Starting phenix.real_space_refine (version: dev) on Fri Dec 16 23:31:43 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i0y_0322/12_2022/6i0y_0322.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i0y_0322/12_2022/6i0y_0322.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i0y_0322/12_2022/6i0y_0322.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i0y_0322/12_2022/6i0y_0322.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i0y_0322/12_2022/6i0y_0322.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i0y_0322/12_2022/6i0y_0322.pdb" } resolution = 3.2 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= 0.011 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 "h ARG 6": "NH1" <-> "NH2" Residue "h ARG 7": "NH1" <-> "NH2" Residue "h ARG 82": "NH1" <-> "NH2" Residue "h ARG 86": "NH1" <-> "NH2" Residue "h ARG 94": "NH1" <-> "NH2" Residue "7 ASP 16": "OD1" <-> "OD2" Residue "J TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 93619 Number of models: 1 Model: "" Number of chains: 48 Chain: "h" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "0" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "1" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 409 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "2" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "3" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "4" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "5" Number of atoms: 1117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1117 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 5, 'TRANS': 142} Chain: "6" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 227 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "7" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 139 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 1, 'TRANS': 14} Chain: "8" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "A" Number of atoms: 61274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2854, 61274 Classifications: {'RNA': 2854} Modifications used: {'rna2p_pur': 268, 'rna2p_pyr': 144, 'rna3p_pur': 1380, 'rna3p_pyr': 1062} Link IDs: {'rna2p': 412, 'rna3p': 2441} Chain breaks: 3 Chain: "B" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2529 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 6, 'rna3p_pur': 56, 'rna3p_pyr': 48} Link IDs: {'rna2p': 14, 'rna3p': 103} Chain: "C" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "D" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "F" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "G" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1313 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 8, 'TRANS': 166} Chain: "H" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 384 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "I" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1032 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "K" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "M" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "N" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "T" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "V" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1649 Classifications: {'RNA': 77} Modifications used: {'p5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 33, 'rna3p_pyr': 32} Link IDs: {'rna2p': 11, 'rna3p': 65} Chain: "W" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 596 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "X" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "Z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "z" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 688 Classifications: {'peptide': 89} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 84} Chain: "4" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 151 Unusual residues: {' MG': 136} Classifications: {'peptide': 1, 'undetermined': 136} Modifications used: {'COO': 1} Link IDs: {None: 136} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 415 Classifications: {'water': 415} Link IDs: {None: 414} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "L" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2598 SG CYS 4 11 117.476 81.135 174.955 1.00 27.97 S ATOM 2623 SG CYS 4 14 116.674 82.419 173.551 1.00 12.31 S ATOM 2726 SG CYS 4 27 118.523 82.794 174.395 1.00 25.55 S Time building chain proxies: 39.21, per 1000 atoms: 0.42 Number of scatterers: 93619 At special positions: 0 Unit cell: (201.4, 213.06, 260.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 93 16.00 P 3049 15.00 Mg 143 11.99 O 26533 8.00 N 17294 7.00 C 46506 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 Atom "ATOM 89722 O4' C V 56 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 41.78 Conformation dependent library (CDL) restraints added in 3.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 4 102 " pdb="ZN ZN 4 102 " - pdb=" SG CYS 4 11 " pdb="ZN ZN 4 102 " - pdb=" ND1 HIS 4 33 " pdb="ZN ZN 4 102 " - pdb=" SG CYS 4 27 " pdb="ZN ZN 4 102 " - pdb=" SG CYS 4 14 " Number of angles added : 3 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6490 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 53 sheets defined 29.2% alpha, 13.6% beta 984 base pairs and 1493 stacking pairs defined. Time for finding SS restraints: 32.00 Creating SS restraints... Processing helix chain '0' and resid 8 through 16 Processing helix chain '0' and resid 17 through 19 No H-bonds generated for 'chain '0' and resid 17 through 19' Processing helix chain '2' and resid 8 through 17 Processing helix chain '2' and resid 17 through 23 Processing helix chain '2' and resid 24 through 37 Processing helix chain '3' and resid 6 through 11 removed outlier: 3.551A pdb=" N ALA 3 10 " --> pdb=" O VAL 3 6 " (cutoff:3.500A) Processing helix chain '3' and resid 36 through 43 Processing helix chain '3' and resid 53 through 61 Processing helix chain '4' and resid 30 through 34 Processing helix chain '5' and resid 3 through 8 Processing helix chain '5' and resid 8 through 19 removed outlier: 3.708A pdb=" N SER 5 16 " --> pdb=" O VAL 5 12 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU 5 17 " --> pdb=" O ALA 5 13 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL 5 18 " --> pdb=" O GLU 5 14 " (cutoff:3.500A) Processing helix chain '5' and resid 33 through 47 removed outlier: 4.190A pdb=" N LYS 5 37 " --> pdb=" O VAL 5 33 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU 5 40 " --> pdb=" O ASP 5 36 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG 5 42 " --> pdb=" O MET 5 38 " (cutoff:3.500A) Processing helix chain '5' and resid 59 through 64 Processing helix chain '5' and resid 94 through 104 removed outlier: 3.665A pdb=" N PHE 5 99 " --> pdb=" O LEU 5 95 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA 5 100 " --> pdb=" O PHE 5 96 " (cutoff:3.500A) Processing helix chain '5' and resid 133 through 138 removed outlier: 3.890A pdb=" N ILE 5 136 " --> pdb=" O GLU 5 133 " (cutoff:3.500A) Processing helix chain '5' and resid 139 through 148 removed outlier: 3.737A pdb=" N MET 5 143 " --> pdb=" O LEU 5 139 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU 5 145 " --> pdb=" O ALA 5 141 " (cutoff:3.500A) Processing helix chain '6' and resid 3 through 7 Processing helix chain '6' and resid 15 through 20 Processing helix chain '6' and resid 24 through 29 removed outlier: 3.885A pdb=" N GLU 6 28 " --> pdb=" O SER 6 24 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS 6 29 " --> pdb=" O ALA 6 25 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 24 through 29' Processing helix chain '7' and resid 11 through 16 Processing helix chain '7' and resid 16 through 22 removed outlier: 3.898A pdb=" N HIS 7 22 " --> pdb=" O LYS 7 18 " (cutoff:3.500A) Processing helix chain '8' and resid 13 through 23 Processing helix chain '8' and resid 44 through 52 Processing helix chain '8' and resid 54 through 59 removed outlier: 3.744A pdb=" N SER 8 58 " --> pdb=" O ALA 8 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 130 through 134 Processing helix chain 'C' and resid 197 through 202 Processing helix chain 'C' and resid 206 through 212 removed outlier: 4.147A pdb=" N ALA C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 224 Processing helix chain 'C' and resid 262 through 264 No H-bonds generated for 'chain 'C' and resid 262 through 264' Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 61 through 70 removed outlier: 3.502A pdb=" N LYS D 70 " --> pdb=" O GLY D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 102 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 24 through 37 removed outlier: 3.592A pdb=" N VAL E 31 " --> pdb=" O LEU E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 113 Processing helix chain 'E' and resid 130 through 142 removed outlier: 3.623A pdb=" N LEU E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 160 Processing helix chain 'E' and resid 176 through 183 removed outlier: 3.548A pdb=" N ILE E 181 " --> pdb=" O PRO E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 200 removed outlier: 3.584A pdb=" N LYS E 194 " --> pdb=" O ALA E 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 9 Processing helix chain 'F' and resid 11 through 20 removed outlier: 3.600A pdb=" N THR F 17 " --> pdb=" O LYS F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 27 Processing helix chain 'F' and resid 40 through 44 removed outlier: 3.903A pdb=" N ALA F 44 " --> pdb=" O GLU F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 60 removed outlier: 3.907A pdb=" N ASP F 50 " --> pdb=" O LYS F 46 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN F 51 " --> pdb=" O LYS F 47 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA F 52 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 105 Processing helix chain 'F' and resid 133 through 137 removed outlier: 4.246A pdb=" N ILE F 136 " --> pdb=" O GLU F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 145 Processing helix chain 'F' and resid 161 through 171 Processing helix chain 'G' and resid 61 through 81 Processing helix chain 'G' and resid 136 through 150 removed outlier: 3.578A pdb=" N TYR G 150 " --> pdb=" O ASP G 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 13 Processing helix chain 'H' and resid 22 through 29 Processing helix chain 'H' and resid 30 through 34 Processing helix chain 'I' and resid 23 through 28 removed outlier: 3.619A pdb=" N LEU I 27 " --> pdb=" O GLY I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 37 removed outlier: 3.920A pdb=" N PHE I 37 " --> pdb=" O ILE I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 44 Processing helix chain 'I' and resid 106 through 111 Processing helix chain 'I' and resid 112 through 116 removed outlier: 3.636A pdb=" N ASP I 115 " --> pdb=" O LYS I 112 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N MET I 116 " --> pdb=" O ALA I 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 112 through 116' Processing helix chain 'I' and resid 122 through 132 removed outlier: 3.928A pdb=" N ILE I 128 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLY I 130 " --> pdb=" O ARG I 126 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 11 removed outlier: 3.777A pdb=" N VAL J 11 " --> pdb=" O PRO J 8 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 38 removed outlier: 3.892A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 62 Processing helix chain 'J' and resid 67 through 72 Processing helix chain 'J' and resid 88 through 95 Processing helix chain 'J' and resid 98 through 107 Processing helix chain 'J' and resid 112 through 120 removed outlier: 3.572A pdb=" N ARG J 120 " --> pdb=" O ARG J 116 " (cutoff:3.500A) Processing helix chain 'J' and resid 132 through 136 Processing helix chain 'K' and resid 71 through 75 removed outlier: 3.812A pdb=" N GLY K 74 " --> pdb=" O ARG K 71 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER K 75 " --> pdb=" O PRO K 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 71 through 75' Processing helix chain 'K' and resid 104 through 108 Processing helix chain 'K' and resid 112 through 118 Processing helix chain 'L' and resid 21 through 26 removed outlier: 4.404A pdb=" N SER L 25 " --> pdb=" O ARG L 21 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLY L 26 " --> pdb=" O GLY L 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 21 through 26' Processing helix chain 'L' and resid 56 through 61 Processing helix chain 'L' and resid 70 through 72 No H-bonds generated for 'chain 'L' and resid 70 through 72' Processing helix chain 'L' and resid 82 through 86 removed outlier: 4.379A pdb=" N GLU L 86 " --> pdb=" O ALA L 83 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 137 Processing helix chain 'M' and resid 43 through 58 removed outlier: 3.873A pdb=" N ALA M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL M 57 " --> pdb=" O MET M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 122 removed outlier: 3.650A pdb=" N GLU M 115 " --> pdb=" O GLU M 111 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 32 Processing helix chain 'N' and resid 38 through 56 removed outlier: 3.528A pdb=" N ARG N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 59 through 69 removed outlier: 3.564A pdb=" N ARG N 63 " --> pdb=" O SER N 59 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 82 removed outlier: 4.466A pdb=" N PHE N 80 " --> pdb=" O VAL N 76 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN N 81 " --> pdb=" O ALA N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 87 Processing helix chain 'O' and resid 4 through 22 removed outlier: 4.274A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 60 Processing helix chain 'O' and resid 67 through 85 removed outlier: 3.552A pdb=" N ALA O 79 " --> pdb=" O GLY O 75 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU O 80 " --> pdb=" O LYS O 76 " (cutoff:3.500A) Processing helix chain 'O' and resid 103 through 113 removed outlier: 5.069A pdb=" N ALA O 109 " --> pdb=" O ALA O 105 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 10 removed outlier: 4.125A pdb=" N GLN P 6 " --> pdb=" O ASN P 2 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU P 7 " --> pdb=" O ILE P 3 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N GLU P 8 " --> pdb=" O ILE P 4 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 55 Processing helix chain 'P' and resid 77 through 81 Processing helix chain 'P' and resid 96 through 102 Processing helix chain 'P' and resid 103 through 107 Processing helix chain 'Q' and resid 6 through 20 removed outlier: 3.726A pdb=" N ARG Q 10 " --> pdb=" O GLY Q 6 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN Q 19 " --> pdb=" O LYS Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 Processing helix chain 'Q' and resid 30 through 71 removed outlier: 4.149A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 85 Processing helix chain 'Q' and resid 93 through 95 No H-bonds generated for 'chain 'Q' and resid 93 through 95' Processing helix chain 'Q' and resid 96 through 101 removed outlier: 3.546A pdb=" N PHE Q 100 " --> pdb=" O ASP Q 96 " (cutoff:3.500A) Processing helix chain 'Q' and resid 101 through 117 removed outlier: 3.602A pdb=" N ALA Q 115 " --> pdb=" O LYS Q 111 " (cutoff:3.500A) Processing helix chain 'S' and resid 20 through 24 Processing helix chain 'S' and resid 28 through 38 removed outlier: 3.643A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 62 removed outlier: 3.533A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 24 Processing helix chain 'T' and resid 40 through 50 removed outlier: 3.598A pdb=" N ALA T 46 " --> pdb=" O GLU T 42 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 53 No H-bonds generated for 'chain 'T' and resid 51 through 53' Processing helix chain 'X' and resid 53 through 62 Processing helix chain 'X' and resid 62 through 72 removed outlier: 3.958A pdb=" N LEU X 70 " --> pdb=" O VAL X 66 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG X 71 " --> pdb=" O LEU X 67 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 23 removed outlier: 3.617A pdb=" N LEU Y 14 " --> pdb=" O SER Y 10 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASN Y 15 " --> pdb=" O VAL Y 11 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR Y 16 " --> pdb=" O GLU Y 12 " (cutoff:3.500A) Processing helix chain 'Y' and resid 23 through 34 Processing helix chain 'Y' and resid 40 through 59 removed outlier: 3.956A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL Y 46 " --> pdb=" O LEU Y 42 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG Y 47 " --> pdb=" O LEU Y 43 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ASP Y 49 " --> pdb=" O GLN Y 45 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU Y 57 " --> pdb=" O VAL Y 53 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN Y 58 " --> pdb=" O LYS Y 54 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 40 through 50 Processing helix chain 'Z' and resid 51 through 54 Processing sheet with id=AA1, first strand: chain 'h' and resid 65 through 66 Processing sheet with id=AA2, first strand: chain 'h' and resid 41 through 46 removed outlier: 3.531A pdb=" N GLN h 46 " --> pdb=" O GLY h 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'h' and resid 83 through 88 Processing sheet with id=AA4, first strand: chain '0' and resid 27 through 29 Processing sheet with id=AA5, first strand: chain '0' and resid 47 through 48 removed outlier: 3.611A pdb=" N ARG 0 51 " --> pdb=" O TYR 0 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '1' and resid 19 through 24 Processing sheet with id=AA7, first strand: chain '4' and resid 17 through 19 Processing sheet with id=AA8, first strand: chain '8' and resid 62 through 65 removed outlier: 7.010A pdb=" N ILE 8 4 " --> pdb=" O VAL 8 64 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N ASN 8 5 " --> pdb=" O ASP 8 43 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ASP 8 43 " --> pdb=" O ASN 8 5 " (cutoff:3.500A) removed outlier: 9.163A pdb=" N LYS 8 25 " --> pdb=" O GLN 8 87 " (cutoff:3.500A) removed outlier: 10.115A pdb=" N ILE 8 89 " --> pdb=" O LYS 8 25 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N PHE 8 91 " --> pdb=" O PRO 8 27 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE 8 29 " --> pdb=" O PHE 8 91 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ARG 8 93 " --> pdb=" O ILE 8 29 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N TYR 8 31 " --> pdb=" O ARG 8 93 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLN 8 78 " --> pdb=" O GLN 8 87 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE 8 89 " --> pdb=" O ASP 8 76 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASP 8 76 " --> pdb=" O ILE 8 89 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N PHE 8 91 " --> pdb=" O ALA 8 74 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ALA 8 74 " --> pdb=" O PHE 8 91 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ARG 8 93 " --> pdb=" O VAL 8 72 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL 8 72 " --> pdb=" O ARG 8 93 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=AB1, first strand: chain 'C' and resid 33 through 34 Processing sheet with id=AB2, first strand: chain 'C' and resid 74 through 75 Processing sheet with id=AB3, first strand: chain 'C' and resid 79 through 81 removed outlier: 3.731A pdb=" N ARG C 79 " --> pdb=" O LEU C 92 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 162 through 165 removed outlier: 5.876A pdb=" N ILE C 163 " --> pdb=" O ARG C 174 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ARG C 174 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA C 165 " --> pdb=" O THR C 172 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N MET C 180 " --> pdb=" O VAL C 267 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 12 through 15 Processing sheet with id=AB6, first strand: chain 'D' and resid 12 through 15 Processing sheet with id=AB7, first strand: chain 'D' and resid 33 through 38 removed outlier: 6.560A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N VAL D 37 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ALA D 47 " --> pdb=" O VAL D 37 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 65 through 68 Processing sheet with id=AB9, first strand: chain 'G' and resid 8 through 9 Processing sheet with id=AC1, first strand: chain 'G' and resid 22 through 24 Processing sheet with id=AC2, first strand: chain 'G' and resid 86 through 87 Processing sheet with id=AC3, first strand: chain 'G' and resid 94 through 95 Processing sheet with id=AC4, first strand: chain 'G' and resid 101 through 102 Processing sheet with id=AC5, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AC6, first strand: chain 'I' and resid 58 through 59 removed outlier: 3.564A pdb=" N THR I 67 " --> pdb=" O THR I 59 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 122 through 123 removed outlier: 6.344A pdb=" N TYR J 16 " --> pdb=" O ILE J 55 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N LEU J 57 " --> pdb=" O TYR J 16 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL J 18 " --> pdb=" O LEU J 57 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 75 through 77 Processing sheet with id=AC9, first strand: chain 'K' and resid 92 through 94 removed outlier: 4.938A pdb=" N GLN K 93 " --> pdb=" O ASN K 88 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ILE K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N VAL K 24 " --> pdb=" O ILE K 38 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N CYS K 84 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASN K 9 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LEU K 86 " --> pdb=" O ASN K 9 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 76 through 79 removed outlier: 6.780A pdb=" N ALA P 57 " --> pdb=" O ILE P 49 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ILE P 49 " --> pdb=" O ALA P 57 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR P 59 " --> pdb=" O ILE P 47 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 74 through 76 removed outlier: 3.599A pdb=" N LYS L 109 " --> pdb=" O ALA L 75 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 89 through 91 Processing sheet with id=AD4, first strand: chain 'M' and resid 63 through 65 removed outlier: 3.692A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 39 through 42 Processing sheet with id=AD6, first strand: chain 'M' and resid 74 through 75 removed outlier: 3.960A pdb=" N ASN M 88 " --> pdb=" O GLU M 75 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 33 through 37 Processing sheet with id=AD8, first strand: chain 'O' and resid 47 through 50 removed outlier: 6.726A pdb=" N VAL O 39 " --> pdb=" O LEU O 48 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ALA O 50 " --> pdb=" O ALA O 37 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ALA O 37 " --> pdb=" O ALA O 50 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N HIS O 29 " --> pdb=" O TYR O 36 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'P' and resid 37 through 43 removed outlier: 3.780A pdb=" N SER P 82 " --> pdb=" O LYS P 28 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'R' and resid 11 through 14 removed outlier: 3.686A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLN R 6 " --> pdb=" O VAL R 38 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL R 38 " --> pdb=" O GLN R 6 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'R' and resid 20 through 23 removed outlier: 3.876A pdb=" N ALA R 65 " --> pdb=" O ASP R 95 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'R' and resid 72 through 78 removed outlier: 4.212A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'S' and resid 4 through 11 removed outlier: 5.632A pdb=" N SER S 101 " --> pdb=" O HIS S 9 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N SER S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N VAL S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'S' and resid 82 through 83 Processing sheet with id=AE6, first strand: chain 'S' and resid 86 through 88 removed outlier: 3.548A pdb=" N MET S 86 " --> pdb=" O ASP S 94 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG S 88 " --> pdb=" O ARG S 92 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG S 92 " --> pdb=" O ARG S 88 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'T' and resid 11 through 14 Processing sheet with id=AE8, first strand: chain 'T' and resid 61 through 63 removed outlier: 3.836A pdb=" N LEU T 61 " --> pdb=" O LYS T 82 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'T' and resid 67 through 68 Processing sheet with id=AF1, first strand: chain 'W' and resid 49 through 50 removed outlier: 3.830A pdb=" N VAL W 50 " --> pdb=" O PHE W 59 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE W 59 " --> pdb=" O VAL W 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'W' and resid 65 through 66 Processing sheet with id=AF3, first strand: chain 'X' and resid 12 through 14 Processing sheet with id=AF4, first strand: chain 'X' and resid 35 through 38 Processing sheet with id=AF5, first strand: chain 'Z' and resid 35 through 37 Processing sheet with id=AF6, first strand: chain 'z' and resid 11 through 13 removed outlier: 3.665A pdb=" N LYS z 85 " --> pdb=" O VAL z 11 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL z 13 " --> pdb=" O LYS z 85 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'z' and resid 19 through 24 removed outlier: 3.523A pdb=" N PHE z 21 " --> pdb=" O LEU z 58 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HIS z 56 " --> pdb=" O ILE z 23 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'z' and resid 74 through 75 828 hydrogen bonds defined for protein. 2163 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2475 hydrogen bonds 3952 hydrogen bond angles 0 basepair planarities 984 basepair parallelities 1493 stacking parallelities Total time for adding SS restraints: 178.66 Time building geometry restraints manager: 44.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 7397 1.28 - 1.43: 45735 1.43 - 1.57: 41927 1.57 - 1.72: 6030 1.72 - 1.87: 168 Bond restraints: 101257 Sorted by residual: bond pdb=" CA ARG S 88 " pdb=" C ARG S 88 " ideal model delta sigma weight residual 1.523 1.374 0.149 1.25e-02 6.40e+03 1.43e+02 bond pdb=" CA MET S 86 " pdb=" C MET S 86 " ideal model delta sigma weight residual 1.524 1.389 0.135 1.26e-02 6.30e+03 1.15e+02 bond pdb=" O3' A A2602 " pdb=" P G A2603 " ideal model delta sigma weight residual 1.607 1.486 0.121 1.50e-02 4.44e+03 6.49e+01 bond pdb=" C ASP S 94 " pdb=" O ASP S 94 " ideal model delta sigma weight residual 1.235 1.141 0.094 1.22e-02 6.72e+03 5.88e+01 bond pdb=" C ALA S 89 " pdb=" O ALA S 89 " ideal model delta sigma weight residual 1.234 1.139 0.096 1.28e-02 6.10e+03 5.57e+01 ... (remaining 101252 not shown) Histogram of bond angle deviations from ideal: 54.46 - 72.71: 1 72.71 - 90.95: 2 90.95 - 109.19: 37989 109.19 - 127.43: 107213 127.43 - 145.67: 6624 Bond angle restraints: 151829 Sorted by residual: angle pdb=" C4' G A2608 " pdb=" C3' G A2608 " pdb=" O3' G A2608 " ideal model delta sigma weight residual 113.00 141.45 -28.45 1.50e+00 4.44e-01 3.60e+02 angle pdb=" C MET S 86 " pdb=" N PRO S 87 " pdb=" CD PRO S 87 " ideal model delta sigma weight residual 125.00 54.46 70.54 4.10e+00 5.95e-02 2.96e+02 angle pdb=" N ARG S 88 " pdb=" CA ARG S 88 " pdb=" C ARG S 88 " ideal model delta sigma weight residual 109.41 85.93 23.48 1.52e+00 4.33e-01 2.39e+02 angle pdb=" C4' A A 751 " pdb=" C3' A A 751 " pdb=" O3' A A 751 " ideal model delta sigma weight residual 113.00 135.48 -22.48 1.50e+00 4.44e-01 2.25e+02 angle pdb=" C THR D 151 " pdb=" N PRO D 152 " pdb=" CA PRO D 152 " ideal model delta sigma weight residual 119.19 104.05 15.14 1.06e+00 8.90e-01 2.04e+02 ... (remaining 151824 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.26: 51566 35.26 - 70.52: 2106 70.52 - 105.78: 170 105.78 - 141.04: 17 141.04 - 176.30: 20 Dihedral angle restraints: 53879 sinusoidal: 43809 harmonic: 10070 Sorted by residual: dihedral pdb=" CA ALA S 89 " pdb=" C ALA S 89 " pdb=" N LYS S 90 " pdb=" CA LYS S 90 " ideal model delta harmonic sigma weight residual -180.00 -133.19 -46.81 0 5.00e+00 4.00e-02 8.77e+01 dihedral pdb=" O4' U A 546 " pdb=" C1' U A 546 " pdb=" N1 U A 546 " pdb=" C2 U A 546 " ideal model delta sinusoidal sigma weight residual 200.00 28.30 171.70 1 1.50e+01 4.44e-03 8.49e+01 dihedral pdb=" O4' U A2076 " pdb=" C1' U A2076 " pdb=" N1 U A2076 " pdb=" C2 U A2076 " ideal model delta sinusoidal sigma weight residual 200.00 29.46 170.54 1 1.50e+01 4.44e-03 8.48e+01 ... (remaining 53876 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.349: 19424 0.349 - 0.699: 30 0.699 - 1.048: 2 1.048 - 1.398: 2 1.398 - 1.747: 6 Chirality restraints: 19464 Sorted by residual: chirality pdb=" CB VAL 5 27 " pdb=" CA VAL 5 27 " pdb=" CG1 VAL 5 27 " pdb=" CG2 VAL 5 27 " both_signs ideal model delta sigma weight residual False -2.63 -0.88 -1.75 2.00e-01 2.50e+01 7.63e+01 chirality pdb=" CG LEU 5 81 " pdb=" CB LEU 5 81 " pdb=" CD1 LEU 5 81 " pdb=" CD2 LEU 5 81 " both_signs ideal model delta sigma weight residual False -2.59 -0.93 -1.66 2.00e-01 2.50e+01 6.90e+01 chirality pdb=" CB ILE 5 123 " pdb=" CA ILE 5 123 " pdb=" CG1 ILE 5 123 " pdb=" CG2 ILE 5 123 " both_signs ideal model delta sigma weight residual False 2.64 1.04 1.61 2.00e-01 2.50e+01 6.47e+01 ... (remaining 19461 not shown) Planarity restraints: 7881 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G V 39 " -0.183 2.00e-02 2.50e+03 1.75e-01 9.19e+02 pdb=" N9 G V 39 " 0.018 2.00e-02 2.50e+03 pdb=" C8 G V 39 " 0.261 2.00e-02 2.50e+03 pdb=" N7 G V 39 " 0.190 2.00e-02 2.50e+03 pdb=" C5 G V 39 " 0.054 2.00e-02 2.50e+03 pdb=" C6 G V 39 " -0.084 2.00e-02 2.50e+03 pdb=" O6 G V 39 " -0.212 2.00e-02 2.50e+03 pdb=" N1 G V 39 " -0.015 2.00e-02 2.50e+03 pdb=" C2 G V 39 " 0.027 2.00e-02 2.50e+03 pdb=" N2 G V 39 " 0.307 2.00e-02 2.50e+03 pdb=" N3 G V 39 " -0.262 2.00e-02 2.50e+03 pdb=" C4 G V 39 " -0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C V 4 " -0.305 2.00e-02 2.50e+03 1.69e-01 6.43e+02 pdb=" N1 C V 4 " 0.015 2.00e-02 2.50e+03 pdb=" C2 C V 4 " 0.070 2.00e-02 2.50e+03 pdb=" O2 C V 4 " 0.089 2.00e-02 2.50e+03 pdb=" N3 C V 4 " 0.025 2.00e-02 2.50e+03 pdb=" C4 C V 4 " 0.039 2.00e-02 2.50e+03 pdb=" N4 C V 4 " -0.289 2.00e-02 2.50e+03 pdb=" C5 C V 4 " 0.208 2.00e-02 2.50e+03 pdb=" C6 C V 4 " 0.149 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G V 3 " -0.091 2.00e-02 2.50e+03 1.43e-01 6.11e+02 pdb=" N9 G V 3 " -0.082 2.00e-02 2.50e+03 pdb=" C8 G V 3 " -0.195 2.00e-02 2.50e+03 pdb=" N7 G V 3 " 0.040 2.00e-02 2.50e+03 pdb=" C5 G V 3 " 0.221 2.00e-02 2.50e+03 pdb=" C6 G V 3 " -0.026 2.00e-02 2.50e+03 pdb=" O6 G V 3 " -0.038 2.00e-02 2.50e+03 pdb=" N1 G V 3 " -0.130 2.00e-02 2.50e+03 pdb=" C2 G V 3 " 0.027 2.00e-02 2.50e+03 pdb=" N2 G V 3 " -0.163 2.00e-02 2.50e+03 pdb=" N3 G V 3 " 0.221 2.00e-02 2.50e+03 pdb=" C4 G V 3 " 0.214 2.00e-02 2.50e+03 ... (remaining 7878 not shown) Histogram of nonbonded interaction distances: 0.68 - 1.53: 9 1.53 - 2.37: 938 2.37 - 3.21: 90509 3.21 - 4.06: 314076 4.06 - 4.90: 474379 Warning: very small nonbonded interaction distances. Nonbonded interactions: 879911 Sorted by model distance: nonbonded pdb=" O PRO 7 24 " pdb=" O2' A V 76 " model vdw 0.682 2.440 nonbonded pdb=" NH1 ARG F 79 " pdb=" C1' C V 56 " model vdw 0.878 3.550 nonbonded pdb=" O2 U A 746 " pdb=" O TRP A3001 " model vdw 1.149 3.040 nonbonded pdb=" NE2 GLN h 46 " pdb=" CG2 VAL h 59 " model vdw 1.233 3.540 nonbonded pdb=" NH1 ARG F 79 " pdb=" O4' C V 56 " model vdw 1.238 2.520 ... (remaining 879906 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 3049 5.49 5 Mg 143 5.21 5 S 93 5.16 5 C 46506 2.51 5 N 17294 2.21 5 O 26533 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=0.89 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: 2.920 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: 16.020 Check model and map are aligned: 1.050 Convert atoms to be neutral: 0.600 Process input model: 371.490 Find NCS groups from input model: 1.590 Set up NCS constraints: 0.210 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: 0.010 Load rotamer database and sin/cos tables:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 396.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5773 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 : 0.010 0.149 101257 Z= 0.616 Angle : 1.487 70.535 151829 Z= 0.790 Chirality : 0.072 1.747 19464 Planarity : 0.010 0.291 7881 Dihedral : 15.555 176.301 47389 Min Nonbonded Distance : 0.682 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 6.52 % Allowed : 16.02 % Favored : 77.47 % Rotamer Outliers : 11.41 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.00 (0.11), residues: 3484 helix: -3.74 (0.11), residues: 854 sheet: -2.80 (0.20), residues: 597 loop : -3.42 (0.12), residues: 2033 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1659 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 328 poor density : 1331 time to evaluate : 3.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 328 outliers final: 97 residues processed: 1502 average time/residue: 1.0036 time to fit residues: 2433.5855 Evaluate side-chains 1001 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 904 time to evaluate : 4.050 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 97 outliers final: 3 residues processed: 97 average time/residue: 0.7413 time to fit residues: 135.4498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 543 optimal weight: 5.9990 chunk 488 optimal weight: 2.9990 chunk 270 optimal weight: 40.0000 chunk 166 optimal weight: 50.0000 chunk 329 optimal weight: 8.9990 chunk 260 optimal weight: 0.9980 chunk 504 optimal weight: 0.6980 chunk 195 optimal weight: 9.9990 chunk 306 optimal weight: 7.9990 chunk 375 optimal weight: 2.9990 chunk 584 optimal weight: 7.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** h 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 18 HIS ** 7 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 44 HIS 8 78 GLN ** 8 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 HIS C 196 ASN C 238 ASN D 130 GLN D 150 GLN E 46 GLN E 90 GLN E 97 ASN E 156 ASN E 195 GLN F 26 GLN G 21 GLN ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 HIS J 135 GLN ** K 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 97 GLN N 9 GLN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 29 HIS P 11 GLN ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 HIS ** S 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 60 HIS T 15 HIS T 59 ASN X 15 ASN Y 15 ASN z 20 HIS z 74 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6195 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.114 101257 Z= 0.237 Angle : 0.799 16.314 151829 Z= 0.406 Chirality : 0.041 0.336 19464 Planarity : 0.007 0.104 7881 Dihedral : 14.366 177.212 40480 Min Nonbonded Distance : 1.660 Molprobity Statistics. All-atom Clashscore : 18.96 Ramachandran Plot: Outliers : 2.84 % Allowed : 11.85 % Favored : 85.30 % Rotamer Outliers : 7.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -3.71 (0.13), residues: 3484 helix: -1.81 (0.15), residues: 885 sheet: -2.53 (0.19), residues: 637 loop : -2.82 (0.12), residues: 1962 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1263 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 1034 time to evaluate : 4.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 229 outliers final: 114 residues processed: 1147 average time/residue: 0.8878 time to fit residues: 1714.7119 Evaluate side-chains 1008 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 894 time to evaluate : 3.944 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 114 outliers final: 1 residues processed: 114 average time/residue: 0.7276 time to fit residues: 157.8260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 325 optimal weight: 10.0000 chunk 181 optimal weight: 10.0000 chunk 486 optimal weight: 4.9990 chunk 398 optimal weight: 3.9990 chunk 161 optimal weight: 9.9990 chunk 585 optimal weight: 9.9990 chunk 632 optimal weight: 1.9990 chunk 521 optimal weight: 10.0000 chunk 580 optimal weight: 0.9990 chunk 199 optimal weight: 10.0000 chunk 470 optimal weight: 50.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 45 HIS ** h 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 4 GLN 2 13 ASN ** 8 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 GLN ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 23 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 98 GLN Q 36 GLN ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS S 15 GLN ** S 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 19 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6568 moved from start: 0.5695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.137 101257 Z= 0.325 Angle : 0.812 14.577 151829 Z= 0.412 Chirality : 0.042 0.334 19464 Planarity : 0.007 0.153 7881 Dihedral : 14.489 178.720 40480 Min Nonbonded Distance : 1.626 Molprobity Statistics. All-atom Clashscore : 19.68 Ramachandran Plot: Outliers : 2.44 % Allowed : 13.23 % Favored : 84.33 % Rotamer Outliers : 7.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.13), residues: 3484 helix: -1.55 (0.15), residues: 901 sheet: -2.14 (0.20), residues: 601 loop : -2.81 (0.12), residues: 1982 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1206 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 996 time to evaluate : 4.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 210 outliers final: 106 residues processed: 1095 average time/residue: 0.8708 time to fit residues: 1625.9538 Evaluate side-chains 990 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 884 time to evaluate : 3.957 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 106 outliers final: 2 residues processed: 106 average time/residue: 0.7218 time to fit residues: 148.3099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 578 optimal weight: 9.9990 chunk 440 optimal weight: 5.9990 chunk 304 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 279 optimal weight: 9.9990 chunk 393 optimal weight: 2.9990 chunk 587 optimal weight: 8.9990 chunk 622 optimal weight: 0.6980 chunk 307 optimal weight: 10.0000 chunk 557 optimal weight: 0.9980 chunk 167 optimal weight: 50.0000 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 74 ASN 5 57 ASN 8 49 ASN ** 8 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 HIS C 114 GLN H 28 ASN ** K 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 HIS ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 71 ASN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6613 moved from start: 0.6611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.138 101257 Z= 0.270 Angle : 0.721 15.261 151829 Z= 0.368 Chirality : 0.039 0.323 19464 Planarity : 0.006 0.145 7881 Dihedral : 14.350 178.570 40480 Min Nonbonded Distance : 1.704 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 2.27 % Allowed : 11.62 % Favored : 86.11 % Rotamer Outliers : 5.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -3.08 (0.13), residues: 3484 helix: -0.97 (0.17), residues: 889 sheet: -2.16 (0.20), residues: 627 loop : -2.60 (0.13), residues: 1968 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1113 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 947 time to evaluate : 3.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 166 outliers final: 95 residues processed: 1026 average time/residue: 0.8492 time to fit residues: 1498.3194 Evaluate side-chains 989 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 894 time to evaluate : 3.934 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 95 outliers final: 1 residues processed: 95 average time/residue: 0.7086 time to fit residues: 128.7805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 518 optimal weight: 9.9990 chunk 353 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 463 optimal weight: 20.0000 chunk 256 optimal weight: 10.0000 chunk 531 optimal weight: 0.9980 chunk 430 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 317 optimal weight: 10.0000 chunk 558 optimal weight: 7.9990 chunk 157 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 69 ASN ** h 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 3 GLN 8 49 ASN ** 8 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 GLN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 HIS E 97 ASN G 21 GLN G 138 GLN ** K 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 18 GLN R 86 GLN S 7 HIS ** S 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 61 ASN ** W 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 22 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.8283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.089 101257 Z= 0.468 Angle : 0.990 16.044 151829 Z= 0.490 Chirality : 0.049 0.312 19464 Planarity : 0.007 0.136 7881 Dihedral : 15.539 179.702 40480 Min Nonbonded Distance : 1.561 Molprobity Statistics. All-atom Clashscore : 27.74 Ramachandran Plot: Outliers : 2.38 % Allowed : 14.29 % Favored : 83.32 % Rotamer Outliers : 7.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.26 % 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: -3.47 (0.13), residues: 3484 helix: -1.52 (0.16), residues: 898 sheet: -1.91 (0.20), residues: 620 loop : -2.92 (0.12), residues: 1966 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1143 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 936 time to evaluate : 4.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 207 outliers final: 122 residues processed: 1042 average time/residue: 0.8641 time to fit residues: 1535.8640 Evaluate side-chains 997 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 875 time to evaluate : 3.946 Switching outliers to nearest non-outliers outliers start: 122 outliers final: 0 residues processed: 122 average time/residue: 0.6810 time to fit residues: 161.2120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 209 optimal weight: 10.0000 chunk 560 optimal weight: 2.9990 chunk 123 optimal weight: 10.0000 chunk 365 optimal weight: 3.9990 chunk 153 optimal weight: 10.0000 chunk 623 optimal weight: 7.9990 chunk 517 optimal weight: 7.9990 chunk 288 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 206 optimal weight: 10.0000 chunk 327 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 88 HIS 8 49 ASN ** 8 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 HIS C 114 GLN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 GLN H 20 ASN ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 ASN ** K 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 61 GLN O 98 GLN P 76 HIS ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 60 HIS ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.8657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.072 101257 Z= 0.376 Angle : 0.813 14.951 151829 Z= 0.410 Chirality : 0.043 0.342 19464 Planarity : 0.006 0.133 7881 Dihedral : 15.053 179.053 40480 Min Nonbonded Distance : 0.954 Molprobity Statistics. All-atom Clashscore : 22.44 Ramachandran Plot: Outliers : 2.24 % Allowed : 12.74 % Favored : 85.02 % Rotamer Outliers : 4.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -3.25 (0.13), residues: 3484 helix: -1.30 (0.16), residues: 907 sheet: -1.78 (0.21), residues: 605 loop : -2.79 (0.12), residues: 1972 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1041 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 925 time to evaluate : 4.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 116 outliers final: 70 residues processed: 984 average time/residue: 0.8834 time to fit residues: 1492.8066 Evaluate side-chains 941 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 871 time to evaluate : 4.110 Switching outliers to nearest non-outliers outliers start: 70 outliers final: 0 residues processed: 70 average time/residue: 0.7190 time to fit residues: 98.2704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 600 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 chunk 355 optimal weight: 10.0000 chunk 455 optimal weight: 1.9990 chunk 352 optimal weight: 8.9990 chunk 524 optimal weight: 0.8980 chunk 347 optimal weight: 10.0000 chunk 620 optimal weight: 9.9990 chunk 388 optimal weight: 2.9990 chunk 378 optimal weight: 2.9990 chunk 286 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 49 ASN ** 8 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN C 199 HIS ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN ** F 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 GLN H 28 ASN ** K 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 23 ASN N 107 ASN P 76 HIS Q 71 ASN R 89 HIS S 31 GLN ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 60 HIS ** W 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 62 ASN z 74 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.8839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.086 101257 Z= 0.247 Angle : 0.711 14.707 151829 Z= 0.362 Chirality : 0.038 0.408 19464 Planarity : 0.006 0.132 7881 Dihedral : 14.693 179.914 40480 Min Nonbonded Distance : 0.997 Molprobity Statistics. All-atom Clashscore : 19.08 Ramachandran Plot: Outliers : 2.12 % Allowed : 12.20 % Favored : 85.68 % Rotamer Outliers : 3.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.97 (0.13), residues: 3484 helix: -0.96 (0.17), residues: 897 sheet: -1.68 (0.20), residues: 619 loop : -2.66 (0.13), residues: 1968 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1018 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 911 time to evaluate : 4.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 107 outliers final: 69 residues processed: 949 average time/residue: 0.8526 time to fit residues: 1393.0439 Evaluate side-chains 936 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 867 time to evaluate : 3.950 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 0 residues processed: 69 average time/residue: 0.7611 time to fit residues: 99.1938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 384 optimal weight: 4.9990 chunk 247 optimal weight: 10.0000 chunk 370 optimal weight: 2.9990 chunk 186 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 394 optimal weight: 6.9990 chunk 422 optimal weight: 9.9990 chunk 306 optimal weight: 10.0000 chunk 57 optimal weight: 0.6980 chunk 487 optimal weight: 0.8980 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 99 ASN 0 37 HIS 8 49 ASN ** 8 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 HIS ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 ASN ** F 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 GLN ** K 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 23 ASN N 62 ASN N 81 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 GLN ** S 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 61 ASN ** W 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 25 GLN z 62 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.9069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 101257 Z= 0.234 Angle : 0.690 14.694 151829 Z= 0.351 Chirality : 0.037 0.350 19464 Planarity : 0.006 0.132 7881 Dihedral : 14.532 179.835 40480 Min Nonbonded Distance : 1.002 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 2.18 % Allowed : 11.97 % Favored : 85.85 % Rotamer Outliers : 2.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.14), residues: 3484 helix: -0.76 (0.18), residues: 896 sheet: -1.66 (0.20), residues: 625 loop : -2.56 (0.13), residues: 1963 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 985 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 910 time to evaluate : 4.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 75 outliers final: 41 residues processed: 939 average time/residue: 0.8563 time to fit residues: 1380.8002 Evaluate side-chains 913 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 872 time to evaluate : 3.946 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 41 outliers final: 1 residues processed: 41 average time/residue: 0.7216 time to fit residues: 58.5981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 564 optimal weight: 5.9990 chunk 594 optimal weight: 0.8980 chunk 542 optimal weight: 3.9990 chunk 578 optimal weight: 5.9990 chunk 348 optimal weight: 10.0000 chunk 251 optimal weight: 10.0000 chunk 454 optimal weight: 10.0000 chunk 177 optimal weight: 20.0000 chunk 522 optimal weight: 3.9990 chunk 547 optimal weight: 10.0000 chunk 576 optimal weight: 9.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 99 ASN 8 49 ASN ** 8 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 HIS C 116 GLN C 199 HIS ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 GLN ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 23 ASN N 62 ASN N 107 ASN ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 61 ASN ** W 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.9325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 101257 Z= 0.272 Angle : 0.728 14.761 151829 Z= 0.368 Chirality : 0.039 0.425 19464 Planarity : 0.006 0.132 7881 Dihedral : 14.593 179.766 40480 Min Nonbonded Distance : 0.986 Molprobity Statistics. All-atom Clashscore : 19.63 Ramachandran Plot: Outliers : 2.07 % Allowed : 12.86 % Favored : 85.07 % Rotamer Outliers : 1.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.14), residues: 3484 helix: -0.69 (0.18), residues: 884 sheet: -1.59 (0.21), residues: 598 loop : -2.59 (0.13), residues: 2002 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 947 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 890 time to evaluate : 4.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 34 residues processed: 911 average time/residue: 0.8634 time to fit residues: 1355.4180 Evaluate side-chains 881 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 847 time to evaluate : 4.004 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.7272 time to fit residues: 50.2140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 379 optimal weight: 7.9990 chunk 611 optimal weight: 10.0000 chunk 373 optimal weight: 2.9990 chunk 290 optimal weight: 10.0000 chunk 425 optimal weight: 3.9990 chunk 641 optimal weight: 50.0000 chunk 590 optimal weight: 0.0770 chunk 510 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 394 optimal weight: 0.2980 chunk 313 optimal weight: 9.9990 overall best weight: 3.0744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 99 ASN ** 4 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 HIS ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 GLN ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 23 ASN N 62 ASN Q 19 GLN Q 36 GLN ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 61 ASN ** W 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.9477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.071 101257 Z= 0.216 Angle : 0.674 14.774 151829 Z= 0.343 Chirality : 0.036 0.381 19464 Planarity : 0.005 0.132 7881 Dihedral : 14.415 179.938 40480 Min Nonbonded Distance : 1.021 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 1.98 % Allowed : 12.00 % Favored : 86.02 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.14), residues: 3484 helix: -0.56 (0.18), residues: 881 sheet: -1.63 (0.21), residues: 601 loop : -2.51 (0.13), residues: 2002 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 923 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 899 time to evaluate : 4.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 16 residues processed: 907 average time/residue: 0.8595 time to fit residues: 1345.8696 Evaluate side-chains 881 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 865 time to evaluate : 3.960 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.6709 time to fit residues: 24.8557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 405 optimal weight: 1.9990 chunk 544 optimal weight: 4.9990 chunk 156 optimal weight: 9.9990 chunk 471 optimal weight: 50.0000 chunk 75 optimal weight: 10.0000 chunk 141 optimal weight: 10.0000 chunk 511 optimal weight: 5.9990 chunk 214 optimal weight: 10.0000 chunk 525 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** h 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 49 ASN ** 8 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 HIS ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 23 ASN N 62 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 5 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.167292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.137646 restraints weight = 202620.515| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.71 r_work: 0.3618 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4096 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4096 r_free = 0.4096 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4096 r_free = 0.4096 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4096 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.9784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.091 101257 Z= 0.402 Angle : 0.861 15.608 151829 Z= 0.428 Chirality : 0.044 0.398 19464 Planarity : 0.006 0.130 7881 Dihedral : 15.020 179.151 40480 Min Nonbonded Distance : 0.950 Molprobity Statistics. All-atom Clashscore : 24.82 Ramachandran Plot: Outliers : 2.04 % Allowed : 14.61 % Favored : 83.35 % Rotamer Outliers : 1.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.13), residues: 3484 helix: -0.88 (0.17), residues: 891 sheet: -1.59 (0.21), residues: 618 loop : -2.68 (0.13), residues: 1975 =============================================================================== Job complete usr+sys time: 24491.30 seconds wall clock time: 430 minutes 37.13 seconds (25837.13 seconds total)