z= 0.339 Chirality : 0.039 0.317 20600 Planarity : 0.005 0.067 8340 Dihedral : 15.872 179.851 42954 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.89 % Favored : 92.03 % Rotamer Outliers : 2.24 % 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: -1.77 (0.13), residues: 3651 helix: 0.45 (0.16), residues: 1010 sheet: -1.49 (0.19), residues: 691 loop : -1.98 (0.13), residues: 1950 *********************** 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 768 residues out of total 2993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 701 time to evaluate : 4.225 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. outliers start: 67 outliers final: 43 residues processed: 730 average time/residue: 0.9335 time to fit residues: 1151.9458 Evaluate side-chains 698 residues out of total 2993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 655 time to evaluate : 4.235 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.6832 time to fit residues: 60.8820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 373 optimal weight: 0.9980 chunk 479 optimal weight: 1.9990 chunk 371 optimal weight: 20.0000 chunk 552 optimal weight: 3.9990 chunk 366 optimal weight: 2.9990 chunk 653 optimal weight: 0.1980 chunk 408 optimal weight: 0.9990 chunk 398 optimal weight: 9.9990 chunk 301 optimal weight: 10.0000 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 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** ** N 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 79 ASN ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 12 ASN e 59 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 106834 Z= 0.160 Angle : 0.539 9.877 160475 Z= 0.276 Chirality : 0.033 0.260 20600 Planarity : 0.004 0.064 8340 Dihedral : 15.587 179.065 42954 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.78 % Favored : 94.14 % Rotamer Outliers : 1.24 % 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: -1.40 (0.14), residues: 3651 helix: 0.78 (0.17), residues: 1002 sheet: -1.27 (0.20), residues: 669 loop : -1.76 (0.13), residues: 1980 *********************** 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 741 residues out of total 2993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 704 time to evaluate : 4.266 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. outliers start: 37 outliers final: 18 residues processed: 721 average time/residue: 0.9526 time to fit residues: 1165.8373 Evaluate side-chains 676 residues out of total 2993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 658 time to evaluate : 4.244 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.7200 time to fit residues: 29.1415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 404 optimal weight: 0.0870 chunk 260 optimal weight: 8.9990 chunk 390 optimal weight: 0.0370 chunk 196 optimal weight: 7.9990 chunk 128 optimal weight: 7.9990 chunk 126 optimal weight: 7.9990 chunk 415 optimal weight: 5.9990 chunk 445 optimal weight: 0.2980 chunk 323 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 513 optimal weight: 20.0000 overall best weight: 2.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 20 ASN ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 GLN ** M 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 64 ASN Z 35 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.066 106834 Z= 0.277 Angle : 0.596 9.968 160475 Z= 0.302 Chirality : 0.035 0.293 20600 Planarity : 0.005 0.065 8340 Dihedral : 15.636 179.630 42954 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.04 % Favored : 92.91 % Rotamer Outliers : 1.60 % 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: -1.43 (0.14), residues: 3651 helix: 0.64 (0.16), residues: 1007 sheet: -1.20 (0.21), residues: 644 loop : -1.74 (0.13), residues: 2000 *********************** 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 725 residues out of total 2993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 677 time to evaluate : 4.250 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: symmetry clash outliers start: 48 outliers final: 33 residues processed: 694 average time/residue: 0.9312 time to fit residues: 1091.8922 Evaluate side-chains 690 residues out of total 2993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 657 time to evaluate : 4.319 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.6991 time to fit residues: 48.1910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 571 optimal weight: 1.9990 chunk 608 optimal weight: 0.6980 chunk 625 optimal weight: 1.9990 chunk 366 optimal weight: 0.6980 chunk 265 optimal weight: 5.9990 chunk 478 optimal weight: 0.5980 chunk 186 optimal weight: 5.9990 chunk 550 optimal weight: 2.9990 chunk 575 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 86 GLN ** K 147 GLN ** 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** Z 35 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 106834 Z= 0.158 Angle : 0.531 11.042 160475 Z= 0.271 Chirality : 0.032 0.254 20600 Planarity : 0.004 0.062 8340 Dihedral : 15.487 179.179 42954 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.31 % Favored : 94.63 % Rotamer Outliers : 0.77 % 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: 0.85 (0.17), residues: 1002 sheet: -1.06 (0.21), residues: 646 loop : -1.62 (0.13), residues: 2003 *********************** 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 721 residues out of total 2993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 698 time to evaluate : 5.481 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. outliers start: 23 outliers final: 13 residues processed: 707 average time/residue: 0.9280 time to fit residues: 1119.2348 Evaluate side-chains 684 residues out of total 2993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 671 time to evaluate : 4.159 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.6904 time to fit residues: 21.7084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 606 optimal weight: 0.9990 chunk 399 optimal weight: 5.9990 chunk 643 optimal weight: 2.9990 chunk 393 optimal weight: 6.9990 chunk 305 optimal weight: 7.9990 chunk 447 optimal weight: 5.9990 chunk 675 optimal weight: 0.6980 chunk 621 optimal weight: 5.9990 chunk 537 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 415 optimal weight: 1.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 GLN ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 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** S 88 GLN W 64 ASN X 29 GLN Z 35 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.4284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 106834 Z= 0.265 Angle : 0.584 10.995 160475 Z= 0.296 Chirality : 0.035 0.287 20600 Planarity : 0.005 0.065 8340 Dihedral : 15.550 179.658 42954 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.68 % Favored : 93.26 % Rotamer Outliers : 0.57 % 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: -1.25 (0.14), residues: 3651 helix: 0.68 (0.17), residues: 1009 sheet: -1.02 (0.21), residues: 621 loop : -1.60 (0.13), residues: 2021 ********************** 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 686 residues out of total 2993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 669 time to evaluate : 4.287 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. outliers start: 17 outliers final: 13 residues processed: 674 average time/residue: 0.9488 time to fit residues: 1085.9516 Evaluate side-chains 665 residues out of total 2993 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 652 time to evaluate : 4.229 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.6907 time to fit residues: 21.6457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 678 random chunks: chunk 329 optimal weight: 9.9990 chunk 427 optimal weight: 0.4980 chunk 572 optimal weight: 3.9990 chunk 164 optimal weight: 6.9990 chunk 495 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 538 optimal weight: 0.8980 chunk 225 optimal weight: 4.9990 chunk 553 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 20 ASN ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 118 GLN ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 ASN 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** S 88 GLN Z 35 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.127759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.098833 restraints weight = 205592.491| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.13 r_work: 0.3115 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 106834 Z= 0.181 Angle : 0.551 12.008 160475 Z= 0.280 Chirality : 0.033 0.266 20600 Planarity : 0.004 0.063 8340 Dihedral : 15.513 179.510 42954 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.72 % Favored : 94.25 % Rotamer Outliers : 0.57 % 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: -1.17 (0.14), residues: 3651 helix: 0.78 (0.17), residues: 1003 sheet: -1.00 (0.21), residues: 641 loop : -1.55 (0.13), residues: 2007 =============================================================================== Job complete usr+sys time: 19739.46 seconds wall clock time: 349 minutes 12.49 seconds (20952.49 seconds total)