Starting phenix.real_space_refine on Tue Nov 21 03:43:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i0y_0322/11_2023/6i0y_0322.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i0y_0322/11_2023/6i0y_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_0322/11_2023/6i0y_0322.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i0y_0322/11_2023/6i0y_0322.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i0y_0322/11_2023/6i0y_0322.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i0y_0322/11_2023/6i0y_0322.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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 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. 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-1.21rc1-5144/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: 35.78, per 1000 atoms: 0.38 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: 45.54 Conformation dependent library (CDL) restraints added in 4.5 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: 36.02 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: 176.35 Time building geometry restraints manager: 48.73 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 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: 2.750 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: 0.060 Extract box with map and model: 13.640 Check model and map are aligned: 1.030 Set scattering table: 0.620 Process input model: 377.130 Find NCS groups from input model: 1.600 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 400.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5603 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 : 13.02 Ramachandran Plot: Outliers : 6.52 % Allowed : 16.02 % Favored : 77.47 % Rotamer: Outliers : 11.41 % Allowed : 13.05 % Favored : 75.54 % 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 : 3.855 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: 1.0306 time to fit residues: 2498.4767 Evaluate side-chains 1001 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 904 time to evaluate : 3.944 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 97 outliers final: 3 residues processed: 97 average time/residue: 0.8184 time to fit residues: 149.9405 ------------------------------------------------------------------------------- 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: 10.0000 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 ** h 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 18 HIS 7 22 HIS 8 44 HIS 8 78 GLN ** 8 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 238 ASN D 130 GLN D 150 GLN E 46 GLN E 90 GLN E 156 ASN E 195 GLN F 26 GLN G 21 GLN ** J 47 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** 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 15 GLN ** S 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 60 HIS T 15 HIS T 59 ASN X 15 ASN Y 15 ASN Y 41 HIS z 20 HIS z 74 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5995 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 101257 Z= 0.244 Angle : 0.785 15.474 151829 Z= 0.400 Chirality : 0.041 0.328 19464 Planarity : 0.006 0.108 7881 Dihedral : 14.297 177.369 40480 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 2.84 % Allowed : 12.03 % Favored : 85.13 % Rotamer: Outliers : 7.79 % Allowed : 23.21 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % 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: -3.73 (0.12), residues: 3484 helix: -1.84 (0.15), residues: 885 sheet: -2.48 (0.19), residues: 637 loop : -2.86 (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 1244 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 1020 time to evaluate : 4.053 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 outliers start: 224 outliers final: 115 residues processed: 1131 average time/residue: 0.9225 time to fit residues: 1758.7728 Evaluate side-chains 1011 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 896 time to evaluate : 3.892 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 115 outliers final: 1 residues processed: 115 average time/residue: 0.7376 time to fit residues: 160.2704 ------------------------------------------------------------------------------- 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: 2.9990 chunk 398 optimal weight: 7.9990 chunk 161 optimal weight: 10.0000 chunk 585 optimal weight: 9.9990 chunk 632 optimal weight: 2.9990 chunk 521 optimal weight: 8.9990 chunk 580 optimal weight: 0.0570 chunk 199 optimal weight: 10.0000 chunk 470 optimal weight: 50.0000 overall best weight: 4.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** h 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 4 GLN 2 13 ASN 8 49 ASN ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 GLN E 97 ASN ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 16 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 65 ASN Q 71 ASN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS ** 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6413 moved from start: 0.5902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.167 101257 Z= 0.340 Angle : 0.853 15.130 151829 Z= 0.430 Chirality : 0.043 0.379 19464 Planarity : 0.008 0.151 7881 Dihedral : 14.626 179.566 40480 Min Nonbonded Distance : 1.527 Molprobity Statistics. All-atom Clashscore : 21.30 Ramachandran Plot: Outliers : 2.41 % Allowed : 13.26 % Favored : 84.33 % Rotamer: Outliers : 7.72 % Allowed : 26.72 % Favored : 65.55 % 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: -3.55 (0.13), residues: 3484 helix: -1.65 (0.15), residues: 899 sheet: -2.21 (0.20), residues: 594 loop : -2.84 (0.12), residues: 1991 *********************** 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 1240 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 1018 time to evaluate : 4.027 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 outliers start: 222 outliers final: 107 residues processed: 1119 average time/residue: 0.9543 time to fit residues: 1815.6713 Evaluate side-chains 997 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 890 time to evaluate : 3.918 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 107 outliers final: 2 residues processed: 107 average time/residue: 0.7124 time to fit residues: 148.3341 ------------------------------------------------------------------------------- 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: 4.9990 chunk 440 optimal weight: 10.0000 chunk 304 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 279 optimal weight: 10.0000 chunk 393 optimal weight: 4.9990 chunk 587 optimal weight: 5.9990 chunk 622 optimal weight: 5.9990 chunk 307 optimal weight: 10.0000 chunk 557 optimal weight: 0.9980 chunk 167 optimal weight: 50.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 66 GLN 5 57 ASN C 57 HIS ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 97 GLN N 31 HIS ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN ** S 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 60 HIS ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6468 moved from start: 0.6855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 101257 Z= 0.301 Angle : 0.751 15.231 151829 Z= 0.382 Chirality : 0.041 0.322 19464 Planarity : 0.006 0.137 7881 Dihedral : 14.497 177.825 40480 Min Nonbonded Distance : 1.659 Molprobity Statistics. All-atom Clashscore : 18.80 Ramachandran Plot: Outliers : 2.27 % Allowed : 11.83 % Favored : 85.91 % Rotamer: Outliers : 6.19 % Allowed : 29.92 % Favored : 63.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -3.24 (0.13), residues: 3484 helix: -1.29 (0.16), residues: 898 sheet: -2.08 (0.20), residues: 615 loop : -2.68 (0.13), residues: 1971 *********************** 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 1153 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 975 time to evaluate : 3.964 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: 178 outliers final: 106 residues processed: 1063 average time/residue: 0.9347 time to fit residues: 1714.4323 Evaluate side-chains 1023 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 917 time to evaluate : 4.593 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 106 outliers final: 1 residues processed: 106 average time/residue: 0.7758 time to fit residues: 158.7224 ------------------------------------------------------------------------------- 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: 7.9990 chunk 353 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 463 optimal weight: 30.0000 chunk 256 optimal weight: 10.0000 chunk 531 optimal weight: 3.9990 chunk 430 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 317 optimal weight: 10.0000 chunk 558 optimal weight: 5.9990 chunk 157 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 69 ASN 5 4 ASN 8 49 ASN ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 GLN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN D 150 GLN E 29 HIS ** G 138 GLN ** 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 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** Q 19 GLN R 18 GLN R 86 GLN ** S 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 49 ASN ** W 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 31 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.8058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.113 101257 Z= 0.382 Angle : 0.862 14.295 151829 Z= 0.432 Chirality : 0.044 0.404 19464 Planarity : 0.007 0.131 7881 Dihedral : 14.999 178.814 40480 Min Nonbonded Distance : 1.563 Molprobity Statistics. All-atom Clashscore : 23.99 Ramachandran Plot: Outliers : 2.35 % Allowed : 13.98 % Favored : 83.67 % Rotamer: Outliers : 6.37 % Allowed : 31.63 % Favored : 62.00 % Cbeta Deviations : 0.03 % 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: -3.38 (0.13), residues: 3484 helix: -1.45 (0.16), residues: 902 sheet: -1.92 (0.20), residues: 613 loop : -2.83 (0.12), residues: 1969 *********************** 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 1118 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 935 time to evaluate : 3.947 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 outliers start: 183 outliers final: 113 residues processed: 1023 average time/residue: 0.8945 time to fit residues: 1568.5938 Evaluate side-chains 998 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 885 time to evaluate : 3.992 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 113 outliers final: 1 residues processed: 113 average time/residue: 0.6948 time to fit residues: 152.6670 ------------------------------------------------------------------------------- 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: 6.9990 chunk 123 optimal weight: 10.0000 chunk 365 optimal weight: 0.7980 chunk 153 optimal weight: 10.0000 chunk 623 optimal weight: 0.7980 chunk 517 optimal weight: 7.9990 chunk 288 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 206 optimal weight: 10.0000 chunk 327 optimal weight: 8.9990 overall best weight: 4.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 49 ASN ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN D 136 ASN F 126 ASN G 127 GLN ** K 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 9 GLN N 81 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 98 GLN Q 19 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 18 GLN ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN R 89 HIS ** S 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 60 HIS S 61 ASN X 22 ASN z 62 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6577 moved from start: 0.8378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 101257 Z= 0.289 Angle : 0.734 15.035 151829 Z= 0.373 Chirality : 0.040 0.367 19464 Planarity : 0.006 0.131 7881 Dihedral : 14.662 179.364 40480 Min Nonbonded Distance : 1.421 Molprobity Statistics. All-atom Clashscore : 19.17 Ramachandran Plot: Outliers : 2.27 % Allowed : 12.26 % Favored : 85.48 % Rotamer: Outliers : 3.86 % Allowed : 34.13 % Favored : 62.00 % 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: -3.10 (0.13), residues: 3484 helix: -1.18 (0.16), residues: 903 sheet: -1.76 (0.21), residues: 597 loop : -2.68 (0.13), residues: 1984 *********************** 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 1047 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 936 time to evaluate : 4.138 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 outliers start: 111 outliers final: 67 residues processed: 979 average time/residue: 0.9092 time to fit residues: 1531.6130 Evaluate side-chains 932 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 865 time to evaluate : 4.466 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 0 residues processed: 67 average time/residue: 0.7321 time to fit residues: 96.3522 ------------------------------------------------------------------------------- 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: 5.9990 chunk 70 optimal weight: 10.0000 chunk 355 optimal weight: 10.0000 chunk 455 optimal weight: 7.9990 chunk 352 optimal weight: 10.0000 chunk 524 optimal weight: 9.9990 chunk 347 optimal weight: 10.0000 chunk 620 optimal weight: 5.9990 chunk 388 optimal weight: 10.0000 chunk 378 optimal weight: 2.9990 chunk 286 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** h 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 37 HIS 5 88 HIS ** 8 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 ASN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 GLN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS ** K 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 62 ASN N 107 ASN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 62 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.9047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 101257 Z= 0.404 Angle : 0.875 15.089 151829 Z= 0.437 Chirality : 0.045 0.405 19464 Planarity : 0.007 0.129 7881 Dihedral : 15.218 179.492 40480 Min Nonbonded Distance : 0.830 Molprobity Statistics. All-atom Clashscore : 25.53 Ramachandran Plot: Outliers : 2.18 % Allowed : 14.32 % Favored : 83.50 % Rotamer: Outliers : 4.00 % Allowed : 34.79 % Favored : 61.20 % 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: -3.19 (0.13), residues: 3484 helix: -1.21 (0.17), residues: 880 sheet: -1.62 (0.21), residues: 562 loop : -2.81 (0.12), residues: 2042 *********************** 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 1049 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 934 time to evaluate : 4.109 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: 115 outliers final: 76 residues processed: 987 average time/residue: 0.9018 time to fit residues: 1527.7711 Evaluate side-chains 961 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 885 time to evaluate : 5.388 Switching outliers to nearest non-outliers outliers start: 76 outliers final: 0 residues processed: 76 average time/residue: 0.7455 time to fit residues: 109.6200 ------------------------------------------------------------------------------- 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: 6.9990 chunk 247 optimal weight: 10.0000 chunk 370 optimal weight: 3.9990 chunk 186 optimal weight: 9.9990 chunk 121 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 394 optimal weight: 7.9990 chunk 422 optimal weight: 7.9990 chunk 306 optimal weight: 8.9990 chunk 57 optimal weight: 9.9990 chunk 487 optimal weight: 0.7980 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 69 ASN h 99 ASN ** 5 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 49 ASN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 GLN ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 ASN ** K 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 62 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN ** S 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 61 ASN ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 74 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 0.9286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 101257 Z= 0.340 Angle : 0.793 16.503 151829 Z= 0.399 Chirality : 0.042 0.442 19464 Planarity : 0.006 0.133 7881 Dihedral : 14.983 179.300 40480 Min Nonbonded Distance : 0.959 Molprobity Statistics. All-atom Clashscore : 22.20 Ramachandran Plot: Outliers : 2.12 % Allowed : 12.83 % Favored : 85.05 % Rotamer: Outliers : 2.71 % Allowed : 36.60 % Favored : 60.68 % 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: -3.09 (0.13), residues: 3484 helix: -1.05 (0.17), residues: 892 sheet: -1.70 (0.21), residues: 607 loop : -2.75 (0.13), residues: 1985 *********************** 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 975 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 897 time to evaluate : 4.838 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 outliers start: 78 outliers final: 62 residues processed: 919 average time/residue: 0.8972 time to fit residues: 1420.7555 Evaluate side-chains 923 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 861 time to evaluate : 4.037 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 0 residues processed: 62 average time/residue: 0.7466 time to fit residues: 90.8167 ------------------------------------------------------------------------------- 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: 2.9990 chunk 594 optimal weight: 5.9990 chunk 542 optimal weight: 0.9990 chunk 578 optimal weight: 0.6980 chunk 348 optimal weight: 10.0000 chunk 251 optimal weight: 10.0000 chunk 454 optimal weight: 9.9990 chunk 177 optimal weight: 20.0000 chunk 522 optimal weight: 4.9990 chunk 547 optimal weight: 5.9990 chunk 576 optimal weight: 0.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 99 ASN ** 5 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 49 ASN C 116 GLN C 199 HIS ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN G 127 GLN J 80 HIS ** K 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 62 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 GLN ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 49 ASN ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 0.9389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 101257 Z= 0.184 Angle : 0.659 15.419 151829 Z= 0.336 Chirality : 0.035 0.461 19464 Planarity : 0.005 0.127 7881 Dihedral : 14.464 179.919 40480 Min Nonbonded Distance : 1.065 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 2.01 % Allowed : 12.08 % Favored : 85.91 % Rotamer: Outliers : 1.60 % Allowed : 38.07 % Favored : 60.33 % 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: -2.78 (0.13), residues: 3484 helix: -0.69 (0.17), residues: 877 sheet: -1.59 (0.21), residues: 598 loop : -2.57 (0.13), residues: 2009 *********************** 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 971 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 925 time to evaluate : 3.997 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: 46 outliers final: 23 residues processed: 941 average time/residue: 0.8833 time to fit residues: 1435.9354 Evaluate side-chains 891 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 868 time to evaluate : 3.972 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.7556 time to fit residues: 36.6170 ------------------------------------------------------------------------------- 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: 6.9990 chunk 611 optimal weight: 20.0000 chunk 373 optimal weight: 2.9990 chunk 290 optimal weight: 10.0000 chunk 425 optimal weight: 0.5980 chunk 641 optimal weight: 50.0000 chunk 590 optimal weight: 0.0770 chunk 510 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 394 optimal weight: 6.9990 chunk 313 optimal weight: 10.0000 overall best weight: 3.3344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 69 ASN h 99 ASN ** 8 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 HIS C 199 HIS ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 HIS ** K 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 62 ASN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 71 ASN ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 61 ASN Y 20 ASN Y 31 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6576 moved from start: 0.9528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 101257 Z= 0.238 Angle : 0.696 15.043 151829 Z= 0.351 Chirality : 0.037 0.457 19464 Planarity : 0.005 0.127 7881 Dihedral : 14.492 179.820 40480 Min Nonbonded Distance : 1.003 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 1.95 % Allowed : 12.77 % Favored : 85.28 % Rotamer: Outliers : 0.97 % Allowed : 40.15 % Favored : 58.87 % 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: -2.71 (0.14), residues: 3484 helix: -0.61 (0.17), residues: 871 sheet: -1.51 (0.21), residues: 596 loop : -2.54 (0.13), residues: 2017 ********************** 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 912 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 884 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 outliers start: 28 outliers final: 24 residues processed: 893 average time/residue: 0.9039 time to fit residues: 1398.3202 Evaluate side-chains 878 residues out of total 2874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 854 time to evaluate : 4.057 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.8095 time to fit residues: 39.0647 ------------------------------------------------------------------------------- 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: 9.9990 chunk 544 optimal weight: 0.9980 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: 9.9990 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: 7.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 99 ASN ** 0 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 26 ASN 8 49 ASN ** 8 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN ** D 173 GLN ** 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 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 62 ASN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.166261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.136308 restraints weight = 205798.531| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.83 r_work: 0.3598 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3567 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3567 r_free = 0.3567 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3567 r_free = 0.3567 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3567 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.9824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.110 101257 Z= 0.469 Angle : 0.913 15.192 151829 Z= 0.451 Chirality : 0.047 0.463 19464 Planarity : 0.007 0.127 7881 Dihedral : 15.220 178.950 40480 Min Nonbonded Distance : 0.954 Molprobity Statistics. All-atom Clashscore : 26.62 Ramachandran Plot: Outliers : 1.87 % Allowed : 14.84 % Favored : 83.30 % Rotamer: Outliers : 1.67 % Allowed : 39.39 % Favored : 58.94 % 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: -2.98 (0.13), residues: 3484 helix: -0.96 (0.17), residues: 874 sheet: -1.52 (0.21), residues: 602 loop : -2.71 (0.13), residues: 2008 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26101.46 seconds wall clock time: 458 minutes 15.79 seconds (27495.79 seconds total)