Starting phenix.real_space_refine on Mon Sep 30 07:17:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wqn_21872/09_2024/6wqn_21872_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wqn_21872/09_2024/6wqn_21872.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wqn_21872/09_2024/6wqn_21872.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wqn_21872/09_2024/6wqn_21872.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wqn_21872/09_2024/6wqn_21872_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wqn_21872/09_2024/6wqn_21872_trim.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 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: 6 Type Number sf(0) Gaussians P 2793 5.49 5 S 53 5.16 5 C 39728 2.51 5 N 14987 2.21 5 O 23136 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 134 residue(s): 1.28s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 80700 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 907 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain: "B" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2094 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 17, 'TRANS': 256} Chain: "C" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 943 Classifications: {'peptide': 116} Link IDs: {'TRANS': 115} Chain: "D" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 785 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 97} Chain: "E" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 845 Classifications: {'peptide': 110} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 105} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 654 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain breaks: 1 Chain: "G" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 702 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} Chain breaks: 1 Chain: "H" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 727 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "J" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 463 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain: "K" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 436 Classifications: {'peptide': 53} Link IDs: {'TRANS': 52} Chain: "L" Number of atoms: 1621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1621 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 206} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "M" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 432 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "N" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 397 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 3, 'TRANS': 46} Chain: "O" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 390 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "P" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 372 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "Q" Number of atoms: 521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 521 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "R" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 296 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "S" Number of atoms: 1472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1472 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 9, 'TRANS': 182} Chain: "V" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1138 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "W" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 911 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "X" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1082 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 5, 'TRANS': 138} Chain: "Y" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1089 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "Z" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 951 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain: "a" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 1, 'TRANS': 108} Chain breaks: 1 Chain: "1" Number of atoms: 57631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2687, 57631 Inner-chain residues flagged as termini: ['pdbres=" A 1 318 "', 'pdbres=" A 11459 "', 'pdbres=" G 11556 "'] Classifications: {'RNA': 2687} Modifications used: {'5*END': 4, 'rna2p_pur': 269, 'rna2p_pyr': 127, 'rna3p_pur': 1283, 'rna3p_pyr': 1008} Link IDs: {'rna2p': 396, 'rna3p': 2290} Chain breaks: 8 Chain: "2" Number of atoms: 2358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 2358 Classifications: {'RNA': 111} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 50, 'rna3p_pyr': 49} Link IDs: {'rna2p': 12, 'rna3p': 98} Chain: "I" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 597 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "1" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'ZC0': 1} Classifications: {'undetermined': 1} Time building chain proxies: 33.11, per 1000 atoms: 0.41 Number of scatterers: 80700 At special positions: 0 Unit cell: (210.325, 236.28, 184.37, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 53 16.00 P 2793 15.00 F 3 9.00 O 23136 8.00 N 14987 7.00 C 39728 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 30 " - pdb=" SG CYS N 33 " distance=2.87 Simple disulfide: pdb=" SG CYS N 33 " - pdb=" SG CYS N 43 " distance=2.02 Simple disulfide: pdb=" SG CYS R 14 " - pdb=" SG CYS R 27 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.97 Conformation dependent library (CDL) restraints added in 3.0 seconds 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4812 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 40 sheets defined 25.7% alpha, 20.1% beta 531 base pairs and 1502 stacking pairs defined. Time for finding SS restraints: 25.24 Creating SS restraints... Processing helix chain 'A' and resid 11 through 15 removed outlier: 3.631A pdb=" N LEU A 15 " --> pdb=" O LYS A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 103 removed outlier: 3.685A pdb=" N ARG A 103 " --> pdb=" O TYR A 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'B' and resid 133 through 135 No H-bonds generated for 'chain 'B' and resid 133 through 135' Processing helix chain 'B' and resid 207 through 213 removed outlier: 4.047A pdb=" N SER B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TRP B 213 " --> pdb=" O GLY B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 225 removed outlier: 3.578A pdb=" N MET B 225 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 268 Processing helix chain 'C' and resid 9 through 20 removed outlier: 3.754A pdb=" N ARG C 13 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR C 17 " --> pdb=" O ARG C 13 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU C 20 " --> pdb=" O LYS C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 30 Processing helix chain 'C' and resid 31 through 70 removed outlier: 3.665A pdb=" N GLN C 37 " --> pdb=" O LYS C 33 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ARG C 51 " --> pdb=" O PHE C 47 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LYS C 54 " --> pdb=" O ARG C 50 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG C 55 " --> pdb=" O ARG C 51 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE C 57 " --> pdb=" O ARG C 53 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG C 58 " --> pdb=" O LYS C 54 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR C 63 " --> pdb=" O LYS C 59 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA C 67 " --> pdb=" O THR C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 73 No H-bonds generated for 'chain 'C' and resid 71 through 73' Processing helix chain 'C' and resid 75 through 86 removed outlier: 3.506A pdb=" N ALA C 86 " --> pdb=" O GLY C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.505A pdb=" N GLU C 97 " --> pdb=" O LYS C 93 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER C 101 " --> pdb=" O GLU C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 116 removed outlier: 3.639A pdb=" N LEU C 109 " --> pdb=" O ALA C 105 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL C 110 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR C 111 " --> pdb=" O ALA C 107 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA C 116 " --> pdb=" O LYS C 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 22 removed outlier: 3.824A pdb=" N LEU E 19 " --> pdb=" O ARG E 15 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL E 20 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP E 22 " --> pdb=" O ARG E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 39 removed outlier: 4.048A pdb=" N ALA E 34 " --> pdb=" O ALA E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 61 removed outlier: 3.542A pdb=" N SER E 53 " --> pdb=" O LYS E 49 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU E 59 " --> pdb=" O LEU E 55 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN E 61 " --> pdb=" O ASN E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 69 Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'F' and resid 34 through 47 removed outlier: 3.593A pdb=" N LYS F 39 " --> pdb=" O LYS F 35 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET F 40 " --> pdb=" O THR F 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 25 Processing helix chain 'H' and resid 45 through 56 removed outlier: 3.505A pdb=" N VAL H 51 " --> pdb=" O GLU H 47 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG H 53 " --> pdb=" O ILE H 49 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU H 54 " --> pdb=" O LYS H 50 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL H 55 " --> pdb=" O VAL H 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 19 removed outlier: 3.575A pdb=" N GLN K 17 " --> pdb=" O GLU K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 35 Processing helix chain 'K' and resid 40 through 61 removed outlier: 4.427A pdb=" N ARG K 44 " --> pdb=" O THR K 40 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR K 45 " --> pdb=" O ALA K 41 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA K 51 " --> pdb=" O ARG K 47 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 79 removed outlier: 3.870A pdb=" N HIS L 76 " --> pdb=" O PRO L 72 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA L 77 " --> pdb=" O ALA L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 110 Processing helix chain 'L' and resid 129 through 134 Processing helix chain 'M' and resid 16 through 27 removed outlier: 3.647A pdb=" N THR M 22 " --> pdb=" O THR M 18 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU M 24 " --> pdb=" O ARG M 20 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU M 26 " --> pdb=" O THR M 22 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY M 27 " --> pdb=" O VAL M 23 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 50 removed outlier: 3.583A pdb=" N GLN M 46 " --> pdb=" O ALA M 42 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS M 49 " --> pdb=" O GLY M 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 17 removed outlier: 3.518A pdb=" N LYS N 15 " --> pdb=" O THR N 11 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG N 17 " --> pdb=" O LYS N 13 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 18 removed outlier: 3.584A pdb=" N SER P 14 " --> pdb=" O LYS P 10 " (cutoff:3.500A) Processing helix chain 'P' and resid 18 through 23 Processing helix chain 'P' and resid 25 through 39 removed outlier: 3.556A pdb=" N LEU P 32 " --> pdb=" O GLY P 28 " (cutoff:3.500A) Processing helix chain 'Q' and resid 7 through 12 removed outlier: 3.612A pdb=" N LYS Q 12 " --> pdb=" O ARG Q 8 " (cutoff:3.500A) Processing helix chain 'Q' and resid 32 through 36 removed outlier: 3.532A pdb=" N LYS Q 36 " --> pdb=" O PHE Q 33 " (cutoff:3.500A) Processing helix chain 'Q' and resid 37 through 43 Processing helix chain 'Q' and resid 44 through 46 No H-bonds generated for 'chain 'Q' and resid 44 through 46' Processing helix chain 'Q' and resid 51 through 56 removed outlier: 4.062A pdb=" N LYS Q 56 " --> pdb=" O LYS Q 52 " (cutoff:3.500A) Processing helix chain 'Q' and resid 59 through 63 Processing helix chain 'R' and resid 29 through 32 Processing helix chain 'S' and resid 29 through 43 removed outlier: 3.933A pdb=" N GLU S 35 " --> pdb=" O SER S 31 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER S 43 " --> pdb=" O LEU S 39 " (cutoff:3.500A) Processing helix chain 'S' and resid 102 through 119 removed outlier: 3.551A pdb=" N ALA S 113 " --> pdb=" O ALA S 109 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL S 118 " --> pdb=" O LEU S 114 " (cutoff:3.500A) Processing helix chain 'S' and resid 135 through 147 Processing helix chain 'S' and resid 160 through 169 removed outlier: 3.854A pdb=" N ALA S 167 " --> pdb=" O VAL S 163 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ASN S 169 " --> pdb=" O LEU S 165 " (cutoff:3.500A) Processing helix chain 'S' and resid 177 through 181 removed outlier: 4.098A pdb=" N LEU S 181 " --> pdb=" O ALA S 178 " (cutoff:3.500A) Processing helix chain 'S' and resid 182 through 189 Processing helix chain 'S' and resid 196 through 206 removed outlier: 3.625A pdb=" N LYS S 200 " --> pdb=" O GLU S 196 " (cutoff:3.500A) Processing helix chain 'V' and resid 25 through 39 removed outlier: 4.332A pdb=" N GLU V 32 " --> pdb=" O ARG V 28 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER V 35 " --> pdb=" O SER V 31 " (cutoff:3.500A) Processing helix chain 'V' and resid 59 through 63 Processing helix chain 'V' and resid 68 through 73 Processing helix chain 'V' and resid 90 through 95 removed outlier: 3.752A pdb=" N ARG V 95 " --> pdb=" O GLY V 91 " (cutoff:3.500A) Processing helix chain 'V' and resid 97 through 108 removed outlier: 3.586A pdb=" N ILE V 102 " --> pdb=" O PRO V 98 " (cutoff:3.500A) Processing helix chain 'V' and resid 113 through 120 removed outlier: 3.811A pdb=" N LYS V 118 " --> pdb=" O ARG V 114 " (cutoff:3.500A) Processing helix chain 'V' and resid 133 through 137 Processing helix chain 'W' and resid 104 through 109 removed outlier: 4.011A pdb=" N GLU W 108 " --> pdb=" O ARG W 104 " (cutoff:3.500A) Processing helix chain 'W' and resid 111 through 118 removed outlier: 3.711A pdb=" N VAL W 115 " --> pdb=" O PHE W 111 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER W 116 " --> pdb=" O MET W 112 " (cutoff:3.500A) Processing helix chain 'X' and resid 56 through 61 Processing helix chain 'X' and resid 92 through 97 Processing helix chain 'X' and resid 131 through 137 Processing helix chain 'Y' and resid 44 through 59 removed outlier: 3.627A pdb=" N ALA Y 53 " --> pdb=" O SER Y 49 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N MET Y 54 " --> pdb=" O ALA Y 50 " (cutoff:3.500A) Processing helix chain 'Y' and resid 112 through 118 removed outlier: 3.549A pdb=" N LEU Y 118 " --> pdb=" O ALA Y 114 " (cutoff:3.500A) Processing helix chain 'Y' and resid 118 through 123 removed outlier: 3.745A pdb=" N HIS Y 123 " --> pdb=" O ARG Y 119 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 28 removed outlier: 3.617A pdb=" N LYS Z 14 " --> pdb=" O SER Z 10 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA Z 15 " --> pdb=" O ASP Z 11 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU Z 17 " --> pdb=" O ARG Z 13 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE Z 25 " --> pdb=" O ALA Z 21 " (cutoff:3.500A) Processing helix chain 'Z' and resid 34 through 52 removed outlier: 4.008A pdb=" N GLU Z 39 " --> pdb=" O ALA Z 35 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N SER Z 42 " --> pdb=" O LYS Z 38 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS Z 46 " --> pdb=" O SER Z 42 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU Z 47 " --> pdb=" O VAL Z 43 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE Z 48 " --> pdb=" O VAL Z 44 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR Z 49 " --> pdb=" O GLU Z 45 " (cutoff:3.500A) Processing helix chain 'Z' and resid 55 through 63 removed outlier: 3.675A pdb=" N ALA Z 63 " --> pdb=" O ARG Z 59 " (cutoff:3.500A) Processing helix chain 'Z' and resid 80 through 85 Processing helix chain 'a' and resid 6 through 19 removed outlier: 3.751A pdb=" N VAL a 10 " --> pdb=" O ASP a 6 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS a 13 " --> pdb=" O LYS a 9 " (cutoff:3.500A) Processing helix chain 'a' and resid 69 through 87 removed outlier: 3.717A pdb=" N GLU a 78 " --> pdb=" O THR a 74 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA a 79 " --> pdb=" O LYS a 75 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS a 87 " --> pdb=" O LYS a 83 " (cutoff:3.500A) Processing helix chain 'a' and resid 103 through 114 removed outlier: 3.627A pdb=" N ALA a 107 " --> pdb=" O GLY a 103 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 90 removed outlier: 6.502A pdb=" N ILE A 83 " --> pdb=" O ARG A 33 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ARG A 33 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS A 85 " --> pdb=" O HIS A 31 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU A 87 " --> pdb=" O ARG A 29 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N THR A 27 " --> pdb=" O LYS A 89 " (cutoff:3.500A) removed outlier: 9.202A pdb=" N GLU A 46 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ILE A 66 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N THR A 62 " --> pdb=" O ILE A 50 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ARG A 52 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR A 60 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 3 through 5 Processing sheet with id=AA3, first strand: chain 'B' and resid 34 through 36 Processing sheet with id=AA4, first strand: chain 'B' and resid 101 through 105 removed outlier: 6.769A pdb=" N ILE B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE B 81 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU B 93 " --> pdb=" O ASP B 79 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 129 through 131 removed outlier: 4.663A pdb=" N LEU B 173 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LYS B 167 " --> pdb=" O TYR B 171 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N TYR B 171 " --> pdb=" O LYS B 167 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL B 181 " --> pdb=" O VAL B 271 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 11 through 14 removed outlier: 6.465A pdb=" N PHE D 2 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N VAL D 41 " --> pdb=" O PHE D 2 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE D 4 " --> pdb=" O LEU D 39 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 19 through 22 removed outlier: 3.608A pdb=" N ILE D 20 " --> pdb=" O LEU D 95 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N THR D 59 " --> pdb=" O ASP D 98 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL D 58 " --> pdb=" O PHE D 35 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 19 through 22 removed outlier: 3.608A pdb=" N ILE D 20 " --> pdb=" O LEU D 95 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY D 66 " --> pdb=" O TYR D 92 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS D 64 " --> pdb=" O LYS D 94 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 71 through 77 removed outlier: 4.465A pdb=" N SER D 82 " --> pdb=" O LYS D 77 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 10 removed outlier: 5.962A pdb=" N SER E 101 " --> pdb=" O THR E 9 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N HIS E 102 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA E 76 " --> pdb=" O HIS E 102 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N THR E 104 " --> pdb=" O ALA E 74 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ALA E 74 " --> pdb=" O THR E 104 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL E 106 " --> pdb=" O LYS E 72 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 82 through 87 Processing sheet with id=AB3, first strand: chain 'F' and resid 7 through 10 removed outlier: 6.519A pdb=" N ASP F 28 " --> pdb=" O LYS F 8 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N THR F 26 " --> pdb=" O PRO F 10 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ARG F 76 " --> pdb=" O VAL F 29 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N LYS F 77 " --> pdb=" O ILE F 55 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ILE F 55 " --> pdb=" O LYS F 77 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE F 79 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL F 53 " --> pdb=" O ILE F 79 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N THR F 81 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LYS F 49 " --> pdb=" O LYS F 83 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 63 through 64 removed outlier: 3.537A pdb=" N ALA G 25 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY G 21 " --> pdb=" O VAL G 9 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ASN G 8 " --> pdb=" O LEU G 71 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU G 71 " --> pdb=" O ASN G 8 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU G 70 " --> pdb=" O THR G 79 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 40 through 43 removed outlier: 3.538A pdb=" N LYS G 43 " --> pdb=" O LEU G 57 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 81 through 83 Processing sheet with id=AB7, first strand: chain 'H' and resid 7 through 8 removed outlier: 3.765A pdb=" N VAL H 39 " --> pdb=" O VAL H 31 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL H 31 " --> pdb=" O VAL H 39 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL H 43 " --> pdb=" O VAL H 27 " (cutoff:3.500A) removed outlier: 8.774A pdb=" N LYS H 26 " --> pdb=" O THR H 87 " (cutoff:3.500A) removed outlier: 9.476A pdb=" N ILE H 89 " --> pdb=" O LYS H 26 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N PHE H 91 " --> pdb=" O PRO H 28 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL H 30 " --> pdb=" O PHE H 91 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE H 86 " --> pdb=" O PHE H 79 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N PHE H 79 " --> pdb=" O ILE H 86 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N HIS H 88 " --> pdb=" O TYR H 77 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N TYR H 77 " --> pdb=" O HIS H 88 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ASP H 90 " --> pdb=" O ALA H 75 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 63 through 65 Processing sheet with id=AB9, first strand: chain 'J' and resid 13 through 16 Processing sheet with id=AC1, first strand: chain 'J' and resid 33 through 38 Processing sheet with id=AC2, first strand: chain 'L' and resid 177 through 183 removed outlier: 5.195A pdb=" N THR L 179 " --> pdb=" O GLY L 120 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N GLY L 120 " --> pdb=" O THR L 179 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N GLN L 181 " --> pdb=" O VAL L 118 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL L 118 " --> pdb=" O GLN L 181 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N VAL L 121 " --> pdb=" O LEU L 208 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LEU L 208 " --> pdb=" O VAL L 121 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LYS L 9 " --> pdb=" O GLU L 29 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLU L 29 " --> pdb=" O LYS L 9 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY L 11 " --> pdb=" O VAL L 27 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL L 194 " --> pdb=" O VAL L 188 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N VAL L 188 " --> pdb=" O VAL L 194 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU L 196 " --> pdb=" O VAL L 186 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 88 through 91 removed outlier: 3.630A pdb=" N ILE L 49 " --> pdb=" O PHE L 91 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLN L 37 " --> pdb=" O GLN L 50 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLY L 52 " --> pdb=" O VAL L 35 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N VAL L 35 " --> pdb=" O GLY L 52 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASN L 33 " --> pdb=" O VAL L 105 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 126 through 128 Processing sheet with id=AC5, first strand: chain 'M' and resid 34 through 37 removed outlier: 3.563A pdb=" N THR M 7 " --> pdb=" O THR M 55 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'N' and resid 27 through 29 Processing sheet with id=AC7, first strand: chain 'O' and resid 17 through 22 removed outlier: 3.599A pdb=" N LYS O 41 " --> pdb=" O CYS O 36 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'Q' and resid 14 through 16 removed outlier: 3.662A pdb=" N ARG Q 48 " --> pdb=" O ARG Q 24 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'R' and resid 2 through 3 removed outlier: 6.573A pdb=" N LYS R 2 " --> pdb=" O ARG R 35 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'R' and resid 15 through 18 Processing sheet with id=AD2, first strand: chain 'S' and resid 123 through 126 removed outlier: 6.015A pdb=" N LEU S 153 " --> pdb=" O VAL S 193 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N THR S 195 " --> pdb=" O LEU S 153 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N VAL S 155 " --> pdb=" O THR S 195 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'V' and resid 123 through 125 removed outlier: 6.724A pdb=" N TRP V 16 " --> pdb=" O GLU V 139 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'V' and resid 74 through 78 removed outlier: 3.565A pdb=" N ARG V 77 " --> pdb=" O LYS V 86 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'W' and resid 7 through 10 removed outlier: 3.593A pdb=" N VAL W 10 " --> pdb=" O ARG W 17 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ARG W 17 " --> pdb=" O VAL W 10 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ALA W 16 " --> pdb=" O ALA W 46 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ALA W 46 " --> pdb=" O ALA W 16 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLU W 18 " --> pdb=" O LYS W 44 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL W 40 " --> pdb=" O ILE W 22 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N VAL W 24 " --> pdb=" O VAL W 38 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N VAL W 38 " --> pdb=" O VAL W 24 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALA W 83 " --> pdb=" O VAL W 63 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N CYS W 84 " --> pdb=" O ARG W 7 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LYS W 9 " --> pdb=" O CYS W 84 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ILE W 86 " --> pdb=" O LYS W 9 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'X' and resid 75 through 77 removed outlier: 3.784A pdb=" N LYS X 127 " --> pdb=" O ILE X 109 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'X' and resid 90 through 91 Processing sheet with id=AD8, first strand: chain 'Y' and resid 63 through 66 removed outlier: 6.634A pdb=" N LEU Y 34 " --> pdb=" O LEU Y 103 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLU Y 105 " --> pdb=" O PHE Y 32 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N PHE Y 32 " --> pdb=" O GLU Y 105 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Y' and resid 40 through 43 removed outlier: 3.541A pdb=" N SER Y 40 " --> pdb=" O VAL Y 97 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL Y 97 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N VAL Y 90 " --> pdb=" O LYS Y 76 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N LYS Y 76 " --> pdb=" O VAL Y 90 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY Y 92 " --> pdb=" O TYR Y 74 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Z' and resid 29 through 33 removed outlier: 5.961A pdb=" N SER Z 116 " --> pdb=" O GLN Z 106 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'a' and resid 51 through 57 removed outlier: 6.719A pdb=" N ILE a 44 " --> pdb=" O LEU a 53 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N GLN a 55 " --> pdb=" O ALA a 42 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ALA a 42 " --> pdb=" O GLN a 55 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 30 through 31 removed outlier: 6.687A pdb=" N LEU I 67 " --> pdb=" O LEU I 45 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 38 through 39 removed outlier: 3.590A pdb=" N GLY I 73 " --> pdb=" O VAL I 39 " (cutoff:3.500A) 598 hydrogen bonds defined for protein. 1641 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1253 hydrogen bonds 1928 hydrogen bond angles 0 basepair planarities 531 basepair parallelities 1502 stacking parallelities Total time for adding SS restraints: 108.17 Time building geometry restraints manager: 16.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 6939 1.31 - 1.44: 40598 1.44 - 1.56: 34946 1.56 - 1.69: 5578 1.69 - 1.81: 92 Bond restraints: 88153 Sorted by residual: bond pdb=" C LYS N 5 " pdb=" N ARG N 6 " ideal model delta sigma weight residual 1.330 1.453 -0.123 1.45e-02 4.76e+03 7.19e+01 bond pdb=" C04 ZC0 13001 " pdb=" C05 ZC0 13001 " ideal model delta sigma weight residual 1.363 1.516 -0.153 2.00e-02 2.50e+03 5.87e+01 bond pdb=" C04 ZC0 13001 " pdb=" N03 ZC0 13001 " ideal model delta sigma weight residual 1.353 1.503 -0.150 2.00e-02 2.50e+03 5.61e+01 bond pdb=" C ARG X 71 " pdb=" N LYS X 72 " ideal model delta sigma weight residual 1.330 1.417 -0.088 1.32e-02 5.74e+03 4.40e+01 bond pdb=" C ARG N 6 " pdb=" N ARG N 7 " ideal model delta sigma weight residual 1.330 1.416 -0.086 1.31e-02 5.83e+03 4.33e+01 ... (remaining 88148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.18: 132164 3.18 - 6.35: 578 6.35 - 9.53: 47 9.53 - 12.70: 17 12.70 - 15.88: 1 Bond angle restraints: 132807 Sorted by residual: angle pdb=" C4' A 1 254 " pdb=" C3' A 1 254 " pdb=" O3' A 1 254 " ideal model delta sigma weight residual 113.00 128.88 -15.88 1.50e+00 4.44e-01 1.12e+02 angle pdb=" N ASP L 159 " pdb=" CA ASP L 159 " pdb=" C ASP L 159 " ideal model delta sigma weight residual 111.07 99.78 11.29 1.07e+00 8.73e-01 1.11e+02 angle pdb=" C4' A 12078 " pdb=" C3' A 12078 " pdb=" O3' A 12078 " ideal model delta sigma weight residual 109.40 96.84 12.56 1.50e+00 4.44e-01 7.01e+01 angle pdb=" C4' G 11405 " pdb=" C3' G 11405 " pdb=" O3' G 11405 " ideal model delta sigma weight residual 113.00 124.51 -11.51 1.50e+00 4.44e-01 5.89e+01 angle pdb=" C4' G 12850 " pdb=" C3' G 12850 " pdb=" O3' G 12850 " ideal model delta sigma weight residual 113.00 124.48 -11.48 1.50e+00 4.44e-01 5.86e+01 ... (remaining 132802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 49508 36.00 - 72.00: 6117 72.00 - 108.00: 685 108.00 - 144.00: 12 144.00 - 180.00: 12 Dihedral angle restraints: 56334 sinusoidal: 48847 harmonic: 7487 Sorted by residual: dihedral pdb=" O4' U 1 556 " pdb=" C1' U 1 556 " pdb=" N1 U 1 556 " pdb=" C2 U 1 556 " ideal model delta sinusoidal sigma weight residual -160.00 12.76 -172.76 1 1.50e+01 4.44e-03 8.50e+01 dihedral pdb=" O4' U 1 895 " pdb=" C1' U 1 895 " pdb=" N1 U 1 895 " pdb=" C2 U 1 895 " ideal model delta sinusoidal sigma weight residual -160.00 9.56 -169.56 1 1.50e+01 4.44e-03 8.46e+01 dihedral pdb=" CB CYS N 33 " pdb=" SG CYS N 33 " pdb=" SG CYS N 43 " pdb=" CB CYS N 43 " ideal model delta sinusoidal sigma weight residual -86.00 -168.85 82.85 1 1.00e+01 1.00e-02 8.41e+01 ... (remaining 56331 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 16591 0.095 - 0.189: 419 0.189 - 0.284: 92 0.284 - 0.379: 13 0.379 - 0.473: 8 Chirality restraints: 17123 Sorted by residual: chirality pdb=" C3' G 11466 " pdb=" C4' G 11466 " pdb=" O3' G 11466 " pdb=" C2' G 11466 " both_signs ideal model delta sigma weight residual False -2.48 -2.00 -0.47 2.00e-01 2.50e+01 5.60e+00 chirality pdb=" C3' U 12557 " pdb=" C4' U 12557 " pdb=" O3' U 12557 " pdb=" C2' U 12557 " both_signs ideal model delta sigma weight residual False -2.48 -2.05 -0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" C3' A 1 254 " pdb=" C4' A 1 254 " pdb=" O3' A 1 254 " pdb=" C2' A 1 254 " both_signs ideal model delta sigma weight residual False -2.48 -2.06 -0.42 2.00e-01 2.50e+01 4.39e+00 ... (remaining 17120 not shown) Planarity restraints: 6394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 102 " 0.023 2.00e-02 2.50e+03 4.70e-02 2.21e+01 pdb=" C LEU A 102 " -0.081 2.00e-02 2.50e+03 pdb=" O LEU A 102 " 0.030 2.00e-02 2.50e+03 pdb=" N ARG A 103 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 1 254 " -0.038 2.00e-02 2.50e+03 2.29e-02 1.44e+01 pdb=" N9 A 1 254 " 0.064 2.00e-02 2.50e+03 pdb=" C8 A 1 254 " -0.011 2.00e-02 2.50e+03 pdb=" N7 A 1 254 " -0.004 2.00e-02 2.50e+03 pdb=" C5 A 1 254 " -0.005 2.00e-02 2.50e+03 pdb=" C6 A 1 254 " -0.005 2.00e-02 2.50e+03 pdb=" N6 A 1 254 " -0.002 2.00e-02 2.50e+03 pdb=" N1 A 1 254 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A 1 254 " -0.002 2.00e-02 2.50e+03 pdb=" N3 A 1 254 " 0.002 2.00e-02 2.50e+03 pdb=" C4 A 1 254 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 12850 " -0.036 2.00e-02 2.50e+03 1.83e-02 1.00e+01 pdb=" N9 G 12850 " 0.050 2.00e-02 2.50e+03 pdb=" C8 G 12850 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G 12850 " -0.006 2.00e-02 2.50e+03 pdb=" C5 G 12850 " -0.005 2.00e-02 2.50e+03 pdb=" C6 G 12850 " -0.005 2.00e-02 2.50e+03 pdb=" O6 G 12850 " -0.002 2.00e-02 2.50e+03 pdb=" N1 G 12850 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G 12850 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G 12850 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G 12850 " 0.005 2.00e-02 2.50e+03 pdb=" C4 G 12850 " 0.004 2.00e-02 2.50e+03 ... (remaining 6391 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 323 2.54 - 3.13: 54782 3.13 - 3.72: 136283 3.72 - 4.31: 216780 4.31 - 4.90: 289772 Nonbonded interactions: 697940 Sorted by model distance: nonbonded pdb=" OG1 THR a 68 " pdb=" OP2 A 2 48 " model vdw 1.951 3.040 nonbonded pdb=" O2' A 2 46 " pdb=" O4' C 2 47 " model vdw 1.962 3.040 nonbonded pdb=" OP1 C 11865 " pdb=" O2' A 11954 " model vdw 1.996 3.040 nonbonded pdb=" O2' G 1 101 " pdb=" OP2 A 1 102 " model vdw 2.013 3.040 nonbonded pdb=" O2' A 1 229 " pdb=" OP1 A 1 230 " model vdw 2.035 3.040 ... (remaining 697935 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.00 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: 5.800 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: 0.110 Extract box with map and model: 2.450 Check model and map are aligned: 0.470 Set scattering table: 0.570 Process input model: 218.960 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.260 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: 0.030 Load rotamer database and sin/cos tables:11.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 240.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 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 : 0.003 0.153 88153 Z= 0.197 Angle : 0.495 15.879 132807 Z= 0.356 Chirality : 0.034 0.473 17123 Planarity : 0.003 0.047 6394 Dihedral : 23.041 179.997 51513 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.31 % Allowed : 25.63 % Favored : 72.06 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 1.15 % 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: -3.39 (0.14), residues: 2590 helix: -2.86 (0.17), residues: 596 sheet: -1.39 (0.21), residues: 546 loop : -2.35 (0.13), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 213 HIS 0.004 0.001 HIS V 133 PHE 0.012 0.001 PHE A 76 TYR 0.007 0.001 TYR F 71 ARG 0.004 0.000 ARG O 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 460 time to evaluate : 3.133 Fit side-chains revert: symmetry clash REVERT: A 12 LYS cc_start: 0.7808 (ttpt) cc_final: 0.7459 (ttpt) REVERT: A 14 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7659 (mt0) REVERT: C 41 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8723 (tttt) REVERT: D 6 GLU cc_start: 0.6425 (tt0) cc_final: 0.6035 (tp30) REVERT: D 71 ILE cc_start: 0.8046 (mt) cc_final: 0.7767 (mp) REVERT: F 4 ARG cc_start: 0.6831 (ttp-170) cc_final: 0.6414 (ttm170) REVERT: G 4 LYS cc_start: 0.6312 (mttt) cc_final: 0.5693 (pptt) REVERT: G 7 ASP cc_start: 0.6802 (p0) cc_final: 0.6481 (p0) REVERT: J 14 THR cc_start: 0.7940 (m) cc_final: 0.7696 (p) REVERT: J 20 HIS cc_start: 0.7328 (t-90) cc_final: 0.7084 (t70) REVERT: M 5 GLN cc_start: 0.7561 (tt0) cc_final: 0.7235 (tp40) REVERT: M 29 LYS cc_start: 0.6635 (OUTLIER) cc_final: 0.5709 (mptt) REVERT: P 10 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8547 (ttmm) REVERT: V 9 GLU cc_start: 0.6373 (tt0) cc_final: 0.6158 (tp30) REVERT: V 80 ASN cc_start: 0.7706 (m-40) cc_final: 0.7305 (m-40) REVERT: W 30 ARG cc_start: 0.8308 (ttt180) cc_final: 0.8072 (ttt180) REVERT: Y 45 ARG cc_start: 0.7104 (mtp85) cc_final: 0.6735 (mtt90) REVERT: Y 63 LYS cc_start: 0.6704 (mmmm) cc_final: 0.6432 (mtpp) REVERT: Y 116 GLU cc_start: 0.6999 (tp30) cc_final: 0.6796 (tp30) REVERT: Z 89 ILE cc_start: 0.8098 (mm) cc_final: 0.7482 (mt) outliers start: 51 outliers final: 14 residues processed: 499 average time/residue: 1.7876 time to fit residues: 1165.6897 Evaluate side-chains 386 residues out of total 2211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 368 time to evaluate : 3.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain M residue 29 LYS Chi-restraints excluded: chain P residue 10 LYS Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain V residue 74 VAL Chi-restraints excluded: chain Y residue 7 VAL Chi-restraints excluded: chain Z residue 78 THR Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 43 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 535 random chunks: chunk 451 optimal weight: 10.0000 chunk 405 optimal weight: 8.9990 chunk 225 optimal weight: 0.0980 chunk 138 optimal weight: 10.0000 chunk 273 optimal weight: 8.9990 chunk 216 optimal weight: 9.9990 chunk 419 optimal weight: 10.0000 chunk 162 optimal weight: 0.7980 chunk 254 optimal weight: 10.0000 chunk 312 optimal weight: 10.0000 chunk 485 optimal weight: 8.9990 overall best weight: 5.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 61 ASN G 45 GLN L 50 GLN N 45 ASN P 27 ASN V 97 ASN V 131 HIS W 110 ASN X 78 ASN X 81 GLN Z 12 GLN I 86 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 88153 Z= 0.403 Angle : 0.869 9.710 132807 Z= 0.437 Chirality : 0.048 0.365 17123 Planarity : 0.006 0.050 6394 Dihedral : 23.366 176.324 46216 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 8.06 % Allowed : 23.14 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: -2.78 (0.14), residues: 2590 helix: -1.90 (0.18), residues: 650 sheet: -1.01 (0.21), residues: 565 loop : -2.19 (0.13), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 213 HIS 0.011 0.002 HIS R 32 PHE 0.016 0.003 PHE K 30 TYR 0.018 0.003 TYR E 62 ARG 0.009 0.001 ARG X 47 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 340 time to evaluate : 3.198 Fit side-chains REVERT: B 163 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7858 (tt0) REVERT: B 268 LYS cc_start: 0.7452 (OUTLIER) cc_final: 0.6932 (tttm) REVERT: C 97 GLU cc_start: 0.6951 (OUTLIER) cc_final: 0.6279 (mp0) REVERT: C 103 GLU cc_start: 0.5939 (OUTLIER) cc_final: 0.5731 (mt-10) REVERT: D 69 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7637 (tttp) REVERT: D 77 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.7754 (mttt) REVERT: E 27 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8278 (mmtt) REVERT: G 4 LYS cc_start: 0.6706 (mttt) cc_final: 0.5829 (pptt) REVERT: H 26 LYS cc_start: 0.6737 (pttt) cc_final: 0.6340 (ptpt) REVERT: H 70 ILE cc_start: 0.6487 (OUTLIER) cc_final: 0.6114 (pp) REVERT: L 168 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8229 (mmtp) REVERT: P 12 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8354 (tttm) REVERT: V 63 ILE cc_start: 0.8201 (OUTLIER) cc_final: 0.7439 (pp) REVERT: V 94 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.5933 (ttm170) REVERT: V 107 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8146 (mptm) REVERT: V 143 LEU cc_start: 0.7263 (mt) cc_final: 0.7040 (mt) REVERT: W 1 MET cc_start: 0.6289 (tmm) cc_final: 0.5991 (tmm) REVERT: W 3 GLN cc_start: 0.7785 (mt0) cc_final: 0.7554 (mt0) REVERT: W 4 GLN cc_start: 0.6727 (OUTLIER) cc_final: 0.6524 (tm-30) REVERT: X 5 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7271 (mt-10) REVERT: Y 63 LYS cc_start: 0.6935 (mmmm) cc_final: 0.6688 (mtpp) REVERT: Y 111 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7329 (tm-30) REVERT: Z 78 THR cc_start: 0.5328 (OUTLIER) cc_final: 0.4946 (m) REVERT: Z 89 ILE cc_start: 0.8108 (mm) cc_final: 0.7840 (mt) outliers start: 178 outliers final: 88 residues processed: 475 average time/residue: 1.7321 time to fit residues: 1085.5657 Evaluate side-chains 433 residues out of total 2211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 328 time to evaluate : 3.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 268 LYS Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 37 LYS Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 42 LYS Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 89 LYS Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain J residue 8 THR Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 30 PHE Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 114 ASP Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain L residue 168 LYS Chi-restraints excluded: chain L residue 189 ASP Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain P residue 12 LYS Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain Q residue 37 SER Chi-restraints excluded: chain Q residue 53 SER Chi-restraints excluded: chain R residue 7 VAL Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain S residue 123 LEU Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain S residue 175 VAL Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain S residue 195 THR Chi-restraints excluded: chain V residue 9 GLU Chi-restraints excluded: chain V residue 18 VAL Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 74 VAL Chi-restraints excluded: chain V residue 94 ARG Chi-restraints excluded: chain V residue 107 LYS Chi-restraints excluded: chain V residue 112 SER Chi-restraints excluded: chain W residue 2 ILE Chi-restraints excluded: chain W residue 4 GLN Chi-restraints excluded: chain X residue 5 GLU Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 122 THR Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 28 THR Chi-restraints excluded: chain Y residue 39 THR Chi-restraints excluded: chain Y residue 43 THR Chi-restraints excluded: chain Y residue 111 GLU Chi-restraints excluded: chain Y residue 129 THR Chi-restraints excluded: chain Z residue 11 ASP Chi-restraints excluded: chain Z residue 32 THR Chi-restraints excluded: chain Z residue 40 VAL Chi-restraints excluded: chain Z residue 42 SER Chi-restraints excluded: chain Z residue 69 VAL Chi-restraints excluded: chain Z residue 71 ILE Chi-restraints excluded: chain Z residue 78 THR Chi-restraints excluded: chain Z residue 91 GLU Chi-restraints excluded: chain Z residue 94 THR Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain a residue 68 THR Chi-restraints excluded: chain a residue 82 LYS Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 43 SER Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 88 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 535 random chunks: chunk 270 optimal weight: 8.9990 chunk 150 optimal weight: 5.9990 chunk 404 optimal weight: 7.9990 chunk 330 optimal weight: 7.9990 chunk 134 optimal weight: 2.9990 chunk 486 optimal weight: 8.9990 chunk 525 optimal weight: 9.9990 chunk 433 optimal weight: 9.9990 chunk 482 optimal weight: 8.9990 chunk 165 optimal weight: 9.9990 chunk 390 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS B 44 ASN B 128 ASN F 73 ASN G 44 HIS G 45 GLN P 13 HIS Q 31 HIS V 97 ASN X 81 GLN Z 12 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 88153 Z= 0.479 Angle : 0.957 11.344 132807 Z= 0.475 Chirality : 0.051 0.401 17123 Planarity : 0.007 0.058 6394 Dihedral : 23.640 176.000 46196 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 9.60 % Allowed : 22.83 % Favored : 67.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: -2.69 (0.14), residues: 2590 helix: -1.83 (0.18), residues: 651 sheet: -0.95 (0.21), residues: 570 loop : -2.14 (0.14), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 213 HIS 0.009 0.002 HIS R 32 PHE 0.016 0.003 PHE K 30 TYR 0.018 0.003 TYR E 62 ARG 0.009 0.001 ARG X 47 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 2211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 337 time to evaluate : 3.324 Fit side-chains REVERT: A 84 GLU cc_start: 0.5914 (OUTLIER) cc_final: 0.5632 (tt0) REVERT: A 115 ILE cc_start: 0.6165 (OUTLIER) cc_final: 0.5844 (pp) REVERT: B 163 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7912 (tt0) REVERT: B 268 LYS cc_start: 0.7477 (OUTLIER) cc_final: 0.6935 (tttm) REVERT: C 51 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.8217 (mtt90) REVERT: C 78 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7187 (mtt-85) REVERT: C 97 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6351 (mp0) REVERT: C 101 SER cc_start: 0.7143 (OUTLIER) cc_final: 0.6910 (m) REVERT: C 103 GLU cc_start: 0.5909 (OUTLIER) cc_final: 0.5704 (mt-10) REVERT: D 69 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7611 (tttp) REVERT: D 77 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.7817 (mttt) REVERT: D 78 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8070 (ptp-170) REVERT: E 27 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8255 (mmtt) REVERT: F 9 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.7169 (mtm-85) REVERT: F 18 GLU cc_start: 0.4955 (OUTLIER) cc_final: 0.4698 (mm-30) REVERT: G 4 LYS cc_start: 0.6652 (mttt) cc_final: 0.5816 (pptt) REVERT: G 17 LYS cc_start: 0.7773 (OUTLIER) cc_final: 0.7266 (ttmt) REVERT: G 41 MET cc_start: 0.6797 (OUTLIER) cc_final: 0.5868 (pp-130) REVERT: L 123 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7436 (mtpp) REVERT: L 198 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7519 (ttmt) REVERT: N 21 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7535 (ttmt) REVERT: O 47 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6044 (tt0) REVERT: P 12 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8401 (tttm) REVERT: Q 43 GLN cc_start: 0.8994 (OUTLIER) cc_final: 0.8576 (mt0) REVERT: R 8 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7896 (pttp) REVERT: R 24 MET cc_start: 0.8392 (mtp) cc_final: 0.8038 (mtt) REVERT: S 157 GLU cc_start: 0.6627 (OUTLIER) cc_final: 0.6267 (mt-10) REVERT: V 63 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.7587 (pp) REVERT: V 94 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.5930 (ttm170) REVERT: V 107 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8508 (mptm) REVERT: V 143 LEU cc_start: 0.7361 (mt) cc_final: 0.7086 (mt) REVERT: W 3 GLN cc_start: 0.7813 (mt0) cc_final: 0.7601 (mt0) REVERT: W 4 GLN cc_start: 0.6672 (OUTLIER) cc_final: 0.6391 (tm-30) REVERT: W 81 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7052 (pt0) REVERT: X 5 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7303 (mt-10) REVERT: X 10 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.6617 (tp30) REVERT: Z 34 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7205 (tp30) REVERT: Z 66 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7417 (tp) REVERT: Z 89 ILE cc_start: 0.8128 (mm) cc_final: 0.7847 (mt) REVERT: I 19 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7366 (tptp) outliers start: 212 outliers final: 114 residues processed: 498 average time/residue: 1.7354 time to fit residues: 1145.3156 Evaluate side-chains 474 residues out of total 2211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 325 time to evaluate : 3.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 268 LYS Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 51 ARG Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 37 LYS Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 72 LYS Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain F residue 9 ARG Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 17 LYS Chi-restraints excluded: chain G residue 41 MET Chi-restraints excluded: chain G residue 42 LYS Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 89 LYS Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain J residue 8 THR Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 48 LYS Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 3 LYS Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 55 ASP Chi-restraints excluded: chain L residue 61 LYS Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 95 ASP Chi-restraints excluded: chain L residue 106 SER Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 114 ASP Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain L residue 123 LYS Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain L residue 189 ASP Chi-restraints excluded: chain L residue 198 LYS Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain N residue 21 LYS Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 47 GLU Chi-restraints excluded: chain P residue 12 LYS Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain Q residue 37 SER Chi-restraints excluded: chain Q residue 43 GLN Chi-restraints excluded: chain Q residue 53 SER Chi-restraints excluded: chain R residue 7 VAL Chi-restraints excluded: chain R residue 8 LYS Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain S residue 123 LEU Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain S residue 143 LEU Chi-restraints excluded: chain S residue 157 GLU Chi-restraints excluded: chain S residue 175 VAL Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain S residue 195 THR Chi-restraints excluded: chain V residue 18 VAL Chi-restraints excluded: chain V residue 35 SER Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 74 VAL Chi-restraints excluded: chain V residue 94 ARG Chi-restraints excluded: chain V residue 107 LYS Chi-restraints excluded: chain W residue 2 ILE Chi-restraints excluded: chain W residue 4 GLN Chi-restraints excluded: chain W residue 28 SER Chi-restraints excluded: chain W residue 81 GLU Chi-restraints excluded: chain X residue 5 GLU Chi-restraints excluded: chain X residue 10 GLU Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 122 THR Chi-restraints excluded: chain X residue 144 GLU Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 28 THR Chi-restraints excluded: chain Y residue 39 THR Chi-restraints excluded: chain Y residue 43 THR Chi-restraints excluded: chain Y residue 94 ILE Chi-restraints excluded: chain Y residue 129 THR Chi-restraints excluded: chain Z residue 11 ASP Chi-restraints excluded: chain Z residue 32 THR Chi-restraints excluded: chain Z residue 34 GLU Chi-restraints excluded: chain Z residue 40 VAL Chi-restraints excluded: chain Z residue 42 SER Chi-restraints excluded: chain Z residue 65 THR Chi-restraints excluded: chain Z residue 66 LEU Chi-restraints excluded: chain Z residue 69 VAL Chi-restraints excluded: chain Z residue 72 LEU Chi-restraints excluded: chain Z residue 91 GLU Chi-restraints excluded: chain Z residue 94 THR Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain a residue 82 LYS Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 43 SER Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 88 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 535 random chunks: chunk 480 optimal weight: 7.9990 chunk 365 optimal weight: 8.9990 chunk 252 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 chunk 232 optimal weight: 0.5980 chunk 326 optimal weight: 7.9990 chunk 488 optimal weight: 7.9990 chunk 517 optimal weight: 10.0000 chunk 255 optimal weight: 9.9990 chunk 462 optimal weight: 9.9990 chunk 139 optimal weight: 6.9990 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 ASN F 73 ASN ** G 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 45 GLN R 32 HIS S 46 GLN X 81 GLN Z 12 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 88153 Z= 0.355 Angle : 0.802 9.733 132807 Z= 0.407 Chirality : 0.045 0.368 17123 Planarity : 0.006 0.059 6394 Dihedral : 23.396 176.229 46194 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 9.47 % Allowed : 24.23 % Favored : 66.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: -2.47 (0.14), residues: 2590 helix: -1.54 (0.18), residues: 656 sheet: -0.82 (0.21), residues: 551 loop : -2.06 (0.14), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 213 HIS 0.007 0.002 HIS a 15 PHE 0.017 0.002 PHE K 30 TYR 0.021 0.002 TYR Y 57 ARG 0.006 0.001 ARG J 28 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 336 time to evaluate : 3.191 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 GLU cc_start: 0.5977 (OUTLIER) cc_final: 0.5721 (tt0) REVERT: A 115 ILE cc_start: 0.6234 (OUTLIER) cc_final: 0.5896 (pp) REVERT: B 163 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7850 (tt0) REVERT: B 247 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.7860 (mmp) REVERT: B 268 LYS cc_start: 0.7484 (OUTLIER) cc_final: 0.7008 (tttm) REVERT: C 78 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7111 (mtt-85) REVERT: C 101 SER cc_start: 0.7127 (OUTLIER) cc_final: 0.6897 (m) REVERT: C 103 GLU cc_start: 0.5934 (OUTLIER) cc_final: 0.5713 (mt-10) REVERT: D 77 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.7782 (mttt) REVERT: D 78 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.8125 (ptp-170) REVERT: F 4 ARG cc_start: 0.6805 (ttp-170) cc_final: 0.6443 (ttm170) REVERT: F 16 SER cc_start: 0.8253 (OUTLIER) cc_final: 0.7847 (t) REVERT: F 18 GLU cc_start: 0.4925 (OUTLIER) cc_final: 0.4707 (mm-30) REVERT: G 4 LYS cc_start: 0.6547 (mttt) cc_final: 0.5649 (pptt) REVERT: G 17 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7551 (ttmt) REVERT: H 19 LYS cc_start: 0.6680 (mtpp) cc_final: 0.6376 (mtpp) REVERT: H 26 LYS cc_start: 0.6539 (mtmt) cc_final: 0.6200 (ptpt) REVERT: H 37 LYS cc_start: 0.5298 (OUTLIER) cc_final: 0.4835 (mtmt) REVERT: H 70 ILE cc_start: 0.6755 (OUTLIER) cc_final: 0.6319 (pp) REVERT: L 123 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7454 (mtpp) REVERT: L 198 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7491 (ttmt) REVERT: O 47 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6034 (tt0) REVERT: R 8 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7822 (pttp) REVERT: S 19 LEU cc_start: 0.0962 (OUTLIER) cc_final: -0.0279 (mm) REVERT: V 63 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7533 (pp) REVERT: V 107 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.7852 (mptm) REVERT: V 143 LEU cc_start: 0.7278 (mt) cc_final: 0.7034 (mt) REVERT: W 1 MET cc_start: 0.6226 (tmm) cc_final: 0.5949 (tmm) REVERT: W 4 GLN cc_start: 0.6627 (OUTLIER) cc_final: 0.6291 (tm-30) REVERT: W 81 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.7104 (pt0) REVERT: W 105 GLU cc_start: 0.7190 (mp0) cc_final: 0.6933 (mp0) REVERT: X 5 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7280 (mt-10) REVERT: X 10 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6566 (tp30) REVERT: Y 63 LYS cc_start: 0.6826 (mmmm) cc_final: 0.6566 (mtpp) REVERT: Y 111 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7325 (tm-30) REVERT: Z 34 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7142 (tp30) REVERT: Z 66 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7358 (tp) REVERT: Z 89 ILE cc_start: 0.8132 (mm) cc_final: 0.7622 (mt) REVERT: I 19 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7358 (tptp) outliers start: 209 outliers final: 120 residues processed: 487 average time/residue: 1.7462 time to fit residues: 1127.6100 Evaluate side-chains 477 residues out of total 2211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 327 time to evaluate : 3.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 268 LYS Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 37 LYS Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 72 LYS Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain G residue 17 LYS Chi-restraints excluded: chain G residue 42 LYS Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 89 LYS Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 37 LYS Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain J residue 8 THR Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain L residue 3 LYS Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 61 LYS Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 95 ASP Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 114 ASP Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain L residue 123 LYS Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 198 LYS Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain N residue 33 CYS Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 47 GLU Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain Q residue 37 SER Chi-restraints excluded: chain Q residue 53 SER Chi-restraints excluded: chain R residue 7 VAL Chi-restraints excluded: chain R residue 8 LYS Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain S residue 123 LEU Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain S residue 143 LEU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain S residue 175 VAL Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain S residue 195 THR Chi-restraints excluded: chain V residue 4 THR Chi-restraints excluded: chain V residue 18 VAL Chi-restraints excluded: chain V residue 35 SER Chi-restraints excluded: chain V residue 40 LYS Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 74 VAL Chi-restraints excluded: chain V residue 94 ARG Chi-restraints excluded: chain V residue 107 LYS Chi-restraints excluded: chain V residue 112 SER Chi-restraints excluded: chain W residue 2 ILE Chi-restraints excluded: chain W residue 4 GLN Chi-restraints excluded: chain W residue 34 ASN Chi-restraints excluded: chain W residue 81 GLU Chi-restraints excluded: chain W residue 120 GLU Chi-restraints excluded: chain X residue 5 GLU Chi-restraints excluded: chain X residue 10 GLU Chi-restraints excluded: chain X residue 69 ILE Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 122 THR Chi-restraints excluded: chain X residue 144 GLU Chi-restraints excluded: chain Y residue 28 THR Chi-restraints excluded: chain Y residue 39 THR Chi-restraints excluded: chain Y residue 43 THR Chi-restraints excluded: chain Y residue 111 GLU Chi-restraints excluded: chain Y residue 129 THR Chi-restraints excluded: chain Z residue 3 TYR Chi-restraints excluded: chain Z residue 11 ASP Chi-restraints excluded: chain Z residue 32 THR Chi-restraints excluded: chain Z residue 34 GLU Chi-restraints excluded: chain Z residue 40 VAL Chi-restraints excluded: chain Z residue 42 SER Chi-restraints excluded: chain Z residue 65 THR Chi-restraints excluded: chain Z residue 66 LEU Chi-restraints excluded: chain Z residue 69 VAL Chi-restraints excluded: chain Z residue 78 THR Chi-restraints excluded: chain Z residue 91 GLU Chi-restraints excluded: chain Z residue 94 THR Chi-restraints excluded: chain Z residue 97 GLN Chi-restraints excluded: chain Z residue 118 ILE Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain a residue 82 LYS Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 88 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.858 > 50: distance: 0 - 1: 14.172 distance: 1 - 2: 18.046 distance: 1 - 4: 20.360 distance: 2 - 3: 23.494 distance: 2 - 8: 12.099 distance: 4 - 5: 15.809 distance: 5 - 6: 9.239 distance: 6 - 7: 14.209 distance: 8 - 9: 14.222 distance: 9 - 10: 16.188 distance: 9 - 12: 10.559 distance: 10 - 11: 14.946 distance: 10 - 16: 39.587 distance: 12 - 13: 21.714 distance: 13 - 14: 19.245 distance: 13 - 15: 10.668 distance: 16 - 17: 32.129 distance: 17 - 18: 21.528 distance: 17 - 20: 26.342 distance: 18 - 19: 21.804 distance: 18 - 24: 33.540 distance: 20 - 21: 30.267 distance: 21 - 22: 42.590 distance: 21 - 23: 33.275 distance: 24 - 25: 19.561 distance: 24 - 30: 31.500 distance: 25 - 26: 27.162 distance: 25 - 28: 30.883 distance: 26 - 27: 10.218 distance: 26 - 31: 24.982 distance: 28 - 29: 33.283 distance: 29 - 30: 7.765 distance: 31 - 32: 14.679 distance: 32 - 33: 31.276 distance: 32 - 35: 29.807 distance: 33 - 34: 9.008 distance: 33 - 40: 22.138 distance: 35 - 36: 6.982 distance: 36 - 37: 5.771 distance: 37 - 38: 16.864 distance: 38 - 39: 25.589 distance: 40 - 41: 11.669 distance: 41 - 42: 38.759 distance: 41 - 44: 14.063 distance: 42 - 43: 9.413 distance: 42 - 51: 11.681 distance: 44 - 45: 15.949 distance: 45 - 46: 24.832 distance: 46 - 47: 14.691 distance: 47 - 48: 21.050 distance: 48 - 49: 28.390 distance: 48 - 50: 27.957 distance: 51 - 52: 16.709 distance: 52 - 53: 20.714 distance: 52 - 55: 17.414 distance: 53 - 54: 7.158 distance: 53 - 58: 11.020 distance: 55 - 56: 14.155 distance: 55 - 57: 12.087 distance: 58 - 59: 19.766 distance: 59 - 60: 25.470 distance: 59 - 62: 11.527 distance: 60 - 61: 15.716 distance: 60 - 67: 20.467 distance: 62 - 63: 12.657 distance: 63 - 64: 15.736 distance: 64 - 65: 3.846 distance: 65 - 66: 9.993 distance: 67 - 68: 9.616 distance: 68 - 69: 6.979 distance: 68 - 71: 10.005 distance: 69 - 70: 10.445 distance: 69 - 79: 20.534 distance: 71 - 72: 9.800 distance: 72 - 73: 3.251 distance: 72 - 74: 8.539 distance: 73 - 75: 8.167 distance: 74 - 76: 10.569 distance: 75 - 77: 9.107 distance: 76 - 77: 4.812 distance: 77 - 78: 6.255