Starting phenix.real_space_refine on Tue Nov 21 01:49:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4uy8_2773/11_2023/4uy8_2773_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4uy8_2773/11_2023/4uy8_2773.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4uy8_2773/11_2023/4uy8_2773_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4uy8_2773/11_2023/4uy8_2773_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4uy8_2773/11_2023/4uy8_2773_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4uy8_2773/11_2023/4uy8_2773.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4uy8_2773/11_2023/4uy8_2773.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4uy8_2773/11_2023/4uy8_2773_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4uy8_2773/11_2023/4uy8_2773_updated.pdb" } resolution = 3.8 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.183 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: 8 Type Number sf(0) Gaussians Zn 1 6.06 5 P 3049 5.49 5 Mg 143 5.21 5 S 91 5.16 5 C 46104 2.51 5 N 17191 2.21 5 O 26408 1.98 5 H 8 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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: 92995 Number of models: 1 Model: "" Number of chains: 47 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: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 170 Classifications: {'peptide': 20} Link IDs: {'PTRANS': 1, 'TRANS': 18} 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': 143, 'rna3p_pur': 1380, 'rna3p_pyr': 1063} Link IDs: {'rna2p': 411, 'rna3p': 2442} 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: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, '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: "U" 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: "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': 1, 'rna3p_pur': 33, 'rna3p_pyr': 31} Link IDs: {'rna2p': 11, 'rna3p': 65} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 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: "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: "7" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Classifications: {'peptide': 2} Modifications used: {'COO': 2, 'NH2NOTPRO': 2} Link IDs: {'TRANS': 1} Chain breaks: 1 Chain: "A" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 135 Unusual residues: {' MG': 135} Classifications: {'undetermined': 135} Link IDs: {None: 134} 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 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: "A" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 416 Classifications: {'water': 416} Link IDs: {None: 415} 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1819 SG CYS 4 11 117.787 76.424 177.464 1.00 27.97 S ATOM 1844 SG CYS 4 14 116.976 77.821 176.178 1.00 12.31 S ATOM 1947 SG CYS 4 27 118.821 78.134 177.054 1.00 25.55 S Time building chain proxies: 35.68, per 1000 atoms: 0.38 Number of scatterers: 92995 At special positions: 0 Unit cell: (201.3, 210.1, 258.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 S 91 16.00 P 3049 15.00 Mg 143 11.99 O 26408 8.00 N 17191 7.00 C 46104 6.00 H 8 1.00 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 89763 O4' C V 56 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 43.03 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 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6338 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 106 helices and 41 sheets defined 24.4% alpha, 10.6% beta 985 base pairs and 1495 stacking pairs defined. Time for finding SS restraints: 41.28 Creating SS restraints... Processing helix chain '0' and resid 9 through 18 removed outlier: 4.721A pdb=" N HIS 0 18 " --> pdb=" O MET 0 14 " (cutoff:3.500A) Processing helix chain '2' and resid 9 through 16 Processing helix chain '2' and resid 18 through 23 Processing helix chain '2' and resid 25 through 36 Processing helix chain '3' and resid 7 through 10 No H-bonds generated for 'chain '3' and resid 7 through 10' Processing helix chain '3' and resid 37 through 43 Processing helix chain '3' and resid 54 through 60 Processing helix chain '4' and resid 31 through 33 No H-bonds generated for 'chain '4' and resid 31 through 33' Processing helix chain '5' and resid 4 through 7 No H-bonds generated for 'chain '5' and resid 4 through 7' Processing helix chain '5' and resid 9 through 18 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: 3.849A pdb=" N VAL 5 18 " --> pdb=" O GLU 5 14 " (cutoff:3.500A) Processing helix chain '5' and resid 34 through 46 removed outlier: 3.584A pdb=" N GLU 5 40 " --> pdb=" O ASP 5 36 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG 5 42 " --> pdb=" O MET 5 38 " (cutoff:3.500A) Processing helix chain '5' and resid 60 through 63 No H-bonds generated for 'chain '5' and resid 60 through 63' Processing helix chain '5' and resid 95 through 103 removed outlier: 3.664A pdb=" N PHE 5 99 " --> pdb=" O LEU 5 95 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA 5 100 " --> pdb=" O PHE 5 96 " (cutoff:3.500A) Processing helix chain '5' and resid 134 through 137 Processing helix chain '5' and resid 140 through 147 removed outlier: 3.790A pdb=" N GLU 5 145 " --> pdb=" O ALA 5 141 " (cutoff:3.500A) Processing helix chain '6' and resid 4 through 6 No H-bonds generated for 'chain '6' and resid 4 through 6' Processing helix chain '6' and resid 16 through 19 No H-bonds generated for 'chain '6' and resid 16 through 19' Processing helix chain '6' and resid 25 through 28 No H-bonds generated for 'chain '6' and resid 25 through 28' Processing helix chain '8' and resid 14 through 23 Processing helix chain '8' and resid 44 through 52 Processing helix chain '8' and resid 54 through 58 Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'C' and resid 131 through 133 No H-bonds generated for 'chain 'C' and resid 131 through 133' Processing helix chain 'C' and resid 198 through 201 Processing helix chain 'C' and resid 207 through 213 removed outlier: 3.503A pdb=" N ARG C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 223 No H-bonds generated for 'chain 'C' and resid 221 through 223' Processing helix chain 'C' and resid 263 through 265 No H-bonds generated for 'chain 'C' and resid 263 through 265' Processing helix chain 'D' and resid 57 through 59 No H-bonds generated for 'chain 'D' and resid 57 through 59' Processing helix chain 'D' and resid 62 through 69 Processing helix chain 'D' and resid 98 through 101 Processing helix chain 'E' and resid 16 through 19 No H-bonds generated for 'chain 'E' and resid 16 through 19' Processing helix chain 'E' and resid 25 through 36 removed outlier: 3.592A pdb=" N VAL E 31 " --> pdb=" O LEU E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 112 Processing helix chain 'E' and resid 131 through 141 Processing helix chain 'E' and resid 155 through 159 Processing helix chain 'E' and resid 177 through 182 removed outlier: 3.546A pdb=" N ILE E 181 " --> pdb=" O PRO E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 199 removed outlier: 3.583A pdb=" N LYS E 194 " --> pdb=" O ALA E 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 8 Processing helix chain 'F' and resid 12 through 19 removed outlier: 3.600A pdb=" N THR F 17 " --> pdb=" O LYS F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 26 No H-bonds generated for 'chain 'F' and resid 24 through 26' Processing helix chain 'F' and resid 41 through 43 No H-bonds generated for 'chain 'F' and resid 41 through 43' Processing helix chain 'F' and resid 47 through 59 removed outlier: 3.672A 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 92 through 104 Processing helix chain 'F' and resid 134 through 136 No H-bonds generated for 'chain 'F' and resid 134 through 136' Processing helix chain 'F' and resid 142 through 144 No H-bonds generated for 'chain 'F' and resid 142 through 144' Processing helix chain 'F' and resid 162 through 171 Processing helix chain 'G' and resid 62 through 80 Processing helix chain 'G' and resid 137 through 151 removed outlier: 3.578A pdb=" N TYR G 150 " --> pdb=" O ASP G 146 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ARG G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 12 No H-bonds generated for 'chain 'H' and resid 10 through 12' Processing helix chain 'H' and resid 23 through 28 Processing helix chain 'H' and resid 43 through 46 No H-bonds generated for 'chain 'H' and resid 43 through 46' Processing helix chain 'I' and resid 24 through 27 removed outlier: 3.621A pdb=" N LEU I 27 " --> pdb=" O GLY I 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 24 through 27' Processing helix chain 'I' and resid 34 through 36 No H-bonds generated for 'chain 'I' and resid 34 through 36' Processing helix chain 'I' and resid 41 through 43 No H-bonds generated for 'chain 'I' and resid 41 through 43' Processing helix chain 'I' and resid 107 through 115 removed outlier: 4.480A pdb=" N LYS I 112 " --> pdb=" O ILE I 108 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA I 113 " --> pdb=" O ALA I 109 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ALA I 114 " --> pdb=" O GLN I 110 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ASP I 115 " --> pdb=" O THR I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 123 through 132 removed outlier: 3.929A pdb=" N ILE I 128 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLY I 130 " --> pdb=" O ARG I 126 " (cutoff:3.500A) Processing helix chain 'J' and resid 8 through 10 No H-bonds generated for 'chain 'J' and resid 8 through 10' Processing helix chain 'J' and resid 27 through 37 removed outlier: 3.893A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 61 No H-bonds generated for 'chain 'J' and resid 59 through 61' Processing helix chain 'J' and resid 68 through 71 No H-bonds generated for 'chain 'J' and resid 68 through 71' Processing helix chain 'J' and resid 89 through 94 Processing helix chain 'J' and resid 97 through 106 removed outlier: 3.940A pdb=" N ILE J 103 " --> pdb=" O VAL J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 121 removed outlier: 3.573A pdb=" N ARG J 120 " --> pdb=" O ARG J 116 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 133 through 135 No H-bonds generated for 'chain 'J' and resid 133 through 135' Processing helix chain 'K' and resid 72 through 74 No H-bonds generated for 'chain 'K' and resid 72 through 74' Processing helix chain 'K' and resid 105 through 107 No H-bonds generated for 'chain 'K' and resid 105 through 107' Processing helix chain 'K' and resid 113 through 117 Processing helix chain 'L' and resid 57 through 60 No H-bonds generated for 'chain 'L' and resid 57 through 60' Processing helix chain 'L' and resid 71 through 73 No H-bonds generated for 'chain 'L' and resid 71 through 73' Processing helix chain 'L' and resid 129 through 138 Processing helix chain 'M' and resid 43 through 57 removed outlier: 3.873A pdb=" N ALA M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL M 57 " --> pdb=" O MET M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 123 removed outlier: 3.651A pdb=" N GLU M 115 " --> pdb=" O GLU M 111 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 31 Processing helix chain 'N' and resid 38 through 56 removed outlier: 3.527A 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: 3.719A 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 60 through 68 Processing helix chain 'N' and resid 73 through 81 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 83 through 87 Processing helix chain 'O' and resid 5 through 21 removed outlier: 4.274A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 56 through 59 No H-bonds generated for 'chain 'O' and resid 56 through 59' Processing helix chain 'O' and resid 68 through 85 removed outlier: 3.551A 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 104 through 112 removed outlier: 5.067A pdb=" N ALA O 109 " --> pdb=" O ALA O 105 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 11 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) removed outlier: 4.489A pdb=" N GLN P 11 " --> pdb=" O LEU P 7 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 55 No H-bonds generated for 'chain 'P' and resid 53 through 55' Processing helix chain 'P' and resid 78 through 80 No H-bonds generated for 'chain 'P' and resid 78 through 80' Processing helix chain 'P' and resid 97 through 101 Processing helix chain 'P' and resid 104 through 106 No H-bonds generated for 'chain 'P' and resid 104 through 106' Processing helix chain 'Q' and resid 7 through 20 removed outlier: 3.968A pdb=" N GLN Q 19 " --> pdb=" O LYS Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 29 Processing helix chain 'Q' and resid 31 through 70 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: 4.078A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 84 Processing helix chain 'Q' and resid 94 through 100 removed outlier: 3.591A pdb=" N PHE Q 100 " --> pdb=" O ILE Q 97 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 116 removed outlier: 3.602A pdb=" N ALA Q 115 " --> pdb=" O LYS Q 111 " (cutoff:3.500A) Processing helix chain 'S' and resid 21 through 23 No H-bonds generated for 'chain 'S' and resid 21 through 23' Processing helix chain 'S' and resid 29 through 38 removed outlier: 3.645A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 61 Processing helix chain 'T' and resid 18 through 23 Processing helix chain 'T' and resid 41 through 52 removed outlier: 3.599A pdb=" N ALA T 46 " --> pdb=" O GLU T 42 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N PHE T 51 " --> pdb=" O VAL T 47 " (cutoff:3.500A) Processing helix chain 'U' and resid 66 through 68 No H-bonds generated for 'chain 'U' and resid 66 through 68' Processing helix chain 'X' and resid 54 through 61 Processing helix chain 'X' and resid 63 through 71 removed outlier: 3.958A pdb=" N LEU X 70 " --> pdb=" O VAL X 66 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG X 71 " --> pdb=" O LEU X 67 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 22 removed outlier: 3.617A pdb=" N LEU Y 14 " --> pdb=" O SER Y 10 " (cutoff:3.500A) removed outlier: 3.863A 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 24 through 33 Processing helix chain 'Y' and resid 40 through 58 removed outlier: 3.985A pdb=" N GLN Y 45 " --> pdb=" O LEU Y 42 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N VAL Y 46 " --> pdb=" O LEU Y 43 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG Y 47 " --> pdb=" O LYS Y 44 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ARG Y 48 " --> pdb=" O GLN Y 45 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU Y 56 " --> pdb=" O VAL Y 53 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LEU Y 57 " --> pdb=" O LYS Y 54 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN Y 58 " --> pdb=" O THR Y 55 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 26 Processing helix chain 'Z' and resid 41 through 49 Processing helix chain 'Z' and resid 51 through 53 No H-bonds generated for 'chain 'Z' and resid 51 through 53' Processing sheet with id= A, first strand: chain '0' and resid 27 through 29 Processing sheet with id= B, first strand: chain '1' and resid 6 through 11 Processing sheet with id= C, first strand: chain '1' and resid 35 through 39 Processing sheet with id= D, first strand: chain '4' and resid 17 through 19 Processing sheet with id= E, first strand: chain '8' and resid 62 through 65 removed outlier: 7.994A pdb=" N ASN 8 5 " --> pdb=" O ASP 8 43 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ASP 8 43 " --> pdb=" O ASN 8 5 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE 8 89 " --> pdb=" O PRO 8 27 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N VAL 8 92 " --> pdb=" O ALA 8 74 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ALA 8 74 " --> pdb=" O VAL 8 92 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 2 through 4 Processing sheet with id= G, 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= H, first strand: chain 'C' and resid 180 through 183 removed outlier: 3.712A pdb=" N ALA C 165 " --> pdb=" O THR C 172 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ARG C 174 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ILE C 163 " --> pdb=" O ARG C 174 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'D' and resid 12 through 15 Processing sheet with id= K, first strand: chain 'D' and resid 25 through 28 Processing sheet with id= L, first strand: chain 'D' and resid 80 through 83 removed outlier: 6.355A pdb=" N THR D 51 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N VAL D 34 " --> pdb=" O THR D 51 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 152 through 157 removed outlier: 6.828A pdb=" N THR F 67 " --> pdb=" O ILE F 84 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N CYS F 86 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU F 65 " --> pdb=" O CYS F 86 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 22 through 24 Processing sheet with id= O, first strand: chain 'G' and resid 40 through 43 Processing sheet with id= P, first strand: chain 'G' and resid 120 through 123 Processing sheet with id= Q, first strand: chain 'J' and resid 17 through 19 removed outlier: 6.415A pdb=" N ILE J 55 " --> pdb=" O VAL J 18 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'J' and resid 75 through 77 Processing sheet with id= S, first strand: chain 'K' and resid 5 through 9 removed outlier: 3.509A pdb=" N CYS K 21 " --> pdb=" O GLN K 5 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N MET K 7 " --> pdb=" O VAL K 19 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL K 19 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N VAL K 24 " --> pdb=" O ILE K 38 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ILE K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'L' and resid 74 through 76 removed outlier: 6.282A pdb=" N PHE L 107 " --> pdb=" O ALA L 75 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'L' and resid 89 through 91 removed outlier: 6.630A pdb=" N THR L 121 " --> pdb=" O VAL L 90 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LYS L 141 " --> pdb=" O VAL L 122 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'M' and resid 129 through 132 removed outlier: 3.693A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'M' and resid 39 through 42 Processing sheet with id= X, first strand: chain 'N' and resid 33 through 37 Processing sheet with id= Y, first strand: chain 'O' and resid 91 through 93 removed outlier: 3.647A pdb=" N HIS O 29 " --> pdb=" O TYR O 36 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'P' and resid 37 through 43 removed outlier: 3.779A pdb=" N SER P 82 " --> pdb=" O LYS P 28 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'P' and resid 70 through 74 removed outlier: 3.772A pdb=" N ALA P 48 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ARG P 61 " --> pdb=" O VAL P 46 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N VAL P 46 " --> pdb=" O ARG P 61 " (cutoff:3.500A) Processing sheet with id= AB, 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: 6.915A pdb=" N GLN R 6 " --> pdb=" O VAL R 38 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL R 38 " --> pdb=" O GLN R 6 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'R' and resid 20 through 23 Processing sheet with id= AD, first strand: chain 'R' and resid 32 through 35 Processing sheet with id= AE, 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= AF, first strand: chain 'S' and resid 4 through 7 removed outlier: 6.577A pdb=" N SER S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N VAL S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'T' and resid 61 through 63 removed outlier: 3.837A pdb=" N LEU T 61 " --> pdb=" O LYS T 82 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'T' and resid 11 through 14 removed outlier: 6.627A pdb=" N LYS T 33 " --> pdb=" O ARG T 12 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'U' and resid 21 through 23 Processing sheet with id= AJ, first strand: chain 'U' and resid 40 through 45 Processing sheet with id= AK, first strand: chain 'U' and resid 82 through 84 Processing sheet with id= AL, first strand: chain 'U' and resid 24 through 27 removed outlier: 6.883A pdb=" N ILE U 34 " --> pdb=" O LYS U 25 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'X' and resid 12 through 14 Processing sheet with id= AN, first strand: chain 'X' and resid 35 through 38 Processing sheet with id= AO, first strand: chain 'Z' and resid 35 through 37 607 hydrogen bonds defined for protein. 1635 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2477 hydrogen bonds 3952 hydrogen bond angles 0 basepair planarities 985 basepair parallelities 1495 stacking parallelities Total time for adding SS restraints: 162.22 Time building geometry restraints manager: 46.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.06: 8 1.06 - 1.26: 7257 1.26 - 1.46: 52856 1.46 - 1.67: 40333 1.67 - 1.87: 168 Bond restraints: 100622 Sorted by residual: bond pdb=" C4 5MU V 54 " pdb=" C5 5MU V 54 " ideal model delta sigma weight residual 1.802 1.441 0.361 2.00e-02 2.50e+03 3.27e+02 bond pdb=" N1 5MU V 54 " pdb=" C6 5MU V 54 " ideal model delta sigma weight residual 1.635 1.382 0.253 2.00e-02 2.50e+03 1.59e+02 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 1.42e+02 bond pdb=" N3 5MU V 54 " pdb=" C4 5MU V 54 " ideal model delta sigma weight residual 1.182 1.404 -0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" CA MET S 86 " pdb=" C MET S 86 " ideal model delta sigma weight residual 1.524 1.388 0.135 1.26e-02 6.30e+03 1.15e+02 ... (remaining 100617 not shown) Histogram of bond angle deviations from ideal: 54.48 - 74.61: 2 74.61 - 94.75: 12 94.75 - 114.88: 83896 114.88 - 135.02: 67032 135.02 - 155.15: 30 Bond angle restraints: 150972 Sorted by residual: angle pdb=" O ARG 7 23 " pdb=" C ARG 7 23 " pdb=" N PRO 7 24 " ideal model delta sigma weight residual 121.32 147.82 -26.50 1.15e+00 7.56e-01 5.31e+02 angle pdb=" C4' U A2585 " pdb=" C3' U A2585 " pdb=" O3' U A2585 " ideal model delta sigma weight residual 113.00 83.11 29.89 1.50e+00 4.44e-01 3.97e+02 angle pdb=" C4' G A2608 " pdb=" C3' G A2608 " pdb=" O3' G A2608 " ideal model delta sigma weight residual 113.00 141.42 -28.42 1.50e+00 4.44e-01 3.59e+02 angle pdb=" N ASN 7 14 " pdb=" CA ASN 7 14 " pdb=" CB ASN 7 14 " ideal model delta sigma weight residual 111.01 138.91 -27.90 1.56e+00 4.11e-01 3.20e+02 angle pdb=" CA ARG 7 23 " pdb=" C ARG 7 23 " pdb=" N PRO 7 24 " ideal model delta sigma weight residual 118.44 90.93 27.51 1.59e+00 3.96e-01 2.99e+02 ... (remaining 150967 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.26: 51207 35.26 - 70.53: 2080 70.53 - 105.79: 164 105.79 - 141.06: 17 141.06 - 176.32: 20 Dihedral angle restraints: 53488 sinusoidal: 43652 harmonic: 9836 Sorted by residual: dihedral pdb=" N ASP 7 16 " pdb=" C ASP 7 16 " pdb=" CA ASP 7 16 " pdb=" CB ASP 7 16 " ideal model delta harmonic sigma weight residual 122.80 94.77 28.03 0 2.50e+00 1.60e-01 1.26e+02 dihedral pdb=" CA ASP 7 21 " pdb=" C ASP 7 21 " pdb=" N HIS 7 22 " pdb=" CA HIS 7 22 " ideal model delta harmonic sigma weight residual 180.00 126.30 53.70 0 5.00e+00 4.00e-02 1.15e+02 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 28.34 171.66 1 1.50e+01 4.44e-03 8.49e+01 ... (remaining 53485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.352: 19315 0.352 - 0.704: 34 0.704 - 1.056: 2 1.056 - 1.408: 2 1.408 - 1.761: 6 Chirality restraints: 19359 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 -0.87 -1.76 2.00e-01 2.50e+01 7.75e+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 -0.91 -1.68 2.00e-01 2.50e+01 7.02e+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 1.03 1.61 2.00e-01 2.50e+01 6.50e+01 ... (remaining 19356 not shown) Planarity restraints: 7768 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 5MU V 54 " 0.006 2.00e-02 2.50e+03 5.78e-01 7.51e+03 pdb=" C4' 5MU V 54 " 0.421 2.00e-02 2.50e+03 pdb=" O4' 5MU V 54 " 0.666 2.00e-02 2.50e+03 pdb=" C3' 5MU V 54 " -0.622 2.00e-02 2.50e+03 pdb=" O3' 5MU V 54 " -0.563 2.00e-02 2.50e+03 pdb=" C2' 5MU V 54 " -0.190 2.00e-02 2.50e+03 pdb=" O2' 5MU V 54 " 0.918 2.00e-02 2.50e+03 pdb=" C1' 5MU V 54 " 0.229 2.00e-02 2.50e+03 pdb=" N1 5MU V 54 " -0.865 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G V 39 " -0.183 2.00e-02 2.50e+03 1.75e-01 9.16e+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 " 0.189 2.00e-02 2.50e+03 pdb=" C5 G V 39 " 0.055 2.00e-02 2.50e+03 pdb=" C6 G V 39 " -0.084 2.00e-02 2.50e+03 pdb=" O6 G V 39 " -0.211 2.00e-02 2.50e+03 pdb=" N1 G V 39 " -0.016 2.00e-02 2.50e+03 pdb=" C2 G V 39 " 0.027 2.00e-02 2.50e+03 pdb=" N2 G V 39 " 0.308 2.00e-02 2.50e+03 pdb=" N3 G V 39 " -0.262 2.00e-02 2.50e+03 pdb=" C4 G V 39 " -0.101 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 6.44e+02 pdb=" N1 C V 4 " 0.015 2.00e-02 2.50e+03 pdb=" C2 C V 4 " 0.071 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 " -0.290 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 ... (remaining 7765 not shown) Histogram of nonbonded interaction distances: 0.88 - 1.62: 7 1.62 - 2.37: 915 2.37 - 3.11: 70847 3.11 - 3.86: 248127 3.86 - 4.60: 370834 Warning: very small nonbonded interaction distances. Nonbonded interactions: 690730 Sorted by model distance: nonbonded pdb=" NH1 ARG F 79 " pdb=" C1' C V 56 " model vdw 0.879 3.250 nonbonded pdb=" O PRO 7 24 " pdb=" O2' A V 76 " model vdw 1.043 2.200 nonbonded pdb=" NH1 ARG F 79 " pdb=" O4' C V 56 " model vdw 1.237 2.350 nonbonded pdb=" OP1 A A2602 " pdb=" OP1 C V 75 " model vdw 1.395 2.800 nonbonded pdb=" O2' G A2061 " pdb=" N4 C A2063 " model vdw 1.396 2.350 ... (remaining 690725 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 group one per residue 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: 3.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 1.190 Extract box with map and model: 13.770 Check model and map are aligned: 1.000 Set scattering table: 0.640 Process input model: 354.660 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 379.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6238 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 0.361 100614 Z= 0.617 Angle : 1.501 70.523 150960 Z= 0.794 Chirality : 0.070 1.761 19359 Planarity : 0.012 0.578 7768 Dihedral : 15.490 176.323 47148 Min Nonbonded Distance : 0.879 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 6.82 % Allowed : 16.31 % Favored : 76.87 % Rotamer: Outliers : 11.16 % Allowed : 12.91 % Favored : 75.94 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.88 % Twisted General : 0.27 % 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: -5.04 (0.12), residues: 3402 helix: -3.74 (0.11), residues: 854 sheet: -2.86 (0.21), residues: 532 loop : -3.44 (0.12), residues: 2016 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1347 residues out of total 2805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 313 poor density : 1034 time to evaluate : 3.768 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 outliers start: 313 outliers final: 93 residues processed: 1232 average time/residue: 1.0618 time to fit residues: 2107.5581 Evaluate side-chains 820 residues out of total 2805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 727 time to evaluate : 3.799 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 93 outliers final: 2 residues processed: 93 average time/residue: 0.8327 time to fit residues: 146.7661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 537 optimal weight: 0.0470 chunk 482 optimal weight: 0.9980 chunk 267 optimal weight: 9.9990 chunk 164 optimal weight: 10.0000 chunk 325 optimal weight: 20.0000 chunk 257 optimal weight: 8.9990 chunk 499 optimal weight: 10.0000 chunk 193 optimal weight: 10.0000 chunk 303 optimal weight: 3.9990 chunk 371 optimal weight: 4.9990 chunk 578 optimal weight: 3.9990 overall best weight: 2.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 30 HIS 5 57 ASN 7 17 ASN 7 22 HIS 8 44 HIS 8 87 GLN ** 8 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN C 152 GLN C 162 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN D 185 ASN ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 GLN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 GLN H 20 ASN H 43 ASN ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 5 GLN ** K 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 18 GLN O 100 HIS O 104 GLN ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 GLN R 18 GLN R 66 HIS ** R 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 33 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 100614 Z= 0.211 Angle : 0.664 15.525 150960 Z= 0.348 Chirality : 0.035 0.281 19359 Planarity : 0.006 0.136 7768 Dihedral : 14.405 178.776 40397 Min Nonbonded Distance : 1.613 Molprobity Statistics. All-atom Clashscore : 39.34 Ramachandran Plot: Outliers : 3.09 % Allowed : 12.99 % Favored : 83.92 % Rotamer: Outliers : 6.02 % Allowed : 23.99 % Favored : 69.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -3.82 (0.13), residues: 3402 helix: -1.93 (0.16), residues: 873 sheet: -2.52 (0.21), residues: 553 loop : -2.93 (0.13), residues: 1976 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1003 residues out of total 2805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 834 time to evaluate : 3.974 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 outliers start: 169 outliers final: 118 residues processed: 906 average time/residue: 0.9865 time to fit residues: 1476.7224 Evaluate side-chains 854 residues out of total 2805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 736 time to evaluate : 3.834 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 118 outliers final: 2 residues processed: 118 average time/residue: 0.7146 time to fit residues: 162.3335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 321 optimal weight: 10.0000 chunk 179 optimal weight: 10.0000 chunk 481 optimal weight: 0.5980 chunk 393 optimal weight: 9.9990 chunk 159 optimal weight: 30.0000 chunk 579 optimal weight: 7.9990 chunk 626 optimal weight: 0.3980 chunk 516 optimal weight: 9.9990 chunk 574 optimal weight: 9.9990 chunk 197 optimal weight: 10.0000 chunk 464 optimal weight: 30.0000 overall best weight: 5.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 13 ASN ** 6 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 17 ASN 7 22 HIS ** 8 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 ASN F 4 HIS ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 ASN H 43 ASN J 47 HIS ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 55 HIS ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 59 ASN U 45 GLN ** W 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 33 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.6364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.129 100614 Z= 0.333 Angle : 0.778 17.697 150960 Z= 0.403 Chirality : 0.040 0.577 19359 Planarity : 0.007 0.133 7768 Dihedral : 15.629 179.597 40397 Min Nonbonded Distance : 1.515 Molprobity Statistics. All-atom Clashscore : 56.87 Ramachandran Plot: Outliers : 2.76 % Allowed : 15.70 % Favored : 81.54 % Rotamer: Outliers : 7.84 % Allowed : 24.42 % Favored : 67.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -3.77 (0.13), residues: 3402 helix: -1.67 (0.16), residues: 853 sheet: -2.32 (0.21), residues: 521 loop : -3.07 (0.12), residues: 2028 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1173 residues out of total 2805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 953 time to evaluate : 3.735 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 outliers start: 220 outliers final: 124 residues processed: 1066 average time/residue: 1.0276 time to fit residues: 1826.9868 Evaluate side-chains 964 residues out of total 2805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 840 time to evaluate : 3.757 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 124 outliers final: 2 residues processed: 124 average time/residue: 0.7781 time to fit residues: 185.2838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 572 optimal weight: 7.9990 chunk 435 optimal weight: 9.9990 chunk 300 optimal weight: 10.0000 chunk 64 optimal weight: 20.0000 chunk 276 optimal weight: 20.0000 chunk 389 optimal weight: 6.9990 chunk 581 optimal weight: 9.9990 chunk 615 optimal weight: 2.9990 chunk 303 optimal weight: 8.9990 chunk 551 optimal weight: 9.9990 chunk 165 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 17 ASN 7 22 HIS ** 8 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 HIS H 2 GLN H 20 ASN ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 ASN ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 5 GLN ** K 89 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 23 ASN O 38 GLN ** P 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 40 GLN ** Q 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 18 GLN ** S 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 40 ASN ** S 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 45 GLN X 19 HIS Y 31 GLN Z 33 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.7883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.119 100614 Z= 0.394 Angle : 0.801 14.053 150960 Z= 0.410 Chirality : 0.040 0.324 19359 Planarity : 0.007 0.122 7768 Dihedral : 16.223 179.398 40397 Min Nonbonded Distance : 1.552 Molprobity Statistics. All-atom Clashscore : 64.51 Ramachandran Plot: Outliers : 2.70 % Allowed : 15.81 % Favored : 81.48 % Rotamer: Outliers : 9.45 % Allowed : 27.24 % Favored : 63.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -3.99 (0.12), residues: 3402 helix: -1.85 (0.16), residues: 818 sheet: -2.31 (0.22), residues: 469 loop : -3.25 (0.12), residues: 2115 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1225 residues out of total 2805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 960 time to evaluate : 3.784 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 outliers start: 265 outliers final: 169 residues processed: 1088 average time/residue: 0.9560 time to fit residues: 1731.8805 Evaluate side-chains 1054 residues out of total 2805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 885 time to evaluate : 5.138 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 169 outliers final: 3 residues processed: 169 average time/residue: 0.7598 time to fit residues: 239.9258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 512 optimal weight: 3.9990 chunk 349 optimal weight: 1.9990 chunk 8 optimal weight: 0.0870 chunk 458 optimal weight: 6.9990 chunk 254 optimal weight: 10.0000 chunk 525 optimal weight: 0.9990 chunk 425 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 314 optimal weight: 10.0000 chunk 552 optimal weight: 0.8980 chunk 155 optimal weight: 20.0000 overall best weight: 1.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 ASN H 20 ASN H 43 ASN ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 HIS ** K 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 ASN ** M 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 23 ASN ** N 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 40 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 18 GLN ** S 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 16 ASN X 19 HIS ** Y 15 ASN ** 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: 0.7280 moved from start: 0.7980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.102 100614 Z= 0.145 Angle : 0.525 13.274 150960 Z= 0.282 Chirality : 0.030 0.298 19359 Planarity : 0.005 0.118 7768 Dihedral : 15.232 177.804 40397 Min Nonbonded Distance : 1.697 Molprobity Statistics. All-atom Clashscore : 49.46 Ramachandran Plot: Outliers : 2.50 % Allowed : 12.49 % Favored : 85.01 % Rotamer: Outliers : 3.42 % Allowed : 31.12 % Favored : 65.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.13), residues: 3402 helix: -0.84 (0.18), residues: 839 sheet: -2.20 (0.22), residues: 474 loop : -2.86 (0.13), residues: 2089 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1023 residues out of total 2805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 927 time to evaluate : 3.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 96 outliers final: 57 residues processed: 964 average time/residue: 0.9695 time to fit residues: 1553.1241 Evaluate side-chains 925 residues out of total 2805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 868 time to evaluate : 3.775 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 57 outliers final: 2 residues processed: 57 average time/residue: 0.7120 time to fit residues: 80.2007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 207 optimal weight: 10.0000 chunk 554 optimal weight: 9.9990 chunk 121 optimal weight: 10.0000 chunk 361 optimal weight: 0.2980 chunk 151 optimal weight: 10.0000 chunk 616 optimal weight: 20.0000 chunk 511 optimal weight: 8.9990 chunk 285 optimal weight: 10.0000 chunk 51 optimal weight: 20.0000 chunk 203 optimal weight: 20.0000 chunk 323 optimal weight: 10.0000 overall best weight: 7.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 ASN ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 18 GLN ** S 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 19 HIS ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.8456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 100614 Z= 0.388 Angle : 0.775 12.771 150960 Z= 0.393 Chirality : 0.038 0.287 19359 Planarity : 0.007 0.122 7768 Dihedral : 15.951 179.589 40397 Min Nonbonded Distance : 1.533 Molprobity Statistics. All-atom Clashscore : 69.10 Ramachandran Plot: Outliers : 2.56 % Allowed : 17.81 % Favored : 79.63 % Rotamer: Outliers : 7.84 % Allowed : 31.12 % Favored : 61.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.76 (0.13), residues: 3402 helix: -1.43 (0.17), residues: 817 sheet: -2.44 (0.22), residues: 509 loop : -3.12 (0.12), residues: 2076 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1113 residues out of total 2805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 893 time to evaluate : 3.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 220 outliers final: 167 residues processed: 988 average time/residue: 0.9485 time to fit residues: 1578.2286 Evaluate side-chains 1042 residues out of total 2805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 875 time to evaluate : 3.814 Switching outliers to nearest non-outliers outliers start: 167 outliers final: 1 residues processed: 167 average time/residue: 0.7230 time to fit residues: 231.2984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 594 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 351 optimal weight: 6.9990 chunk 450 optimal weight: 0.0030 chunk 348 optimal weight: 1.9990 chunk 518 optimal weight: 5.9990 chunk 344 optimal weight: 10.0000 chunk 613 optimal weight: 6.9990 chunk 384 optimal weight: 0.0870 chunk 374 optimal weight: 7.9990 chunk 283 optimal weight: 10.0000 overall best weight: 3.0174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 13 ASN ** 2 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 GLN H 20 ASN ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 23 ASN ** N 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 98 GLN ** P 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 19 HIS ** Y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.8573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 100614 Z= 0.180 Angle : 0.552 13.286 150960 Z= 0.293 Chirality : 0.031 0.272 19359 Planarity : 0.005 0.126 7768 Dihedral : 15.509 179.745 40397 Min Nonbonded Distance : 1.689 Molprobity Statistics. All-atom Clashscore : 53.78 Ramachandran Plot: Outliers : 2.38 % Allowed : 13.40 % Favored : 84.22 % Rotamer: Outliers : 2.35 % Allowed : 32.76 % Favored : 64.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.13), residues: 3402 helix: -0.87 (0.17), residues: 834 sheet: -2.19 (0.23), residues: 469 loop : -2.90 (0.12), residues: 2099 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 960 residues out of total 2805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 894 time to evaluate : 3.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 44 residues processed: 924 average time/residue: 0.9503 time to fit residues: 1468.0882 Evaluate side-chains 904 residues out of total 2805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 860 time to evaluate : 3.844 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 1 residues processed: 44 average time/residue: 0.7511 time to fit residues: 64.7736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 379 optimal weight: 10.0000 chunk 245 optimal weight: 10.0000 chunk 366 optimal weight: 10.0000 chunk 184 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 390 optimal weight: 9.9990 chunk 418 optimal weight: 10.0000 chunk 303 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 482 optimal weight: 9.9990 overall best weight: 9.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 3 GLN ** 1 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 24 ASN ** 8 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 HIS ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 HIS ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 23 ASN ** N 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 2 ASN P 51 ASN ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 45 GLN ** W 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 19 HIS ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.9385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.079 100614 Z= 0.517 Angle : 0.951 12.717 150960 Z= 0.472 Chirality : 0.044 0.359 19359 Planarity : 0.007 0.128 7768 Dihedral : 17.163 179.204 40397 Min Nonbonded Distance : 1.543 Molprobity Statistics. All-atom Clashscore : 80.15 Ramachandran Plot: Outliers : 2.50 % Allowed : 20.43 % Favored : 77.07 % Rotamer: Outliers : 6.06 % Allowed : 32.87 % Favored : 61.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -4.09 (0.13), residues: 3402 helix: -1.77 (0.16), residues: 802 sheet: -2.43 (0.22), residues: 495 loop : -3.37 (0.12), residues: 2105 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1084 residues out of total 2805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 914 time to evaluate : 4.731 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: 170 outliers final: 128 residues processed: 970 average time/residue: 0.9749 time to fit residues: 1577.0490 Evaluate side-chains 1012 residues out of total 2805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 884 time to evaluate : 3.891 Switching outliers to nearest non-outliers outliers start: 128 outliers final: 1 residues processed: 128 average time/residue: 0.7550 time to fit residues: 184.2592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 558 optimal weight: 0.9980 chunk 588 optimal weight: 10.0000 chunk 536 optimal weight: 0.9980 chunk 572 optimal weight: 6.9990 chunk 344 optimal weight: 10.0000 chunk 249 optimal weight: 6.9990 chunk 449 optimal weight: 6.9990 chunk 175 optimal weight: 7.9990 chunk 517 optimal weight: 7.9990 chunk 541 optimal weight: 10.0000 chunk 570 optimal weight: 0.4980 overall best weight: 3.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 ASN ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 98 GLN P 2 ASN ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 73 ASN ** W 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 19 HIS ** X 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.9407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 100614 Z= 0.203 Angle : 0.587 13.072 150960 Z= 0.310 Chirality : 0.033 0.400 19359 Planarity : 0.005 0.132 7768 Dihedral : 16.040 179.711 40397 Min Nonbonded Distance : 1.681 Molprobity Statistics. All-atom Clashscore : 57.02 Ramachandran Plot: Outliers : 2.29 % Allowed : 13.93 % Favored : 83.77 % Rotamer: Outliers : 1.57 % Allowed : 34.69 % Favored : 63.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.13), residues: 3402 helix: -1.02 (0.18), residues: 809 sheet: -2.30 (0.22), residues: 489 loop : -3.09 (0.12), residues: 2104 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 929 residues out of total 2805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 885 time to evaluate : 3.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 29 residues processed: 900 average time/residue: 0.9860 time to fit residues: 1484.4583 Evaluate side-chains 878 residues out of total 2805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 849 time to evaluate : 3.810 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 1 residues processed: 29 average time/residue: 0.7201 time to fit residues: 43.6662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 375 optimal weight: 9.9990 chunk 605 optimal weight: 20.0000 chunk 369 optimal weight: 3.9990 chunk 287 optimal weight: 10.0000 chunk 420 optimal weight: 4.9990 chunk 634 optimal weight: 10.0000 chunk 584 optimal weight: 0.0370 chunk 505 optimal weight: 0.0000 chunk 52 optimal weight: 10.0000 chunk 390 optimal weight: 10.0000 chunk 309 optimal weight: 10.0000 overall best weight: 3.8068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 44 GLN ** 1 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 13 ASN ** 2 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 24 ASN ** 8 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 ASN ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 2 ASN ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.9501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 100614 Z= 0.214 Angle : 0.586 12.913 150960 Z= 0.308 Chirality : 0.032 0.400 19359 Planarity : 0.005 0.133 7768 Dihedral : 16.026 179.749 40397 Min Nonbonded Distance : 1.696 Molprobity Statistics. All-atom Clashscore : 58.29 Ramachandran Plot: Outliers : 2.23 % Allowed : 16.64 % Favored : 81.13 % Rotamer: Outliers : 1.07 % Allowed : 37.33 % Favored : 61.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.13), residues: 3402 helix: -0.88 (0.18), residues: 809 sheet: -2.29 (0.22), residues: 484 loop : -3.03 (0.12), residues: 2109 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6804 Ramachandran restraints generated. 3402 Oldfield, 0 Emsley, 3402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 901 residues out of total 2805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 871 time to evaluate : 3.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 24 residues processed: 882 average time/residue: 0.9837 time to fit residues: 1455.8312 Evaluate side-chains 888 residues out of total 2805 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 864 time to evaluate : 3.880 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 1 residues processed: 24 average time/residue: 0.8028 time to fit residues: 39.1403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 637 random chunks: chunk 401 optimal weight: 0.8980 chunk 538 optimal weight: 0.4980 chunk 154 optimal weight: 20.0000 chunk 465 optimal weight: 9.9990 chunk 74 optimal weight: 20.0000 chunk 140 optimal weight: 20.0000 chunk 506 optimal weight: 4.9990 chunk 211 optimal weight: 10.0000 chunk 519 optimal weight: 10.0000 chunk 64 optimal weight: 20.0000 chunk 93 optimal weight: 10.0000 overall best weight: 5.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 13 ASN ** 2 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 GLN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 2 ASN ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.159799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.135739 restraints weight = 186085.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.138865 restraints weight = 67537.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.140733 restraints weight = 34987.374| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3792 r_free = 0.3792 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3792 r_free = 0.3792 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3792 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.9537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 100614 Z= 0.275 Angle : 0.629 12.869 150960 Z= 0.327 Chirality : 0.034 0.400 19359 Planarity : 0.005 0.133 7768 Dihedral : 16.063 179.410 40397 Min Nonbonded Distance : 1.621 Molprobity Statistics. All-atom Clashscore : 60.75 Ramachandran Plot: Outliers : 2.23 % Allowed : 17.31 % Favored : 80.45 % Rotamer: Outliers : 1.71 % Allowed : 37.15 % Favored : 61.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.49 (0.13), residues: 3402 helix: -0.98 (0.18), residues: 810 sheet: -2.31 (0.22), residues: 491 loop : -3.04 (0.12), residues: 2101 =============================================================================== Job complete usr+sys time: 23722.96 seconds wall clock time: 419 minutes 30.96 seconds (25170.96 seconds total)