Starting phenix.real_space_refine on Mon Sep 23 17:49:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5anb_3146/09_2024/5anb_3146.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5anb_3146/09_2024/5anb_3146.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5anb_3146/09_2024/5anb_3146.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5anb_3146/09_2024/5anb_3146.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5anb_3146/09_2024/5anb_3146.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5anb_3146/09_2024/5anb_3146.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.028 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: 5 Type Number sf(0) Gaussians P 1158 5.49 5 S 138 5.16 5 C 26065 2.51 5 N 8658 2.21 5 O 12474 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 48493 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3176 Classifications: {'peptide': 398} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 12, 'TRANS': 382} Chain: "B" Number of atoms: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1491 Classifications: {'peptide': 188} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 184} Chain: "C" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1571 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 195} Chain: "D" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1245 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 150} Chain: "E" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1017 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'CIS': 4, 'PTRANS': 6, 'TRANS': 125} Chain: "F" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1721 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 209} Chain: "G" Number of atoms: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 586 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "H" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 427 Classifications: {'peptide': 52} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "I" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1686 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 217} Chain: "J" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2015 Classifications: {'peptide': 250} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 242} Chain: "K" Number of atoms: 8800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1120, 8800 Classifications: {'peptide': 1120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 62, 'TRANS': 1057} Chain: "N" Number of atoms: 24758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1162, 24758 Inner-chain residues flagged as termini: ['pdbres=" C N1356 "', 'pdbres=" A N2392 "', 'pdbres=" A N2925 "'] Classifications: {'RNA': 1162} Modifications used: {'5*END': 4, 'rna2p_pur': 101, 'rna2p_pyr': 59, 'rna3p_pur': 523, 'rna3p_pyr': 479} Link IDs: {'rna2p': 160, 'rna3p': 1001} Time building chain proxies: 19.53, per 1000 atoms: 0.40 Number of scatterers: 48493 At special positions: 0 Unit cell: (208.81, 194.18, 214.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 138 16.00 P 1158 15.00 O 12474 8.00 N 8658 7.00 C 26065 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.30 Conformation dependent library (CDL) restraints added in 2.6 seconds 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5632 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 39 sheets defined 28.4% alpha, 11.3% beta 320 base pairs and 533 stacking pairs defined. Time for finding SS restraints: 15.34 Creating SS restraints... Processing helix chain 'A' and resid 13 through 17 removed outlier: 3.513A pdb=" N PHE A 16 " --> pdb=" O ASN A 13 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG A 17 " --> pdb=" O LEU A 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 13 through 17' Processing helix chain 'A' and resid 111 through 120 removed outlier: 3.832A pdb=" N ARG A 115 " --> pdb=" O SER A 111 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU A 118 " --> pdb=" O PHE A 114 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR A 119 " --> pdb=" O ARG A 115 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LYS A 120 " --> pdb=" O ARG A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 157 removed outlier: 3.590A pdb=" N LYS A 145 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER A 146 " --> pdb=" O GLU A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 202 removed outlier: 3.638A pdb=" N ALA A 198 " --> pdb=" O LYS A 194 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N VAL A 199 " --> pdb=" O VAL A 195 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA A 200 " --> pdb=" O ASN A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 377 through 385 removed outlier: 3.504A pdb=" N GLU A 382 " --> pdb=" O HIS A 378 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS A 384 " --> pdb=" O THR A 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 84 Processing helix chain 'B' and resid 148 through 163 Processing helix chain 'C' and resid 35 through 43 removed outlier: 3.600A pdb=" N GLN C 40 " --> pdb=" O SER C 36 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LYS C 41 " --> pdb=" O SER C 37 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE C 42 " --> pdb=" O GLN C 38 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG C 43 " --> pdb=" O LEU C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 66 removed outlier: 3.635A pdb=" N VAL C 63 " --> pdb=" O ILE C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 100 removed outlier: 3.633A pdb=" N VAL C 100 " --> pdb=" O VAL C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 137 removed outlier: 4.096A pdb=" N THR C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER C 135 " --> pdb=" O PRO C 131 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE C 136 " --> pdb=" O THR C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 177 removed outlier: 3.704A pdb=" N GLN C 175 " --> pdb=" O ALA C 171 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS C 176 " --> pdb=" O THR C 172 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU C 177 " --> pdb=" O LEU C 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 171 through 177' Processing helix chain 'D' and resid 45 through 51 Processing helix chain 'D' and resid 79 through 85 removed outlier: 4.024A pdb=" N LEU D 85 " --> pdb=" O VAL D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 92 Processing helix chain 'D' and resid 106 through 118 removed outlier: 3.815A pdb=" N CYS D 110 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS D 111 " --> pdb=" O GLU D 107 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA D 113 " --> pdb=" O ILE D 109 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR D 115 " --> pdb=" O LYS D 111 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N MET D 116 " --> pdb=" O ILE D 112 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE D 118 " --> pdb=" O LYS D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 133 Processing helix chain 'E' and resid 119 through 125 Processing helix chain 'E' and resid 125 through 131 Processing helix chain 'F' and resid 62 through 70 removed outlier: 3.509A pdb=" N ILE F 70 " --> pdb=" O GLU F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 79 removed outlier: 3.603A pdb=" N LYS F 78 " --> pdb=" O LYS F 74 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR F 79 " --> pdb=" O TYR F 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 74 through 79' Processing helix chain 'F' and resid 145 through 158 removed outlier: 3.724A pdb=" N GLU F 150 " --> pdb=" O ALA F 146 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ALA F 151 " --> pdb=" O ASN F 147 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS F 158 " --> pdb=" O ARG F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 187 removed outlier: 3.614A pdb=" N GLN F 182 " --> pdb=" O ARG F 178 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS F 183 " --> pdb=" O GLU F 179 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU F 184 " --> pdb=" O ALA F 180 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS F 185 " --> pdb=" O TYR F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 215 removed outlier: 3.763A pdb=" N ALA F 214 " --> pdb=" O ALA F 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 43 Processing helix chain 'G' and resid 52 through 60 removed outlier: 3.914A pdb=" N ARG G 56 " --> pdb=" O SER G 52 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 69 removed outlier: 3.698A pdb=" N ALA G 68 " --> pdb=" O THR G 64 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS G 69 " --> pdb=" O ASP G 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 64 through 69' Processing helix chain 'H' and resid 1 through 12 Processing helix chain 'I' and resid 32 through 42 removed outlier: 3.664A pdb=" N VAL I 38 " --> pdb=" O PHE I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 88 Processing helix chain 'I' and resid 122 through 134 Processing helix chain 'I' and resid 166 through 178 removed outlier: 3.675A pdb=" N GLN I 170 " --> pdb=" O SER I 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 192 through 196 removed outlier: 3.645A pdb=" N GLY I 196 " --> pdb=" O CYS I 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 192 through 196' Processing helix chain 'I' and resid 211 through 222 removed outlier: 3.523A pdb=" N SER I 216 " --> pdb=" O ALA I 212 " (cutoff:3.500A) Processing helix chain 'J' and resid 35 through 41 removed outlier: 4.212A pdb=" N ARG J 40 " --> pdb=" O VAL J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 50 removed outlier: 3.741A pdb=" N VAL J 50 " --> pdb=" O ASP J 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 46 through 50' Processing helix chain 'J' and resid 67 through 76 Processing helix chain 'J' and resid 79 through 91 removed outlier: 3.707A pdb=" N ILE J 83 " --> pdb=" O ASP J 79 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 117 removed outlier: 3.624A pdb=" N VAL J 115 " --> pdb=" O ILE J 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 129 through 141 removed outlier: 4.420A pdb=" N ILE J 133 " --> pdb=" O THR J 129 " (cutoff:3.500A) Processing helix chain 'J' and resid 149 through 163 removed outlier: 4.027A pdb=" N LYS J 159 " --> pdb=" O LEU J 155 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLN J 160 " --> pdb=" O GLU J 156 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU J 163 " --> pdb=" O LYS J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 179 through 194 removed outlier: 4.060A pdb=" N LYS J 184 " --> pdb=" O VAL J 180 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS J 185 " --> pdb=" O ASN J 181 " (cutoff:3.500A) Proline residue: J 192 - end of helix Processing helix chain 'J' and resid 217 through 229 removed outlier: 4.426A pdb=" N ASP J 221 " --> pdb=" O PHE J 217 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU J 222 " --> pdb=" O ARG J 218 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE J 224 " --> pdb=" O ILE J 220 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS J 225 " --> pdb=" O ASP J 221 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 15 Processing helix chain 'K' and resid 31 through 43 removed outlier: 3.616A pdb=" N LEU K 39 " --> pdb=" O LEU K 35 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 67 Processing helix chain 'K' and resid 102 through 110 Processing helix chain 'K' and resid 124 through 135 removed outlier: 3.793A pdb=" N GLN K 133 " --> pdb=" O ALA K 129 " (cutoff:3.500A) Processing helix chain 'K' and resid 147 through 153 removed outlier: 3.983A pdb=" N LEU K 151 " --> pdb=" O LYS K 147 " (cutoff:3.500A) Processing helix chain 'K' and resid 158 through 178 removed outlier: 3.509A pdb=" N ALA K 162 " --> pdb=" O THR K 158 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR K 163 " --> pdb=" O PRO K 159 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER K 164 " --> pdb=" O GLN K 160 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN K 168 " --> pdb=" O SER K 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 192 Processing helix chain 'K' and resid 201 through 208 removed outlier: 4.192A pdb=" N GLY K 205 " --> pdb=" O ASN K 201 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL K 208 " --> pdb=" O GLN K 204 " (cutoff:3.500A) Processing helix chain 'K' and resid 226 through 231 Processing helix chain 'K' and resid 244 through 256 Processing helix chain 'K' and resid 259 through 267 removed outlier: 3.675A pdb=" N LEU K 263 " --> pdb=" O LYS K 259 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LYS K 265 " --> pdb=" O GLU K 261 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR K 266 " --> pdb=" O VAL K 262 " (cutoff:3.500A) Processing helix chain 'K' and resid 291 through 296 removed outlier: 4.108A pdb=" N GLN K 295 " --> pdb=" O PRO K 291 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU K 296 " --> pdb=" O LEU K 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 291 through 296' Processing helix chain 'K' and resid 299 through 311 removed outlier: 3.781A pdb=" N SER K 303 " --> pdb=" O GLU K 299 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU K 309 " --> pdb=" O TYR K 305 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS K 310 " --> pdb=" O ASP K 306 " (cutoff:3.500A) Processing helix chain 'K' and resid 313 through 321 removed outlier: 3.657A pdb=" N ILE K 319 " --> pdb=" O LYS K 315 " (cutoff:3.500A) Processing helix chain 'K' and resid 338 through 347 removed outlier: 3.956A pdb=" N ASN K 342 " --> pdb=" O LYS K 338 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN K 347 " --> pdb=" O ALA K 343 " (cutoff:3.500A) Processing helix chain 'K' and resid 351 through 362 removed outlier: 4.028A pdb=" N ALA K 357 " --> pdb=" O HIS K 353 " (cutoff:3.500A) Processing helix chain 'K' and resid 367 through 373 removed outlier: 3.870A pdb=" N ALA K 371 " --> pdb=" O LEU K 367 " (cutoff:3.500A) Processing helix chain 'K' and resid 393 through 402 Processing helix chain 'K' and resid 439 through 448 Processing helix chain 'K' and resid 450 through 459 removed outlier: 4.440A pdb=" N ALA K 456 " --> pdb=" O LYS K 452 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN K 459 " --> pdb=" O ALA K 455 " (cutoff:3.500A) Processing helix chain 'K' and resid 469 through 474 removed outlier: 4.361A pdb=" N THR K 473 " --> pdb=" O SER K 469 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N CYS K 474 " --> pdb=" O ALA K 470 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 469 through 474' Processing helix chain 'K' and resid 529 through 535 removed outlier: 3.621A pdb=" N GLU K 533 " --> pdb=" O TYR K 529 " (cutoff:3.500A) Processing helix chain 'K' and resid 629 through 644 removed outlier: 3.828A pdb=" N LYS K 638 " --> pdb=" O VAL K 634 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN K 642 " --> pdb=" O LYS K 638 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA K 643 " --> pdb=" O LEU K 639 " (cutoff:3.500A) Processing helix chain 'K' and resid 663 through 674 removed outlier: 4.125A pdb=" N GLN K 668 " --> pdb=" O GLU K 664 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG K 669 " --> pdb=" O VAL K 665 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP K 672 " --> pdb=" O GLN K 668 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP K 673 " --> pdb=" O ARG K 669 " (cutoff:3.500A) Processing helix chain 'K' and resid 720 through 725 Processing helix chain 'K' and resid 731 through 735 removed outlier: 3.903A pdb=" N VAL K 734 " --> pdb=" O GLY K 731 " (cutoff:3.500A) Processing helix chain 'K' and resid 759 through 768 Processing helix chain 'K' and resid 772 through 777 Processing helix chain 'K' and resid 787 through 796 removed outlier: 4.240A pdb=" N MET K 791 " --> pdb=" O GLU K 787 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE K 792 " --> pdb=" O ASN K 788 " (cutoff:3.500A) Processing helix chain 'K' and resid 808 through 813 removed outlier: 4.085A pdb=" N THR K 812 " --> pdb=" O GLU K 808 " (cutoff:3.500A) Processing helix chain 'K' and resid 858 through 863 Processing helix chain 'K' and resid 866 through 879 removed outlier: 3.711A pdb=" N VAL K 870 " --> pdb=" O GLY K 866 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLN K 874 " --> pdb=" O VAL K 870 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU K 875 " --> pdb=" O SER K 871 " (cutoff:3.500A) Processing helix chain 'K' and resid 907 through 918 Processing helix chain 'K' and resid 935 through 942 removed outlier: 3.691A pdb=" N GLU K 939 " --> pdb=" O SER K 935 " (cutoff:3.500A) Processing helix chain 'K' and resid 957 through 976 removed outlier: 3.825A pdb=" N ARG K 970 " --> pdb=" O LYS K 966 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL K 975 " --> pdb=" O TYR K 971 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS K 976 " --> pdb=" O ALA K 972 " (cutoff:3.500A) Processing helix chain 'K' and resid 992 through 1005 removed outlier: 4.091A pdb=" N GLY K 997 " --> pdb=" O GLY K 993 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ARG K 998 " --> pdb=" O ASP K 994 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL K1002 " --> pdb=" O ARG K 998 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS K1005 " --> pdb=" O ALA K1001 " (cutoff:3.500A) Processing helix chain 'K' and resid 1036 through 1044 removed outlier: 3.585A pdb=" N ILE K1040 " --> pdb=" O PHE K1036 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS K1042 " --> pdb=" O ASP K1038 " (cutoff:3.500A) Processing helix chain 'K' and resid 1070 through 1077 removed outlier: 4.027A pdb=" N TYR K1074 " --> pdb=" O THR K1070 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE K1077 " --> pdb=" O GLU K1073 " (cutoff:3.500A) Processing helix chain 'K' and resid 1086 through 1090 removed outlier: 3.520A pdb=" N LYS K1089 " --> pdb=" O GLN K1086 " (cutoff:3.500A) Processing helix chain 'K' and resid 1112 through 1117 removed outlier: 3.645A pdb=" N LEU K1116 " --> pdb=" O LYS K1112 " (cutoff:3.500A) Processing sheet with id=AA, first strand: chain 'A' and resid 45 through 46 removed outlier: 5.128A pdb=" N ILE A 218 " --> pdb=" O ASN A 282 " (cutoff:3.500A) Processing sheet with id=AB, first strand: chain 'A' and resid 287 through 289 removed outlier: 7.578A pdb=" N HIS A 55 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ILE A 367 " --> pdb=" O HIS A 55 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL A 57 " --> pdb=" O LYS A 365 " (cutoff:3.500A) Processing sheet with id=AC, first strand: chain 'A' and resid 98 through 106 removed outlier: 5.025A pdb=" N LEU A 99 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N THR A 95 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N THR A 101 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL A 93 " --> pdb=" O THR A 101 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS A 103 " --> pdb=" O GLY A 91 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY A 91 " --> pdb=" O LYS A 103 " (cutoff:3.500A) Processing sheet with id=AD, first strand: chain 'A' and resid 229 through 230 removed outlier: 3.514A pdb=" N GLY A 271 " --> pdb=" O ASN A 230 " (cutoff:3.500A) Processing sheet with id=BA, first strand: chain 'B' and resid 8 through 11 Processing sheet with id=BB, first strand: chain 'B' and resid 17 through 20 Processing sheet with id=BC, first strand: chain 'B' and resid 133 through 134 removed outlier: 7.604A pdb=" N GLU B 87 " --> pdb=" O ARG B 182 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ARG B 182 " --> pdb=" O GLU B 87 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LYS B 89 " --> pdb=" O SER B 180 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY B 176 " --> pdb=" O VAL B 93 " (cutoff:3.500A) Processing sheet with id=BD, first strand: chain 'B' and resid 101 through 104 removed outlier: 3.515A pdb=" N VAL B 110 " --> pdb=" O ILE B 124 " (cutoff:3.500A) Processing sheet with id=CA, first strand: chain 'C' and resid 52 through 53 removed outlier: 3.871A pdb=" N ILE C 87 " --> pdb=" O LEU C 53 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS C 25 " --> pdb=" O CYS C 90 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N MET C 26 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE C 191 " --> pdb=" O MET C 26 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N VAL C 28 " --> pdb=" O LYS C 189 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU C 187 " --> pdb=" O GLU C 30 " (cutoff:3.500A) Processing sheet with id=DA, first strand: chain 'D' and resid 13 through 14 Processing sheet with id=EA, first strand: chain 'E' and resid 22 through 24 removed outlier: 5.133A pdb=" N VAL E 36 " --> pdb=" O THR E 61 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR E 61 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA E 38 " --> pdb=" O MET E 59 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL E 58 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N THR E 75 " --> pdb=" O VAL E 58 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ALA E 60 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N VAL E 73 " --> pdb=" O ALA E 60 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N VAL E 62 " --> pdb=" O LYS E 71 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS E 71 " --> pdb=" O VAL E 62 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ALA E 99 " --> pdb=" O VAL E 79 " (cutoff:3.500A) Processing sheet with id=EB, first strand: chain 'E' and resid 85 through 86 Processing sheet with id=EC, first strand: chain 'E' and resid 117 through 118 Processing sheet with id=FA, first strand: chain 'F' and resid 36 through 37 removed outlier: 3.657A pdb=" N LEU F 36 " --> pdb=" O MET F 87 " (cutoff:3.500A) Processing sheet with id=FB, first strand: chain 'F' and resid 134 through 140 removed outlier: 7.076A pdb=" N ILE F 134 " --> pdb=" O SER F 54 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N SER F 54 " --> pdb=" O ILE F 134 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE F 136 " --> pdb=" O LEU F 52 " (cutoff:3.500A) Processing sheet with id=FC, first strand: chain 'F' and resid 58 through 61 removed outlier: 5.977A pdb=" N ILE F 99 " --> pdb=" O PRO F 122 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY F 124 " --> pdb=" O LEU F 97 " (cutoff:3.500A) Processing sheet with id=FD, first strand: chain 'F' and resid 192 through 193 removed outlier: 3.729A pdb=" N ASN F 196 " --> pdb=" O ASP F 193 " (cutoff:3.500A) Processing sheet with id=GA, first strand: chain 'G' and resid 4 through 5 Processing sheet with id=GB, first strand: chain 'G' and resid 19 through 22 Processing sheet with id=HA, first strand: chain 'H' and resid 17 through 19 Processing sheet with id=IA, first strand: chain 'I' and resid 2 through 4 Processing sheet with id=IB, first strand: chain 'I' and resid 17 through 18 Processing sheet with id=IC, first strand: chain 'I' and resid 64 through 65 removed outlier: 3.519A pdb=" N GLN I 95 " --> pdb=" O LEU I 70 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU I 72 " --> pdb=" O GLN I 95 " (cutoff:3.500A) Processing sheet with id=ID, first strand: chain 'I' and resid 109 through 110 Processing sheet with id=IE, first strand: chain 'I' and resid 152 through 154 Processing sheet with id=JA, first strand: chain 'J' and resid 19 through 22 removed outlier: 10.711A pdb=" N ARG J 26 " --> pdb=" O VAL J 56 " (cutoff:3.500A) removed outlier: 9.521A pdb=" N VAL J 56 " --> pdb=" O ARG J 26 " (cutoff:3.500A) removed outlier: 10.155A pdb=" N GLU J 28 " --> pdb=" O HIS J 54 " (cutoff:3.500A) removed outlier: 8.983A pdb=" N HIS J 54 " --> pdb=" O GLU J 28 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ALA J 30 " --> pdb=" O GLN J 52 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLN J 64 " --> pdb=" O VAL J 58 " (cutoff:3.500A) Processing sheet with id=JB, first strand: chain 'J' and resid 196 through 200 removed outlier: 7.360A pdb=" N VAL J 196 " --> pdb=" O ILE J 212 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ILE J 212 " --> pdb=" O VAL J 196 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N GLU J 198 " --> pdb=" O CYS J 210 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N CYS J 210 " --> pdb=" O GLU J 198 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU J 200 " --> pdb=" O ILE J 208 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ILE J 208 " --> pdb=" O GLU J 200 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU J 207 " --> pdb=" O LEU J 178 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL J 209 " --> pdb=" O PHE J 176 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU J 174 " --> pdb=" O LEU J 211 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP J 213 " --> pdb=" O MET J 172 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU J 234 " --> pdb=" O ILE J 177 " (cutoff:3.500A) Processing sheet with id=KA, first strand: chain 'K' and resid 73 through 74 removed outlier: 3.677A pdb=" N SER K 73 " --> pdb=" O ASP K 92 " (cutoff:3.500A) Processing sheet with id=KB, first strand: chain 'K' and resid 78 through 80 removed outlier: 3.791A pdb=" N TYR K 79 " --> pdb=" O TYR K 86 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR K 86 " --> pdb=" O TYR K 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=KB Processing sheet with id=KC, first strand: chain 'K' and resid 113 through 118 removed outlier: 3.527A pdb=" N VAL K 142 " --> pdb=" O CYS K 113 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL K 117 " --> pdb=" O VAL K 144 " (cutoff:3.500A) Processing sheet with id=KD, first strand: chain 'K' and resid 272 through 273 Processing sheet with id=KE, first strand: chain 'K' and resid 412 through 413 Processing sheet with id=KF, first strand: chain 'K' and resid 520 through 523 removed outlier: 3.647A pdb=" N LYS K 520 " --> pdb=" O LEU K 560 " (cutoff:3.500A) Processing sheet with id=KG, first strand: chain 'K' and resid 563 through 564 Processing sheet with id=KH, first strand: chain 'K' and resid 621 through 624 removed outlier: 3.851A pdb=" N ALA K 621 " --> pdb=" O SER K 686 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER K 686 " --> pdb=" O ALA K 621 " (cutoff:3.500A) Processing sheet with id=KI, first strand: chain 'K' and resid 693 through 695 Processing sheet with id=KJ, first strand: chain 'K' and resid 750 through 751 Processing sheet with id=KK, first strand: chain 'K' and resid 754 through 757 removed outlier: 4.475A pdb=" N ILE K 835 " --> pdb=" O VAL K 890 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL K 837 " --> pdb=" O PHE K 892 " (cutoff:3.500A) Processing sheet with id=KL, first strand: chain 'K' and resid 1009 through 1015 removed outlier: 5.867A pdb=" N VAL K1010 " --> pdb=" O VAL K1027 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL K1027 " --> pdb=" O VAL K1010 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLN K1012 " --> pdb=" O LYS K1025 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE K1024 " --> pdb=" O ILE K 989 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE K 989 " --> pdb=" O ILE K1024 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA K1026 " --> pdb=" O CYS K 987 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR K 986 " --> pdb=" O VAL K1053 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL K1053 " --> pdb=" O THR K 986 " (cutoff:3.500A) 585 hydrogen bonds defined for protein. 1608 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 779 hydrogen bonds 1328 hydrogen bond angles 0 basepair planarities 320 basepair parallelities 533 stacking parallelities Total time for adding SS restraints: 38.68 Time building geometry restraints manager: 10.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6276 1.33 - 1.45: 20060 1.45 - 1.58: 23008 1.58 - 1.70: 2284 1.70 - 1.83: 212 Bond restraints: 51840 Sorted by residual: bond pdb=" CA LEU A 249 " pdb=" C LEU A 249 " ideal model delta sigma weight residual 1.522 1.575 -0.053 1.24e-02 6.50e+03 1.82e+01 bond pdb=" O3' C N3316 " pdb=" P C N3317 " ideal model delta sigma weight residual 1.607 1.668 -0.061 1.50e-02 4.44e+03 1.66e+01 bond pdb=" N GLN J 9 " pdb=" CA GLN J 9 " ideal model delta sigma weight residual 1.456 1.500 -0.044 1.16e-02 7.43e+03 1.45e+01 bond pdb=" CA LEU E 49 " pdb=" C LEU E 49 " ideal model delta sigma weight residual 1.528 1.484 0.044 1.18e-02 7.18e+03 1.40e+01 bond pdb=" N VAL A 135 " pdb=" CA VAL A 135 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.25e-02 6.40e+03 1.34e+01 ... (remaining 51835 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.28: 73071 3.28 - 6.55: 2461 6.55 - 9.83: 130 9.83 - 13.10: 10 13.10 - 16.38: 2 Bond angle restraints: 75674 Sorted by residual: angle pdb=" O3' G N2995 " pdb=" C3' G N2995 " pdb=" C2' G N2995 " ideal model delta sigma weight residual 113.70 130.08 -16.38 1.50e+00 4.44e-01 1.19e+02 angle pdb=" O3' G N2515 " pdb=" C3' G N2515 " pdb=" C2' G N2515 " ideal model delta sigma weight residual 113.70 126.29 -12.59 1.50e+00 4.44e-01 7.04e+01 angle pdb=" C4' U N3457 " pdb=" C3' U N3457 " pdb=" O3' U N3457 " ideal model delta sigma weight residual 109.40 121.96 -12.56 1.50e+00 4.44e-01 7.02e+01 angle pdb=" C4' A N2663 " pdb=" C3' A N2663 " pdb=" O3' A N2663 " ideal model delta sigma weight residual 113.00 101.22 11.78 1.50e+00 4.44e-01 6.17e+01 angle pdb=" C4' G N3183 " pdb=" C3' G N3183 " pdb=" O3' G N3183 " ideal model delta sigma weight residual 113.00 101.42 11.58 1.50e+00 4.44e-01 5.96e+01 ... (remaining 75669 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 29336 35.95 - 71.91: 2994 71.91 - 107.86: 317 107.86 - 143.82: 10 143.82 - 179.77: 40 Dihedral angle restraints: 32697 sinusoidal: 23979 harmonic: 8718 Sorted by residual: dihedral pdb=" C5' A N2547 " pdb=" C4' A N2547 " pdb=" C3' A N2547 " pdb=" O3' A N2547 " ideal model delta sinusoidal sigma weight residual 147.00 80.45 66.55 1 8.00e+00 1.56e-02 9.03e+01 dihedral pdb=" O4' C N3169 " pdb=" C1' C N3169 " pdb=" N1 C N3169 " pdb=" C2 C N3169 " ideal model delta sinusoidal sigma weight residual -160.00 18.21 -178.21 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C N2497 " pdb=" C1' C N2497 " pdb=" N1 C N2497 " pdb=" C2 C N2497 " ideal model delta sinusoidal sigma weight residual 200.00 22.63 177.37 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 32694 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 7591 0.122 - 0.244: 1678 0.244 - 0.367: 193 0.367 - 0.489: 10 0.489 - 0.611: 4 Chirality restraints: 9476 Sorted by residual: chirality pdb=" CA PHE K 399 " pdb=" N PHE K 399 " pdb=" C PHE K 399 " pdb=" CB PHE K 399 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.33e+00 chirality pdb=" C3' A N2547 " pdb=" C4' A N2547 " pdb=" O3' A N2547 " pdb=" C2' A N2547 " both_signs ideal model delta sigma weight residual False -2.74 -2.14 -0.60 2.00e-01 2.50e+01 9.06e+00 chirality pdb=" C3' U N3105 " pdb=" C4' U N3105 " pdb=" O3' U N3105 " pdb=" C2' U N3105 " both_signs ideal model delta sigma weight residual False -2.74 -2.16 -0.58 2.00e-01 2.50e+01 8.45e+00 ... (remaining 9473 not shown) Planarity restraints: 5341 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U N2931 " 0.061 2.00e-02 2.50e+03 3.90e-02 3.42e+01 pdb=" N1 U N2931 " -0.034 2.00e-02 2.50e+03 pdb=" C2 U N2931 " -0.003 2.00e-02 2.50e+03 pdb=" O2 U N2931 " 0.004 2.00e-02 2.50e+03 pdb=" N3 U N2931 " -0.046 2.00e-02 2.50e+03 pdb=" C4 U N2931 " -0.013 2.00e-02 2.50e+03 pdb=" O4 U N2931 " 0.073 2.00e-02 2.50e+03 pdb=" C5 U N2931 " -0.031 2.00e-02 2.50e+03 pdb=" C6 U N2931 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C N3209 " -0.042 2.00e-02 2.50e+03 3.79e-02 3.23e+01 pdb=" N1 C N3209 " 0.040 2.00e-02 2.50e+03 pdb=" C2 C N3209 " -0.011 2.00e-02 2.50e+03 pdb=" O2 C N3209 " 0.055 2.00e-02 2.50e+03 pdb=" N3 C N3209 " -0.077 2.00e-02 2.50e+03 pdb=" C4 C N3209 " 0.001 2.00e-02 2.50e+03 pdb=" N4 C N3209 " 0.019 2.00e-02 2.50e+03 pdb=" C5 C N3209 " 0.009 2.00e-02 2.50e+03 pdb=" C6 C N3209 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C N3462 " 0.023 2.00e-02 2.50e+03 3.69e-02 3.06e+01 pdb=" N1 C N3462 " -0.009 2.00e-02 2.50e+03 pdb=" C2 C N3462 " 0.004 2.00e-02 2.50e+03 pdb=" O2 C N3462 " -0.057 2.00e-02 2.50e+03 pdb=" N3 C N3462 " 0.087 2.00e-02 2.50e+03 pdb=" C4 C N3462 " -0.009 2.00e-02 2.50e+03 pdb=" N4 C N3462 " -0.022 2.00e-02 2.50e+03 pdb=" C5 C N3462 " -0.013 2.00e-02 2.50e+03 pdb=" C6 C N3462 " -0.005 2.00e-02 2.50e+03 ... (remaining 5338 not shown) Histogram of nonbonded interaction distances: 1.25 - 1.98: 2 1.98 - 2.71: 3071 2.71 - 3.44: 65297 3.44 - 4.17: 144120 4.17 - 4.90: 207965 Nonbonded interactions: 420455 Sorted by model distance: nonbonded pdb=" N1 A N2425 " pdb=" O4 U N2442 " model vdw 1.245 2.496 nonbonded pdb=" N1 A N2989 " pdb=" O4 U N3046 " model vdw 1.560 2.496 nonbonded pdb=" C2 A N2425 " pdb=" O4 U N2442 " model vdw 2.003 3.340 nonbonded pdb=" NH1 ARG E 45 " pdb=" OP1 C N3379 " model vdw 2.133 3.120 nonbonded pdb=" O2' C N3114 " pdb=" O4' U N3115 " model vdw 2.167 3.040 ... (remaining 420450 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 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: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.330 Check model and map are aligned: 0.260 Set scattering table: 0.340 Process input model: 107.410 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 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 : 0.008 0.061 51840 Z= 0.488 Angle : 1.315 16.375 75674 Z= 0.885 Chirality : 0.099 0.611 9476 Planarity : 0.007 0.101 5341 Dihedral : 23.468 179.769 27065 Min Nonbonded Distance : 1.245 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 3.10 % Allowed : 12.95 % Favored : 83.95 % Rotamer: Outliers : 4.33 % Allowed : 9.62 % Favored : 86.05 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.77 % Cis-general : 0.31 % Twisted Proline : 1.54 % Twisted General : 0.10 % 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: -4.17 (0.12), residues: 3003 helix: -0.76 (0.16), residues: 661 sheet: -3.48 (0.22), residues: 290 loop : -3.64 (0.10), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 58 HIS 0.009 0.002 HIS A 259 PHE 0.030 0.003 PHE K 399 TYR 0.026 0.003 TYR F 17 ARG 0.024 0.002 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 830 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 717 time to evaluate : 2.490 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: A 80 GLU cc_start: 0.6618 (pt0) cc_final: 0.5655 (mt-10) REVERT: A 164 ILE cc_start: 0.8735 (mt) cc_final: 0.8484 (mt) REVERT: A 177 LYS cc_start: 0.1554 (mttt) cc_final: 0.0623 (mttp) REVERT: A 224 THR cc_start: 0.8583 (OUTLIER) cc_final: 0.8274 (m) REVERT: A 251 LYS cc_start: 0.5606 (mptt) cc_final: 0.4522 (mptt) REVERT: A 286 TYR cc_start: 0.5791 (m-10) cc_final: 0.5505 (m-10) REVERT: A 316 MET cc_start: 0.6469 (tmm) cc_final: 0.5973 (ttp) REVERT: A 324 MET cc_start: 0.4691 (tpt) cc_final: 0.3792 (tpp) REVERT: A 364 LEU cc_start: 0.7316 (OUTLIER) cc_final: 0.6771 (mm) REVERT: B 57 LEU cc_start: 0.5845 (tp) cc_final: 0.5500 (tp) REVERT: B 77 ASN cc_start: 0.8366 (m-40) cc_final: 0.7999 (t0) REVERT: B 87 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8140 (tt0) REVERT: B 108 ARG cc_start: 0.7013 (mmt180) cc_final: 0.6359 (ptp-170) REVERT: B 161 LEU cc_start: 0.7721 (tp) cc_final: 0.7460 (mt) REVERT: B 171 ARG cc_start: 0.7182 (OUTLIER) cc_final: 0.6981 (mtm-85) REVERT: C 6 SER cc_start: -0.0907 (OUTLIER) cc_final: -0.1276 (t) REVERT: C 12 PHE cc_start: 0.7111 (m-80) cc_final: 0.6869 (m-80) REVERT: C 14 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7368 (tp30) REVERT: C 15 LYS cc_start: 0.7184 (OUTLIER) cc_final: 0.6270 (mmtm) REVERT: C 54 MET cc_start: 0.3826 (ttt) cc_final: 0.3357 (ttt) REVERT: C 59 MET cc_start: 0.4767 (ptt) cc_final: 0.3920 (ptt) REVERT: D 25 MET cc_start: 0.1364 (OUTLIER) cc_final: -0.3407 (tmm) REVERT: D 74 LEU cc_start: 0.5312 (OUTLIER) cc_final: 0.5059 (pt) REVERT: E 54 VAL cc_start: 0.8886 (m) cc_final: 0.8548 (t) REVERT: E 97 ASP cc_start: 0.6374 (OUTLIER) cc_final: 0.3625 (t0) REVERT: E 102 MET cc_start: 0.6984 (tpt) cc_final: 0.6540 (mmm) REVERT: E 110 LYS cc_start: 0.5241 (ptpt) cc_final: 0.4769 (ptpp) REVERT: E 112 ASN cc_start: 0.7571 (m-40) cc_final: 0.7357 (p0) REVERT: F 21 ARG cc_start: 0.7318 (ptt180) cc_final: 0.7020 (mtm110) REVERT: F 31 ILE cc_start: 0.8124 (pt) cc_final: 0.7764 (mt) REVERT: F 57 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8053 (tttm) REVERT: F 63 GLU cc_start: 0.7607 (pt0) cc_final: 0.6941 (mt-10) REVERT: F 115 MET cc_start: 0.8374 (mmp) cc_final: 0.7920 (mmt) REVERT: F 122 PRO cc_start: 0.9384 (Cg_exo) cc_final: 0.9145 (Cg_endo) REVERT: F 125 THR cc_start: 0.8188 (m) cc_final: 0.7936 (m) REVERT: F 144 MET cc_start: 0.8757 (mmt) cc_final: 0.8466 (mmt) REVERT: F 184 LEU cc_start: 0.8084 (mt) cc_final: 0.7867 (mt) REVERT: F 192 ASN cc_start: 0.7555 (m-40) cc_final: 0.6773 (m110) REVERT: F 198 LYS cc_start: 0.7900 (mttt) cc_final: 0.7381 (mtpp) REVERT: F 203 HIS cc_start: 0.7118 (p-80) cc_final: 0.6861 (p90) REVERT: G 13 ILE cc_start: 0.8286 (mm) cc_final: 0.8059 (mm) REVERT: G 17 ARG cc_start: 0.6947 (OUTLIER) cc_final: 0.5934 (ptp-170) REVERT: G 36 VAL cc_start: 0.7955 (m) cc_final: 0.7573 (p) REVERT: G 51 TRP cc_start: 0.4680 (OUTLIER) cc_final: 0.3508 (m-90) REVERT: H 10 ARG cc_start: 0.7229 (mtt180) cc_final: 0.6487 (mtp180) REVERT: I 7 TYR cc_start: 0.6138 (OUTLIER) cc_final: 0.5565 (t80) REVERT: I 62 LEU cc_start: 0.7732 (tp) cc_final: 0.7272 (tp) REVERT: I 101 PHE cc_start: 0.7633 (t80) cc_final: 0.6955 (t80) REVERT: I 111 ASN cc_start: 0.5905 (m-40) cc_final: 0.5597 (t0) REVERT: I 126 GLU cc_start: 0.7919 (tt0) cc_final: 0.7268 (mt-10) REVERT: I 147 LEU cc_start: 0.7138 (mt) cc_final: 0.6844 (mt) REVERT: I 172 GLU cc_start: 0.6410 (pt0) cc_final: 0.5131 (tp30) REVERT: I 181 LEU cc_start: 0.7974 (mp) cc_final: 0.7662 (mp) REVERT: J 6 PRO cc_start: 0.6193 (Cg_exo) cc_final: 0.5977 (Cg_endo) REVERT: J 19 ARG cc_start: 0.7470 (ptp-170) cc_final: 0.7066 (ttm170) REVERT: J 68 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7697 (mmtt) REVERT: J 82 GLU cc_start: 0.7853 (pt0) cc_final: 0.7218 (tp30) REVERT: J 97 ASP cc_start: 0.6036 (OUTLIER) cc_final: 0.5768 (t0) REVERT: J 207 GLU cc_start: 0.3623 (tt0) cc_final: 0.2548 (mp0) REVERT: J 243 GLU cc_start: -0.0216 (OUTLIER) cc_final: -0.1179 (pp20) REVERT: K 1 MET cc_start: 0.0348 (mtt) cc_final: -0.1092 (mtm) REVERT: K 49 ARG cc_start: 0.3315 (ptt180) cc_final: 0.3008 (mmm160) REVERT: K 55 ARG cc_start: 0.5156 (OUTLIER) cc_final: 0.3328 (mpt180) REVERT: K 63 GLU cc_start: 0.6517 (mt-10) cc_final: 0.6097 (mt-10) REVERT: K 71 LYS cc_start: 0.4213 (mmtm) cc_final: 0.3695 (mmmm) REVERT: K 102 GLU cc_start: 0.1832 (mt-10) cc_final: 0.0604 (mt-10) REVERT: K 186 LEU cc_start: 0.1769 (OUTLIER) cc_final: 0.1388 (mt) REVERT: K 217 ASP cc_start: 0.5565 (t70) cc_final: 0.5202 (t0) REVERT: K 241 TRP cc_start: 0.0425 (m-10) cc_final: -0.1695 (m-10) REVERT: K 280 ILE cc_start: 0.1089 (mt) cc_final: 0.0140 (pt) REVERT: K 293 PHE cc_start: 0.1123 (m-10) cc_final: 0.0540 (m-10) REVERT: K 315 LYS cc_start: 0.4057 (mtpp) cc_final: 0.3830 (tppt) REVERT: K 358 MET cc_start: 0.3837 (ttt) cc_final: 0.2645 (mtm) REVERT: K 363 LEU cc_start: 0.4081 (mt) cc_final: 0.3557 (pp) REVERT: K 365 SER cc_start: 0.7807 (m) cc_final: 0.7600 (t) REVERT: K 400 MET cc_start: -0.0563 (tpt) cc_final: -0.0772 (tpt) REVERT: K 417 MET cc_start: 0.2113 (mtm) cc_final: 0.1014 (mmp) REVERT: K 438 ILE cc_start: 0.4372 (tp) cc_final: 0.3938 (pt) REVERT: K 442 ARG cc_start: 0.3917 (mmt180) cc_final: 0.3394 (ptt180) REVERT: K 555 MET cc_start: 0.1505 (tmm) cc_final: 0.1231 (tmm) REVERT: K 581 ASN cc_start: 0.2568 (p0) cc_final: 0.2248 (p0) REVERT: K 656 GLU cc_start: 0.4999 (tt0) cc_final: 0.4076 (mp0) REVERT: K 747 LYS cc_start: 0.4740 (mttp) cc_final: 0.4498 (ttmt) REVERT: K 774 ARG cc_start: 0.4918 (ptm160) cc_final: 0.4480 (mpt90) REVERT: K 791 MET cc_start: 0.2516 (mmm) cc_final: 0.2299 (tpt) REVERT: K 799 LYS cc_start: 0.4585 (mtmt) cc_final: 0.4311 (tttp) REVERT: K 888 MET cc_start: 0.6176 (mtt) cc_final: 0.5907 (ttt) REVERT: K 977 PRO cc_start: 0.6350 (Cg_endo) cc_final: 0.5968 (Cg_exo) REVERT: K 1041 ARG cc_start: 0.2237 (ttp-170) cc_final: 0.1991 (ptm160) REVERT: K 1091 MET cc_start: 0.4355 (mmm) cc_final: 0.3658 (mpp) outliers start: 113 outliers final: 42 residues processed: 788 average time/residue: 0.5584 time to fit residues: 701.7278 Evaluate side-chains 490 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 430 time to evaluate : 2.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 348 optimal weight: 7.9990 chunk 313 optimal weight: 40.0000 chunk 173 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 chunk 211 optimal weight: 9.9990 chunk 167 optimal weight: 5.9990 chunk 323 optimal weight: 10.0000 chunk 125 optimal weight: 5.9990 chunk 196 optimal weight: 20.0000 chunk 240 optimal weight: 5.9990 chunk 375 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN A 137 GLN A 180 HIS A 207 ASN A 314 ASN A 327 HIS ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 15 ASN B 64 GLN B 188 ASN C 84 ASN C 118 ASN C 178 ASN E 5 GLN E 10 ASN F 112 GLN ** F 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 177 ASN G 7 ASN G 30 HIS I 9 ASN I 21 ASN I 28 GLN ** I 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 111 ASN I 145 ASN ** I 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 200 ASN J 103 GLN ** J 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 4 ASN K 11 GLN K 18 ASN K 21 ASN K 27 HIS K 30 HIS ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 138 ASN K 204 GLN K 254 GLN K 393 GLN K 466 GLN K 668 GLN K 682 HIS K 706 ASN ** K 793 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 931 GLN K1012 GLN K1085 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.113 51840 Z= 0.376 Angle : 0.913 13.805 75674 Z= 0.461 Chirality : 0.048 0.356 9476 Planarity : 0.007 0.145 5341 Dihedral : 23.748 179.137 21038 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.97 % Allowed : 11.42 % Favored : 87.61 % Rotamer: Outliers : 0.23 % Allowed : 5.02 % Favored : 94.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % Cis-general : 0.28 % Twisted Proline : 3.85 % Twisted General : 0.10 % 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: -3.62 (0.13), residues: 3003 helix: 0.02 (0.20), residues: 661 sheet: -3.10 (0.21), residues: 376 loop : -3.36 (0.11), residues: 1966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.004 TRP F 171 HIS 0.009 0.002 HIS I 162 PHE 0.031 0.003 PHE K 181 TYR 0.040 0.003 TYR F 181 ARG 0.013 0.001 ARG K 444 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 545 time to evaluate : 2.519 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: A 71 GLU cc_start: 0.8559 (pp20) cc_final: 0.8208 (pp20) REVERT: A 80 GLU cc_start: 0.7079 (pt0) cc_final: 0.6337 (mt-10) REVERT: A 173 LYS cc_start: 0.5904 (tptt) cc_final: 0.5623 (tttt) REVERT: A 316 MET cc_start: 0.6354 (tmm) cc_final: 0.5883 (ttp) REVERT: B 1 MET cc_start: 0.2214 (mmt) cc_final: 0.0728 (mmt) REVERT: B 108 ARG cc_start: 0.7795 (mmt180) cc_final: 0.6654 (ptp-170) REVERT: B 116 PHE cc_start: 0.8260 (t80) cc_final: 0.8012 (t80) REVERT: B 131 THR cc_start: 0.8604 (m) cc_final: 0.7968 (m) REVERT: C 14 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7569 (tp30) REVERT: D 25 MET cc_start: 0.0124 (pmm) cc_final: -0.0282 (ptp) REVERT: E 54 VAL cc_start: 0.9027 (m) cc_final: 0.8770 (t) REVERT: E 78 VAL cc_start: 0.7136 (p) cc_final: 0.6883 (p) REVERT: E 89 ASP cc_start: 0.7824 (p0) cc_final: 0.6992 (m-30) REVERT: E 102 MET cc_start: 0.7126 (tpt) cc_final: 0.6597 (mmm) REVERT: E 125 TRP cc_start: 0.8642 (m100) cc_final: 0.8327 (m100) REVERT: F 59 GLN cc_start: 0.7395 (mt0) cc_final: 0.7002 (mt0) REVERT: F 63 GLU cc_start: 0.8117 (pt0) cc_final: 0.7176 (mt-10) REVERT: G 13 ILE cc_start: 0.8112 (mm) cc_final: 0.7828 (mm) REVERT: G 53 MET cc_start: 0.4743 (mmt) cc_final: 0.4298 (tpt) REVERT: H 20 ARG cc_start: 0.8539 (mtt180) cc_final: 0.8084 (mtt180) REVERT: I 1 MET cc_start: 0.3472 (ptp) cc_final: 0.3198 (ptp) REVERT: I 101 PHE cc_start: 0.7664 (t80) cc_final: 0.6875 (t80) REVERT: I 133 LEU cc_start: 0.5923 (mt) cc_final: 0.5022 (mt) REVERT: I 147 LEU cc_start: 0.6803 (mt) cc_final: 0.6596 (mt) REVERT: J 31 CYS cc_start: 0.6401 (m) cc_final: 0.6054 (m) REVERT: J 82 GLU cc_start: 0.8232 (pt0) cc_final: 0.7351 (tp30) REVERT: J 100 ARG cc_start: 0.7350 (ttm-80) cc_final: 0.7096 (mtm110) REVERT: J 107 MET cc_start: 0.6278 (mtt) cc_final: 0.5905 (mtt) REVERT: J 207 GLU cc_start: 0.3719 (tt0) cc_final: 0.2276 (mp0) REVERT: K 1 MET cc_start: 0.0736 (mtt) cc_final: -0.0704 (mtm) REVERT: K 49 ARG cc_start: 0.3417 (ptt180) cc_final: 0.3062 (mtt180) REVERT: K 63 GLU cc_start: 0.6654 (mt-10) cc_final: 0.5610 (tt0) REVERT: K 102 GLU cc_start: 0.0445 (mt-10) cc_final: 0.0172 (mt-10) REVERT: K 217 ASP cc_start: 0.5379 (t70) cc_final: 0.4913 (t0) REVERT: K 227 PRO cc_start: 0.7050 (OUTLIER) cc_final: 0.6663 (Cg_exo) REVERT: K 293 PHE cc_start: 0.1540 (m-10) cc_final: 0.0932 (m-10) REVERT: K 356 LEU cc_start: 0.6706 (mp) cc_final: 0.6467 (mt) REVERT: K 358 MET cc_start: 0.3244 (ttt) cc_final: 0.2308 (mtm) REVERT: K 378 MET cc_start: 0.5563 (tpt) cc_final: 0.5291 (tpt) REVERT: K 417 MET cc_start: 0.2334 (mtm) cc_final: 0.1086 (mmp) REVERT: K 438 ILE cc_start: 0.3826 (tp) cc_final: 0.3295 (tt) REVERT: K 442 ARG cc_start: 0.4234 (mmt180) cc_final: 0.3161 (ptt180) REVERT: K 528 LYS cc_start: 0.3344 (tptp) cc_final: 0.3026 (mmmt) REVERT: K 589 GLN cc_start: 0.1389 (tt0) cc_final: 0.0802 (tt0) REVERT: K 652 GLN cc_start: 0.3055 (mm110) cc_final: 0.2823 (mm110) REVERT: K 737 ASP cc_start: 0.5240 (m-30) cc_final: 0.4477 (t0) REVERT: K 747 LYS cc_start: 0.4833 (mttp) cc_final: 0.4465 (ttmt) REVERT: K 774 ARG cc_start: 0.4581 (ptm-80) cc_final: 0.4303 (mpt90) REVERT: K 791 MET cc_start: 0.1939 (mmm) cc_final: 0.1716 (tpt) REVERT: K 799 LYS cc_start: 0.4186 (mtmt) cc_final: 0.3922 (tttt) REVERT: K 810 HIS cc_start: 0.1738 (p-80) cc_final: 0.1533 (p-80) REVERT: K 1023 ILE cc_start: 0.4751 (tt) cc_final: 0.3738 (tt) REVERT: K 1061 PRO cc_start: 0.7340 (Cg_endo) cc_final: 0.6998 (Cg_exo) outliers start: 6 outliers final: 1 residues processed: 548 average time/residue: 0.5456 time to fit residues: 485.8198 Evaluate side-chains 396 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 394 time to evaluate : 2.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 208 optimal weight: 30.0000 chunk 116 optimal weight: 0.0270 chunk 312 optimal weight: 20.0000 chunk 255 optimal weight: 0.9990 chunk 103 optimal weight: 0.5980 chunk 375 optimal weight: 10.0000 chunk 405 optimal weight: 10.0000 chunk 334 optimal weight: 9.9990 chunk 372 optimal weight: 10.0000 chunk 128 optimal weight: 0.9980 chunk 301 optimal weight: 10.0000 overall best weight: 2.5242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 ASN D 66 ASN F 130 ASN F 177 ASN F 192 ASN ** I 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 138 ASN K 165 HIS K 435 GLN ** K 793 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 844 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 51840 Z= 0.206 Angle : 0.715 13.587 75674 Z= 0.368 Chirality : 0.041 0.283 9476 Planarity : 0.006 0.125 5341 Dihedral : 23.456 179.954 21038 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.90 % Allowed : 11.26 % Favored : 87.85 % Rotamer: Outliers : 0.11 % Allowed : 4.10 % Favored : 95.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % Cis-general : 0.28 % Twisted Proline : 3.85 % 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: -3.20 (0.14), residues: 3003 helix: 0.33 (0.20), residues: 668 sheet: -2.51 (0.23), residues: 353 loop : -3.17 (0.12), residues: 1982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP K 348 HIS 0.019 0.002 HIS I 118 PHE 0.020 0.002 PHE A 366 TYR 0.023 0.002 TYR B 94 ARG 0.016 0.001 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 523 time to evaluate : 2.497 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: A 80 GLU cc_start: 0.6602 (pt0) cc_final: 0.5905 (mt-10) REVERT: B 1 MET cc_start: 0.2987 (mmt) cc_final: 0.1128 (mmt) REVERT: B 108 ARG cc_start: 0.7782 (mmt180) cc_final: 0.6557 (ptp-170) REVERT: B 131 THR cc_start: 0.8267 (m) cc_final: 0.7599 (m) REVERT: B 161 LEU cc_start: 0.8056 (tp) cc_final: 0.7502 (mt) REVERT: B 185 LEU cc_start: 0.5110 (mt) cc_final: 0.4342 (pp) REVERT: C 20 PHE cc_start: 0.7677 (m-80) cc_final: 0.6801 (t80) REVERT: C 82 LYS cc_start: 0.6393 (tptt) cc_final: 0.5418 (tptp) REVERT: E 87 ARG cc_start: 0.7013 (ptp90) cc_final: 0.6683 (ptt-90) REVERT: E 102 MET cc_start: 0.6793 (tpt) cc_final: 0.6338 (mmm) REVERT: E 125 TRP cc_start: 0.8650 (m100) cc_final: 0.8304 (m100) REVERT: F 59 GLN cc_start: 0.7403 (mt0) cc_final: 0.6953 (mt0) REVERT: F 63 GLU cc_start: 0.8090 (pt0) cc_final: 0.7207 (mt-10) REVERT: F 96 VAL cc_start: 0.7549 (m) cc_final: 0.7337 (m) REVERT: F 184 LEU cc_start: 0.7928 (mt) cc_final: 0.7688 (mt) REVERT: G 13 ILE cc_start: 0.7515 (mm) cc_final: 0.7238 (mm) REVERT: I 28 GLN cc_start: 0.6275 (tt0) cc_final: 0.5815 (tt0) REVERT: I 62 LEU cc_start: 0.7444 (tp) cc_final: 0.7043 (tp) REVERT: I 85 ARG cc_start: 0.6895 (tpp-160) cc_final: 0.6682 (tpp-160) REVERT: I 101 PHE cc_start: 0.7769 (t80) cc_final: 0.6844 (t80) REVERT: I 133 LEU cc_start: 0.6143 (mt) cc_final: 0.5477 (mt) REVERT: J 20 MET cc_start: 0.8945 (ppp) cc_final: 0.8621 (ppp) REVERT: J 31 CYS cc_start: 0.6443 (m) cc_final: 0.5926 (m) REVERT: J 82 GLU cc_start: 0.8020 (pt0) cc_final: 0.7409 (tp30) REVERT: J 100 ARG cc_start: 0.7233 (ttm-80) cc_final: 0.6976 (mtm110) REVERT: J 107 MET cc_start: 0.6530 (mtt) cc_final: 0.6103 (mtt) REVERT: J 207 GLU cc_start: 0.3178 (tt0) cc_final: 0.1859 (mp0) REVERT: K 1 MET cc_start: 0.0472 (mtt) cc_final: -0.0316 (mtm) REVERT: K 63 GLU cc_start: 0.6392 (mt-10) cc_final: 0.6055 (mt-10) REVERT: K 102 GLU cc_start: 0.0667 (mt-10) cc_final: -0.0209 (mt-10) REVERT: K 217 ASP cc_start: 0.5592 (t70) cc_final: 0.5098 (t0) REVERT: K 293 PHE cc_start: 0.1492 (m-10) cc_final: 0.1259 (m-10) REVERT: K 358 MET cc_start: 0.2650 (ttt) cc_final: 0.1609 (ttm) REVERT: K 378 MET cc_start: 0.5811 (tpt) cc_final: 0.5499 (tpt) REVERT: K 417 MET cc_start: 0.1379 (mtm) cc_final: 0.1092 (mmp) REVERT: K 438 ILE cc_start: 0.4491 (tp) cc_final: 0.4057 (tt) REVERT: K 442 ARG cc_start: 0.4309 (mmt180) cc_final: 0.2939 (ptt180) REVERT: K 449 HIS cc_start: 0.7254 (m90) cc_final: 0.6266 (t-90) REVERT: K 589 GLN cc_start: 0.1181 (tt0) cc_final: 0.0623 (tt0) REVERT: K 637 MET cc_start: 0.1166 (tpp) cc_final: 0.0797 (tpp) REVERT: K 737 ASP cc_start: 0.5056 (m-30) cc_final: 0.4399 (t0) REVERT: K 747 LYS cc_start: 0.4818 (mttp) cc_final: 0.4563 (ttmt) REVERT: K 774 ARG cc_start: 0.4631 (ptm-80) cc_final: 0.4273 (mmt-90) REVERT: K 799 LYS cc_start: 0.4227 (mtmt) cc_final: 0.3837 (ttpt) REVERT: K 810 HIS cc_start: 0.1497 (p-80) cc_final: 0.1273 (p-80) REVERT: K 1061 PRO cc_start: 0.6962 (Cg_endo) cc_final: 0.6680 (Cg_exo) outliers start: 3 outliers final: 0 residues processed: 525 average time/residue: 0.5131 time to fit residues: 441.5916 Evaluate side-chains 403 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 403 time to evaluate : 2.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 371 optimal weight: 10.0000 chunk 282 optimal weight: 20.0000 chunk 194 optimal weight: 30.0000 chunk 41 optimal weight: 7.9990 chunk 179 optimal weight: 4.9990 chunk 252 optimal weight: 7.9990 chunk 377 optimal weight: 9.9990 chunk 399 optimal weight: 10.0000 chunk 197 optimal weight: 5.9990 chunk 357 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 HIS ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 ASN B 15 ASN B 64 GLN B 154 GLN D 65 GLN D 156 GLN E 81 GLN ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 177 ASN G 7 ASN I 28 GLN ** I 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 145 ASN ** I 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 121 ASN J 152 GLN ** J 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 4 ASN K 427 GLN ** K 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 793 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 918 ASN K 927 ASN K 931 GLN K 944 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 51840 Z= 0.421 Angle : 0.966 13.946 75674 Z= 0.484 Chirality : 0.050 0.361 9476 Planarity : 0.007 0.144 5341 Dihedral : 23.698 179.719 21038 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 19.57 Ramachandran Plot: Outliers : 0.87 % Allowed : 13.39 % Favored : 85.75 % Rotamer: Outliers : 0.08 % Allowed : 6.05 % Favored : 93.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % Cis-general : 0.28 % Twisted Proline : 3.85 % Twisted General : 0.07 % 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: -3.48 (0.13), residues: 3003 helix: -0.41 (0.19), residues: 676 sheet: -2.51 (0.24), residues: 375 loop : -3.19 (0.12), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.004 TRP K 135 HIS 0.020 0.002 HIS K 165 PHE 0.032 0.003 PHE F 173 TYR 0.030 0.003 TYR F 17 ARG 0.010 0.001 ARG K 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 484 time to evaluate : 2.511 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: A 80 GLU cc_start: 0.6777 (pt0) cc_final: 0.5608 (pt0) REVERT: A 173 LYS cc_start: 0.6094 (tptt) cc_final: 0.5728 (tttt) REVERT: A 316 MET cc_start: 0.5744 (ttp) cc_final: 0.5529 (ttp) REVERT: B 1 MET cc_start: 0.4045 (mmt) cc_final: 0.1644 (mmt) REVERT: B 108 ARG cc_start: 0.8037 (mmt180) cc_final: 0.6531 (ptp-170) REVERT: B 131 THR cc_start: 0.8606 (m) cc_final: 0.7943 (m) REVERT: C 20 PHE cc_start: 0.7784 (m-80) cc_final: 0.6939 (t80) REVERT: E 24 ASN cc_start: 0.7581 (m-40) cc_final: 0.7299 (m-40) REVERT: E 89 ASP cc_start: 0.8151 (p0) cc_final: 0.7906 (p0) REVERT: E 102 MET cc_start: 0.7013 (tpt) cc_final: 0.6539 (mmm) REVERT: E 125 TRP cc_start: 0.8745 (m100) cc_final: 0.8315 (m100) REVERT: F 59 GLN cc_start: 0.7362 (mt0) cc_final: 0.6909 (mt0) REVERT: F 63 GLU cc_start: 0.8211 (pt0) cc_final: 0.7115 (mt-10) REVERT: F 96 VAL cc_start: 0.7586 (m) cc_final: 0.7251 (m) REVERT: F 102 MET cc_start: 0.6793 (mpp) cc_final: 0.6526 (mtp) REVERT: F 125 THR cc_start: 0.8521 (m) cc_final: 0.8237 (p) REVERT: F 135 ILE cc_start: 0.9193 (pt) cc_final: 0.8945 (pt) REVERT: F 159 PHE cc_start: 0.8492 (m-80) cc_final: 0.8189 (m-10) REVERT: G 13 ILE cc_start: 0.7935 (mm) cc_final: 0.7417 (mm) REVERT: G 53 MET cc_start: 0.4572 (mmt) cc_final: 0.4183 (tpt) REVERT: H 45 ARG cc_start: 0.7420 (ptt90) cc_final: 0.7139 (ptt180) REVERT: I 101 PHE cc_start: 0.7902 (t80) cc_final: 0.7094 (t80) REVERT: I 205 ILE cc_start: 0.6974 (mm) cc_final: 0.6768 (mm) REVERT: J 20 MET cc_start: 0.9217 (ppp) cc_final: 0.8828 (ppp) REVERT: J 31 CYS cc_start: 0.6530 (m) cc_final: 0.6126 (m) REVERT: J 82 GLU cc_start: 0.8387 (pt0) cc_final: 0.7367 (tp30) REVERT: J 84 CYS cc_start: 0.8836 (m) cc_final: 0.8404 (t) REVERT: J 100 ARG cc_start: 0.7294 (ttm-80) cc_final: 0.7000 (mtm110) REVERT: J 207 GLU cc_start: 0.3238 (tt0) cc_final: 0.2290 (mm-30) REVERT: K 1 MET cc_start: 0.0984 (mtt) cc_final: -0.0022 (mtm) REVERT: K 102 GLU cc_start: 0.0982 (mt-10) cc_final: -0.0215 (mt-10) REVERT: K 160 GLN cc_start: 0.5575 (mp10) cc_final: 0.5263 (tm-30) REVERT: K 217 ASP cc_start: 0.5426 (t70) cc_final: 0.4937 (t0) REVERT: K 294 VAL cc_start: 0.1245 (p) cc_final: 0.0927 (p) REVERT: K 358 MET cc_start: 0.2822 (ttt) cc_final: 0.1917 (ttm) REVERT: K 417 MET cc_start: 0.2222 (mtm) cc_final: 0.1495 (mmp) REVERT: K 423 LYS cc_start: 0.6893 (tptp) cc_final: 0.6041 (mtmm) REVERT: K 438 ILE cc_start: 0.4578 (tp) cc_final: 0.4188 (tt) REVERT: K 442 ARG cc_start: 0.4322 (mmt180) cc_final: 0.3073 (ptt180) REVERT: K 747 LYS cc_start: 0.4463 (mttp) cc_final: 0.4107 (ttpt) REVERT: K 756 MET cc_start: -0.2956 (mmt) cc_final: -0.3181 (mmt) REVERT: K 774 ARG cc_start: 0.4945 (ptm-80) cc_final: 0.4390 (mpt90) REVERT: K 799 LYS cc_start: 0.4454 (mtmt) cc_final: 0.4234 (ttpt) REVERT: K 819 ILE cc_start: 0.3153 (mp) cc_final: 0.2816 (tp) REVERT: K 990 MET cc_start: 0.2637 (mmm) cc_final: 0.0754 (mmm) REVERT: K 1061 PRO cc_start: 0.6547 (Cg_endo) cc_final: 0.6235 (Cg_exo) outliers start: 2 outliers final: 1 residues processed: 486 average time/residue: 0.5019 time to fit residues: 402.4637 Evaluate side-chains 390 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 389 time to evaluate : 2.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 332 optimal weight: 9.9990 chunk 226 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 297 optimal weight: 10.0000 chunk 164 optimal weight: 9.9990 chunk 340 optimal weight: 20.0000 chunk 275 optimal weight: 20.0000 chunk 0 optimal weight: 8.9990 chunk 203 optimal weight: 10.0000 chunk 358 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 GLN B 160 GLN D 144 ASN ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 177 ASN ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 74 ASN ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 86 GLN ** J 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 205 GLN ** K 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 254 GLN K 449 HIS ** K 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 632 GLN K 652 GLN ** K 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 769 ASN ** K 793 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.5060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 51840 Z= 0.441 Angle : 0.983 13.684 75674 Z= 0.493 Chirality : 0.051 0.392 9476 Planarity : 0.007 0.120 5341 Dihedral : 23.826 179.799 21038 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 20.54 Ramachandran Plot: Outliers : 1.00 % Allowed : 14.35 % Favored : 84.65 % Rotamer: Outliers : 0.08 % Allowed : 5.33 % Favored : 94.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % Cis-general : 0.28 % Twisted Proline : 3.85 % Twisted General : 0.10 % 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: -3.67 (0.13), residues: 3003 helix: -0.73 (0.19), residues: 662 sheet: -2.51 (0.25), residues: 334 loop : -3.27 (0.12), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.005 TRP F 171 HIS 0.014 0.003 HIS G 30 PHE 0.042 0.003 PHE F 34 TYR 0.029 0.004 TYR B 94 ARG 0.023 0.001 ARG K 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 476 time to evaluate : 2.557 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: A 80 GLU cc_start: 0.6738 (pt0) cc_final: 0.5631 (pt0) REVERT: A 281 ARG cc_start: 0.8124 (mtm180) cc_final: 0.7818 (mtm-85) REVERT: A 316 MET cc_start: 0.5267 (ttp) cc_final: 0.4918 (ttp) REVERT: B 1 MET cc_start: 0.4247 (mmt) cc_final: -0.0510 (ptt) REVERT: B 94 TYR cc_start: 0.4151 (t80) cc_final: 0.3695 (t80) REVERT: B 108 ARG cc_start: 0.8121 (mmt180) cc_final: 0.6530 (mtm180) REVERT: B 131 THR cc_start: 0.8445 (m) cc_final: 0.7987 (m) REVERT: B 154 GLN cc_start: 0.8757 (tp40) cc_final: 0.8450 (tp40) REVERT: E 11 TYR cc_start: 0.5023 (m-10) cc_final: 0.4647 (m-10) REVERT: E 89 ASP cc_start: 0.8162 (p0) cc_final: 0.7930 (p0) REVERT: E 102 MET cc_start: 0.7075 (tpt) cc_final: 0.6678 (mmm) REVERT: E 125 TRP cc_start: 0.8732 (m100) cc_final: 0.8337 (m100) REVERT: F 1 MET cc_start: 0.5227 (tpt) cc_final: 0.4995 (tpt) REVERT: F 59 GLN cc_start: 0.7271 (mt0) cc_final: 0.6890 (mt0) REVERT: F 63 GLU cc_start: 0.8235 (pt0) cc_final: 0.6731 (mt-10) REVERT: F 102 MET cc_start: 0.6929 (mpp) cc_final: 0.6320 (mtp) REVERT: F 150 GLU cc_start: 0.8031 (mp0) cc_final: 0.7603 (mp0) REVERT: F 159 PHE cc_start: 0.8493 (m-80) cc_final: 0.7986 (m-10) REVERT: G 13 ILE cc_start: 0.7739 (mm) cc_final: 0.7155 (mm) REVERT: G 32 ILE cc_start: 0.8532 (mt) cc_final: 0.8127 (mm) REVERT: H 45 ARG cc_start: 0.7705 (ptt90) cc_final: 0.7256 (ptt180) REVERT: I 62 LEU cc_start: 0.7789 (tp) cc_final: 0.7435 (tp) REVERT: I 101 PHE cc_start: 0.7976 (t80) cc_final: 0.6856 (t80) REVERT: J 14 ASN cc_start: 0.6697 (p0) cc_final: 0.5265 (m-40) REVERT: J 20 MET cc_start: 0.9157 (ppp) cc_final: 0.8787 (ppp) REVERT: J 31 CYS cc_start: 0.7086 (m) cc_final: 0.6651 (m) REVERT: J 82 GLU cc_start: 0.8483 (pt0) cc_final: 0.7627 (tp30) REVERT: J 84 CYS cc_start: 0.8783 (m) cc_final: 0.8476 (t) REVERT: J 100 ARG cc_start: 0.7301 (ttm-80) cc_final: 0.7023 (mtm110) REVERT: J 207 GLU cc_start: 0.3485 (tt0) cc_final: 0.1958 (mp0) REVERT: K 1 MET cc_start: 0.1576 (mtt) cc_final: 0.0700 (mtm) REVERT: K 102 GLU cc_start: 0.0580 (mt-10) cc_final: -0.0548 (mt-10) REVERT: K 147 LYS cc_start: -0.1573 (mmtt) cc_final: -0.1805 (mmtp) REVERT: K 217 ASP cc_start: 0.4590 (t70) cc_final: 0.4309 (t0) REVERT: K 227 PRO cc_start: 0.5852 (OUTLIER) cc_final: 0.5612 (Cg_exo) REVERT: K 358 MET cc_start: 0.2344 (ttt) cc_final: 0.1608 (ttm) REVERT: K 417 MET cc_start: 0.2290 (mtm) cc_final: 0.1804 (mmp) REVERT: K 438 ILE cc_start: 0.4966 (tp) cc_final: 0.4464 (tt) REVERT: K 442 ARG cc_start: 0.4034 (mmt180) cc_final: 0.2577 (ptt180) REVERT: K 449 HIS cc_start: 0.6822 (m90) cc_final: 0.6566 (m90) REVERT: K 747 LYS cc_start: 0.4198 (mttp) cc_final: 0.3908 (tttt) REVERT: K 756 MET cc_start: -0.2855 (mmt) cc_final: -0.3106 (mmt) REVERT: K 774 ARG cc_start: 0.4985 (ptm-80) cc_final: 0.4349 (mmp80) REVERT: K 780 THR cc_start: 0.5316 (m) cc_final: 0.4982 (m) REVERT: K 817 ARG cc_start: 0.1596 (mtp85) cc_final: 0.0653 (mtp85) REVERT: K 913 GLU cc_start: 0.5614 (pt0) cc_final: 0.5285 (pt0) REVERT: K 990 MET cc_start: 0.2664 (mmp) cc_final: 0.1392 (mmm) REVERT: K 1061 PRO cc_start: 0.6661 (Cg_endo) cc_final: 0.6261 (Cg_exo) outliers start: 2 outliers final: 0 residues processed: 477 average time/residue: 0.5601 time to fit residues: 438.8255 Evaluate side-chains 398 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 397 time to evaluate : 2.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 134 optimal weight: 8.9990 chunk 359 optimal weight: 8.9990 chunk 78 optimal weight: 20.0000 chunk 234 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 399 optimal weight: 10.0000 chunk 331 optimal weight: 8.9990 chunk 185 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 209 optimal weight: 9.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 ASN ** A 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 HIS ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 GLN C 133 GLN C 147 ASN C 155 ASN ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 130 ASN F 177 ASN G 30 HIS ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 74 ASN ** I 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 86 GLN ** J 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 231 ASN K 435 GLN ** K 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 793 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 944 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.5514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 51840 Z= 0.436 Angle : 0.987 13.770 75674 Z= 0.494 Chirality : 0.051 0.359 9476 Planarity : 0.007 0.128 5341 Dihedral : 23.904 179.070 21038 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 21.80 Ramachandran Plot: Outliers : 0.87 % Allowed : 15.22 % Favored : 83.92 % Rotamer: Outliers : 0.08 % Allowed : 3.60 % Favored : 96.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % Cis-general : 0.28 % Twisted Proline : 3.08 % Twisted General : 0.07 % 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: -3.84 (0.13), residues: 3003 helix: -0.93 (0.19), residues: 653 sheet: -2.63 (0.25), residues: 344 loop : -3.35 (0.12), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.004 TRP F 171 HIS 0.010 0.002 HIS I 118 PHE 0.029 0.003 PHE F 173 TYR 0.026 0.003 TYR B 94 ARG 0.019 0.001 ARG K 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 472 time to evaluate : 2.493 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: A 80 GLU cc_start: 0.6771 (pt0) cc_final: 0.5647 (pt0) REVERT: A 120 LYS cc_start: 0.4822 (mttt) cc_final: 0.4446 (ptmt) REVERT: A 281 ARG cc_start: 0.8223 (mtm180) cc_final: 0.7953 (mtm-85) REVERT: A 316 MET cc_start: 0.5904 (ttp) cc_final: 0.5501 (ttp) REVERT: B 1 MET cc_start: 0.4989 (mmt) cc_final: 0.0687 (ptt) REVERT: B 94 TYR cc_start: 0.4517 (t80) cc_final: 0.4060 (t80) REVERT: B 150 GLU cc_start: 0.7554 (pm20) cc_final: 0.7217 (tt0) REVERT: C 82 LYS cc_start: 0.4964 (tptt) cc_final: 0.3971 (tppt) REVERT: E 11 TYR cc_start: 0.4859 (m-10) cc_final: 0.4562 (m-10) REVERT: E 102 MET cc_start: 0.7117 (tpt) cc_final: 0.6719 (mmm) REVERT: E 125 TRP cc_start: 0.8743 (m100) cc_final: 0.8352 (m100) REVERT: F 14 ASN cc_start: 0.8023 (t0) cc_final: 0.7514 (m-40) REVERT: F 15 LYS cc_start: 0.8554 (mmmt) cc_final: 0.8350 (mmpt) REVERT: F 59 GLN cc_start: 0.7308 (mt0) cc_final: 0.7016 (mt0) REVERT: F 63 GLU cc_start: 0.8222 (pt0) cc_final: 0.6735 (mt-10) REVERT: F 159 PHE cc_start: 0.8478 (m-80) cc_final: 0.8180 (m-10) REVERT: G 13 ILE cc_start: 0.7681 (mm) cc_final: 0.7182 (mm) REVERT: H 20 ARG cc_start: 0.8505 (mtt180) cc_final: 0.8297 (mtt180) REVERT: H 45 ARG cc_start: 0.7586 (ptt90) cc_final: 0.7079 (ptt180) REVERT: I 101 PHE cc_start: 0.7856 (t80) cc_final: 0.7297 (t80) REVERT: I 126 GLU cc_start: 0.8446 (tt0) cc_final: 0.7683 (mt-10) REVERT: J 20 MET cc_start: 0.8967 (ppp) cc_final: 0.8622 (ppp) REVERT: J 31 CYS cc_start: 0.7102 (m) cc_final: 0.6757 (m) REVERT: J 82 GLU cc_start: 0.8496 (pt0) cc_final: 0.7577 (tp30) REVERT: J 84 CYS cc_start: 0.8797 (m) cc_final: 0.8418 (t) REVERT: J 207 GLU cc_start: 0.2519 (tt0) cc_final: 0.1193 (mp0) REVERT: K 1 MET cc_start: 0.1563 (mtt) cc_final: 0.0736 (mtm) REVERT: K 102 GLU cc_start: 0.0799 (mt-10) cc_final: -0.0361 (mt-10) REVERT: K 217 ASP cc_start: 0.4611 (t70) cc_final: 0.4135 (t0) REVERT: K 241 TRP cc_start: 0.1719 (m-10) cc_final: 0.0735 (m-10) REVERT: K 358 MET cc_start: 0.1824 (ttt) cc_final: 0.1472 (ttm) REVERT: K 417 MET cc_start: 0.3192 (mtm) cc_final: 0.2517 (mmp) REVERT: K 423 LYS cc_start: 0.7160 (tptp) cc_final: 0.6593 (mmtt) REVERT: K 438 ILE cc_start: 0.4889 (tp) cc_final: 0.4290 (tt) REVERT: K 442 ARG cc_start: 0.3874 (mmt180) cc_final: 0.2350 (ttp-170) REVERT: K 449 HIS cc_start: 0.6937 (m90) cc_final: 0.6660 (m90) REVERT: K 747 LYS cc_start: 0.4287 (mttp) cc_final: 0.4017 (tttt) REVERT: K 756 MET cc_start: -0.1860 (mmt) cc_final: -0.2182 (mmt) REVERT: K 774 ARG cc_start: 0.4904 (ptm-80) cc_final: 0.4209 (mmp80) REVERT: K 776 MET cc_start: -0.1931 (ttp) cc_final: -0.2226 (ttp) REVERT: K 777 GLU cc_start: 0.4474 (mp0) cc_final: 0.4054 (tt0) REVERT: K 990 MET cc_start: 0.3353 (mmp) cc_final: 0.2154 (mmm) REVERT: K 1021 MET cc_start: 0.5606 (mmm) cc_final: 0.5055 (mmt) outliers start: 2 outliers final: 0 residues processed: 473 average time/residue: 0.5009 time to fit residues: 393.9305 Evaluate side-chains 393 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 393 time to evaluate : 2.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 385 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 227 optimal weight: 0.9980 chunk 291 optimal weight: 9.9990 chunk 226 optimal weight: 5.9990 chunk 336 optimal weight: 10.0000 chunk 223 optimal weight: 7.9990 chunk 398 optimal weight: 9.9990 chunk 249 optimal weight: 5.9990 chunk 242 optimal weight: 20.0000 chunk 183 optimal weight: 2.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN A 277 HIS ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 GLN E 84 HIS E 98 ASN F 177 ASN ** G 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 86 GLN ** J 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 171 HIS ** K 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 793 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.5683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 51840 Z= 0.277 Angle : 0.811 13.546 75674 Z= 0.413 Chirality : 0.044 0.302 9476 Planarity : 0.006 0.110 5341 Dihedral : 23.716 179.964 21038 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.70 % Allowed : 13.82 % Favored : 85.48 % Rotamer: Outliers : 0.04 % Allowed : 1.65 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % Cis-general : 0.28 % Twisted Proline : 2.31 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.71 (0.13), residues: 3003 helix: -0.86 (0.19), residues: 666 sheet: -2.37 (0.26), residues: 337 loop : -3.29 (0.12), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.004 TRP F 171 HIS 0.010 0.002 HIS G 30 PHE 0.019 0.002 PHE I 138 TYR 0.023 0.002 TYR K 862 ARG 0.020 0.001 ARG K 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 479 time to evaluate : 2.504 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: A 80 GLU cc_start: 0.6912 (pt0) cc_final: 0.5735 (pt0) REVERT: A 316 MET cc_start: 0.5785 (ttp) cc_final: 0.5457 (ttp) REVERT: B 1 MET cc_start: 0.4533 (mmt) cc_final: 0.1052 (ptt) REVERT: B 94 TYR cc_start: 0.4618 (t80) cc_final: 0.4104 (t80) REVERT: C 82 LYS cc_start: 0.4834 (tptt) cc_final: 0.3784 (tppt) REVERT: E 27 ASP cc_start: 0.7679 (t0) cc_final: 0.7344 (p0) REVERT: E 102 MET cc_start: 0.7027 (tpt) cc_final: 0.6655 (tpt) REVERT: E 125 TRP cc_start: 0.8698 (m100) cc_final: 0.8220 (m100) REVERT: F 14 ASN cc_start: 0.7886 (t0) cc_final: 0.7534 (m-40) REVERT: F 15 LYS cc_start: 0.8470 (mmmt) cc_final: 0.8260 (mmpt) REVERT: F 59 GLN cc_start: 0.7274 (mt0) cc_final: 0.6995 (mt0) REVERT: F 63 GLU cc_start: 0.8107 (pt0) cc_final: 0.6461 (mt-10) REVERT: F 102 MET cc_start: 0.6644 (mpp) cc_final: 0.6417 (mpp) REVERT: F 135 ILE cc_start: 0.9154 (pt) cc_final: 0.8801 (pt) REVERT: G 13 ILE cc_start: 0.7456 (mm) cc_final: 0.6895 (mm) REVERT: H 45 ARG cc_start: 0.7415 (ptt90) cc_final: 0.6951 (ptt180) REVERT: I 62 LEU cc_start: 0.7634 (tp) cc_final: 0.7263 (tp) REVERT: I 101 PHE cc_start: 0.7757 (t80) cc_final: 0.7526 (t80) REVERT: I 120 ASP cc_start: 0.6906 (t0) cc_final: 0.5759 (m-30) REVERT: I 126 GLU cc_start: 0.8365 (tt0) cc_final: 0.7689 (mt-10) REVERT: I 139 ARG cc_start: 0.7722 (mmm-85) cc_final: 0.7352 (mmm-85) REVERT: J 20 MET cc_start: 0.8985 (ppp) cc_final: 0.8619 (ppp) REVERT: J 31 CYS cc_start: 0.7556 (m) cc_final: 0.7157 (m) REVERT: J 82 GLU cc_start: 0.8459 (pt0) cc_final: 0.7576 (tp30) REVERT: J 207 GLU cc_start: 0.2744 (tt0) cc_final: 0.1230 (mp0) REVERT: K 1 MET cc_start: 0.1968 (mtt) cc_final: 0.0895 (mtm) REVERT: K 102 GLU cc_start: 0.0590 (mt-10) cc_final: -0.0179 (mt-10) REVERT: K 217 ASP cc_start: 0.4645 (t70) cc_final: 0.4173 (t0) REVERT: K 358 MET cc_start: 0.1499 (ttt) cc_final: 0.1179 (ttm) REVERT: K 417 MET cc_start: 0.3540 (mtm) cc_final: 0.2953 (mmt) REVERT: K 423 LYS cc_start: 0.7072 (tptp) cc_final: 0.6574 (mmtt) REVERT: K 438 ILE cc_start: 0.4932 (tp) cc_final: 0.4327 (tt) REVERT: K 442 ARG cc_start: 0.3859 (mmt180) cc_final: 0.2462 (ptt180) REVERT: K 449 HIS cc_start: 0.6919 (m90) cc_final: 0.6639 (m90) REVERT: K 747 LYS cc_start: 0.4207 (mttp) cc_final: 0.3877 (tttt) REVERT: K 756 MET cc_start: -0.1900 (mmt) cc_final: -0.2216 (mmt) REVERT: K 774 ARG cc_start: 0.4896 (ptm-80) cc_final: 0.4228 (mmp80) REVERT: K 776 MET cc_start: -0.2067 (ttp) cc_final: -0.2472 (ttp) REVERT: K 777 GLU cc_start: 0.4378 (mp0) cc_final: 0.3850 (tt0) REVERT: K 780 THR cc_start: 0.5014 (m) cc_final: 0.4756 (p) REVERT: K 990 MET cc_start: 0.3156 (mmp) cc_final: 0.1811 (mmm) REVERT: K 1021 MET cc_start: 0.5821 (mmm) cc_final: 0.5038 (mmt) REVERT: K 1057 TRP cc_start: 0.2945 (m100) cc_final: 0.2368 (m100) outliers start: 1 outliers final: 0 residues processed: 479 average time/residue: 0.4936 time to fit residues: 393.4635 Evaluate side-chains 398 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 398 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 246 optimal weight: 5.9990 chunk 158 optimal weight: 7.9990 chunk 237 optimal weight: 3.9990 chunk 119 optimal weight: 0.2980 chunk 78 optimal weight: 30.0000 chunk 77 optimal weight: 6.9990 chunk 253 optimal weight: 3.9990 chunk 271 optimal weight: 30.0000 chunk 196 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 312 optimal weight: 20.0000 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 HIS A 277 HIS ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 15 ASN B 61 ASN B 64 GLN B 154 GLN ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 177 ASN ** G 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 8 ASN ** J 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 440 GLN ** K 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 793 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.5856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 51840 Z= 0.252 Angle : 0.778 13.502 75674 Z= 0.395 Chirality : 0.043 0.276 9476 Planarity : 0.006 0.105 5341 Dihedral : 23.605 179.872 21038 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.67 % Allowed : 13.79 % Favored : 85.55 % Rotamer: Outliers : 0.08 % Allowed : 1.00 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % Cis-general : 0.28 % Twisted Proline : 2.31 % Twisted General : 0.07 % 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: -3.56 (0.14), residues: 3003 helix: -0.70 (0.19), residues: 661 sheet: -2.44 (0.27), residues: 336 loop : -3.17 (0.12), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP K 348 HIS 0.009 0.002 HIS A 378 PHE 0.021 0.002 PHE B 116 TYR 0.027 0.002 TYR K 862 ARG 0.018 0.001 ARG K 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 469 time to evaluate : 2.547 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: A 80 GLU cc_start: 0.6919 (pt0) cc_final: 0.5726 (pt0) REVERT: A 265 THR cc_start: 0.8459 (p) cc_final: 0.8251 (p) REVERT: A 316 MET cc_start: 0.5840 (ttp) cc_final: 0.5467 (ttp) REVERT: B 1 MET cc_start: 0.4356 (mmt) cc_final: 0.1152 (ptt) REVERT: B 61 ASN cc_start: 0.7009 (p0) cc_final: 0.6459 (p0) REVERT: B 94 TYR cc_start: 0.4645 (t80) cc_final: 0.4132 (t80) REVERT: C 82 LYS cc_start: 0.4706 (tptt) cc_final: 0.3558 (tppt) REVERT: C 129 MET cc_start: 0.4164 (tpt) cc_final: 0.3874 (mmm) REVERT: F 14 ASN cc_start: 0.7796 (t0) cc_final: 0.7560 (m-40) REVERT: F 15 LYS cc_start: 0.8396 (mmmt) cc_final: 0.8195 (mmpt) REVERT: F 59 GLN cc_start: 0.7054 (mt0) cc_final: 0.6778 (mt0) REVERT: G 33 ASN cc_start: 0.8571 (p0) cc_final: 0.8362 (p0) REVERT: H 45 ARG cc_start: 0.7365 (ptt90) cc_final: 0.7066 (ptt180) REVERT: I 62 LEU cc_start: 0.7609 (tp) cc_final: 0.7295 (tp) REVERT: I 100 LYS cc_start: 0.7162 (ptpp) cc_final: 0.5868 (tppt) REVERT: I 101 PHE cc_start: 0.7820 (t80) cc_final: 0.7383 (t80) REVERT: I 120 ASP cc_start: 0.6803 (t0) cc_final: 0.5984 (m-30) REVERT: I 126 GLU cc_start: 0.8383 (tt0) cc_final: 0.7623 (pt0) REVERT: I 139 ARG cc_start: 0.7672 (mmm-85) cc_final: 0.7370 (mmm-85) REVERT: J 31 CYS cc_start: 0.7488 (m) cc_final: 0.6720 (m) REVERT: J 82 GLU cc_start: 0.8456 (pt0) cc_final: 0.7548 (tp30) REVERT: J 207 GLU cc_start: 0.2314 (tt0) cc_final: 0.0865 (mp0) REVERT: K 1 MET cc_start: 0.1755 (mtt) cc_final: 0.0805 (mtm) REVERT: K 102 GLU cc_start: 0.0860 (mt-10) cc_final: -0.0303 (mt-10) REVERT: K 201 ASN cc_start: 0.5943 (m-40) cc_final: 0.4976 (p0) REVERT: K 217 ASP cc_start: 0.4584 (t70) cc_final: 0.4153 (t0) REVERT: K 417 MET cc_start: 0.3830 (mtm) cc_final: 0.3186 (mmt) REVERT: K 423 LYS cc_start: 0.7086 (tptp) cc_final: 0.6596 (mmtt) REVERT: K 438 ILE cc_start: 0.4882 (tp) cc_final: 0.4209 (tt) REVERT: K 442 ARG cc_start: 0.3888 (mmt180) cc_final: 0.2395 (ptt180) REVERT: K 528 LYS cc_start: 0.2592 (tptp) cc_final: 0.0959 (ptmt) REVERT: K 637 MET cc_start: 0.0181 (tpp) cc_final: -0.0168 (mtp) REVERT: K 747 LYS cc_start: 0.4180 (mttp) cc_final: 0.3844 (tttt) REVERT: K 756 MET cc_start: -0.1794 (mmt) cc_final: -0.2078 (mmt) REVERT: K 774 ARG cc_start: 0.4908 (ptm-80) cc_final: 0.4255 (mmp80) REVERT: K 776 MET cc_start: -0.2033 (ttp) cc_final: -0.2305 (ttp) REVERT: K 777 GLU cc_start: 0.4387 (mp0) cc_final: 0.3835 (tt0) REVERT: K 780 THR cc_start: 0.5051 (m) cc_final: 0.4832 (p) REVERT: K 990 MET cc_start: 0.3128 (mmp) cc_final: 0.1720 (mmm) REVERT: K 1021 MET cc_start: 0.5851 (mmm) cc_final: 0.5110 (mmt) outliers start: 2 outliers final: 0 residues processed: 471 average time/residue: 0.5590 time to fit residues: 443.0624 Evaluate side-chains 394 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 394 time to evaluate : 2.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 362 optimal weight: 10.0000 chunk 381 optimal weight: 10.0000 chunk 347 optimal weight: 10.0000 chunk 370 optimal weight: 10.0000 chunk 223 optimal weight: 9.9990 chunk 161 optimal weight: 9.9990 chunk 291 optimal weight: 4.9990 chunk 113 optimal weight: 7.9990 chunk 335 optimal weight: 10.0000 chunk 350 optimal weight: 10.0000 chunk 369 optimal weight: 10.0000 overall best weight: 8.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 HIS A 378 HIS B 5 ASN ** B 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN C 175 GLN ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 177 ASN ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 8 ASN ** J 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 GLN ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 440 GLN ** K 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 657 HIS ** K 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 793 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.6159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.086 51840 Z= 0.485 Angle : 1.041 13.615 75674 Z= 0.518 Chirality : 0.053 0.319 9476 Planarity : 0.008 0.152 5341 Dihedral : 23.940 179.181 21038 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 24.52 Ramachandran Plot: Outliers : 0.77 % Allowed : 17.12 % Favored : 82.12 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % Cis-general : 0.28 % Twisted Proline : 3.85 % Twisted General : 0.07 % 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: -3.88 (0.13), residues: 3003 helix: -1.18 (0.18), residues: 674 sheet: -2.56 (0.27), residues: 324 loop : -3.32 (0.12), residues: 2005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.004 TRP K 348 HIS 0.013 0.002 HIS I 162 PHE 0.033 0.003 PHE F 173 TYR 0.035 0.004 TYR K 862 ARG 0.014 0.001 ARG K 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 448 time to evaluate : 2.523 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: A 80 GLU cc_start: 0.6620 (pt0) cc_final: 0.5607 (pt0) REVERT: A 316 MET cc_start: 0.5713 (ttp) cc_final: 0.5299 (ttp) REVERT: B 1 MET cc_start: 0.4497 (mmt) cc_final: 0.1350 (ptt) REVERT: B 94 TYR cc_start: 0.4613 (t80) cc_final: 0.4272 (t80) REVERT: B 147 ASN cc_start: 0.6979 (m-40) cc_final: 0.6605 (m-40) REVERT: C 82 LYS cc_start: 0.4567 (tptt) cc_final: 0.3282 (tppt) REVERT: E 125 TRP cc_start: 0.8647 (m100) cc_final: 0.8161 (m100) REVERT: F 1 MET cc_start: 0.5058 (tpt) cc_final: 0.4485 (tpt) REVERT: F 8 CYS cc_start: 0.7844 (m) cc_final: 0.7559 (m) REVERT: F 59 GLN cc_start: 0.7304 (mt0) cc_final: 0.7066 (mt0) REVERT: F 63 GLU cc_start: 0.8004 (pt0) cc_final: 0.6389 (mt-10) REVERT: G 55 TYR cc_start: 0.6666 (t80) cc_final: 0.5479 (t80) REVERT: H 45 ARG cc_start: 0.7503 (ptt90) cc_final: 0.7011 (ptt180) REVERT: I 1 MET cc_start: 0.4588 (ptt) cc_final: 0.4285 (ptt) REVERT: I 100 LYS cc_start: 0.7101 (ptpp) cc_final: 0.5928 (tppt) REVERT: I 101 PHE cc_start: 0.7825 (t80) cc_final: 0.7522 (t80) REVERT: I 120 ASP cc_start: 0.7213 (t0) cc_final: 0.6155 (m-30) REVERT: I 126 GLU cc_start: 0.8447 (tt0) cc_final: 0.7695 (mt-10) REVERT: I 139 ARG cc_start: 0.7706 (mmm-85) cc_final: 0.7414 (mmm-85) REVERT: I 205 ILE cc_start: 0.7320 (mm) cc_final: 0.7112 (mm) REVERT: J 20 MET cc_start: 0.9158 (ppp) cc_final: 0.8930 (ppp) REVERT: J 31 CYS cc_start: 0.7046 (m) cc_final: 0.6722 (m) REVERT: J 82 GLU cc_start: 0.8488 (pt0) cc_final: 0.7604 (tp30) REVERT: J 207 GLU cc_start: 0.1797 (tt0) cc_final: 0.0633 (mp0) REVERT: K 1 MET cc_start: 0.1529 (mtt) cc_final: 0.0799 (mtm) REVERT: K 102 GLU cc_start: 0.0729 (mt-10) cc_final: -0.0227 (mt-10) REVERT: K 217 ASP cc_start: 0.4769 (t70) cc_final: 0.4426 (t0) REVERT: K 358 MET cc_start: 0.1362 (ttt) cc_final: 0.1048 (ttm) REVERT: K 417 MET cc_start: 0.3992 (mtm) cc_final: 0.3311 (mmt) REVERT: K 423 LYS cc_start: 0.7247 (tptp) cc_final: 0.6676 (mmtt) REVERT: K 438 ILE cc_start: 0.4846 (tp) cc_final: 0.4055 (tt) REVERT: K 442 ARG cc_start: 0.3819 (mmt180) cc_final: 0.2381 (ptt180) REVERT: K 747 LYS cc_start: 0.4387 (mttp) cc_final: 0.4025 (tttt) REVERT: K 756 MET cc_start: -0.1864 (mmt) cc_final: -0.2147 (mmt) REVERT: K 774 ARG cc_start: 0.4616 (ptm-80) cc_final: 0.3939 (mmp80) REVERT: K 776 MET cc_start: -0.2019 (ttp) cc_final: -0.2224 (ttp) REVERT: K 777 GLU cc_start: 0.4251 (mp0) cc_final: 0.3809 (tt0) REVERT: K 990 MET cc_start: 0.2939 (mmp) cc_final: 0.1405 (mtm) REVERT: K 1021 MET cc_start: 0.5911 (mmm) cc_final: 0.5594 (mmm) outliers start: 0 outliers final: 0 residues processed: 448 average time/residue: 0.5064 time to fit residues: 375.5877 Evaluate side-chains 385 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 385 time to evaluate : 2.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 243 optimal weight: 8.9990 chunk 392 optimal weight: 7.9990 chunk 239 optimal weight: 9.9990 chunk 186 optimal weight: 5.9990 chunk 272 optimal weight: 4.9990 chunk 411 optimal weight: 9.9990 chunk 378 optimal weight: 8.9990 chunk 327 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 253 optimal weight: 0.0370 chunk 200 optimal weight: 10.0000 overall best weight: 4.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 ASN ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 15 ASN ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 ASN ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN E 131 ASN F 147 ASN F 177 ASN ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 GLN K 43 ASN ** K 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 652 GLN K 657 HIS ** K 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 793 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 810 HIS ** K 944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.6229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 51840 Z= 0.268 Angle : 0.809 13.434 75674 Z= 0.411 Chirality : 0.044 0.271 9476 Planarity : 0.006 0.127 5341 Dihedral : 23.733 179.810 21038 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.67 % Allowed : 13.65 % Favored : 85.68 % Rotamer: Outliers : 0.08 % Allowed : 0.34 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % Cis-general : 0.28 % Twisted Proline : 4.62 % Twisted General : 0.07 % 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: -3.74 (0.14), residues: 3003 helix: -0.95 (0.19), residues: 672 sheet: -2.61 (0.26), residues: 344 loop : -3.23 (0.12), residues: 1987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP F 171 HIS 0.009 0.002 HIS A 378 PHE 0.023 0.002 PHE B 116 TYR 0.033 0.002 TYR K 862 ARG 0.018 0.001 ARG K 20 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 466 time to evaluate : 2.530 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: A 80 GLU cc_start: 0.6875 (pt0) cc_final: 0.5692 (pt0) REVERT: A 286 TYR cc_start: 0.6277 (m-10) cc_final: 0.6023 (m-10) REVERT: A 316 MET cc_start: 0.5850 (ttp) cc_final: 0.5500 (ttp) REVERT: A 324 MET cc_start: 0.5897 (tpp) cc_final: 0.2938 (mtp) REVERT: B 1 MET cc_start: 0.4242 (mmt) cc_final: 0.1335 (ptt) REVERT: B 94 TYR cc_start: 0.4761 (t80) cc_final: 0.4474 (t80) REVERT: B 122 ARG cc_start: 0.7902 (tpp-160) cc_final: 0.7675 (mmt-90) REVERT: B 161 LEU cc_start: 0.8111 (tp) cc_final: 0.7530 (mt) REVERT: C 82 LYS cc_start: 0.4542 (tptt) cc_final: 0.3283 (tppt) REVERT: D 146 LYS cc_start: 0.3244 (tppt) cc_final: 0.2312 (tptt) REVERT: E 102 MET cc_start: 0.6716 (tpt) cc_final: 0.6209 (tpt) REVERT: E 113 ILE cc_start: 0.8825 (mp) cc_final: 0.8625 (mp) REVERT: F 1 MET cc_start: 0.5123 (tpt) cc_final: 0.4732 (tpt) REVERT: F 59 GLN cc_start: 0.7307 (mt0) cc_final: 0.7083 (mt0) REVERT: G 33 ASN cc_start: 0.8822 (p0) cc_final: 0.8609 (p0) REVERT: I 62 LEU cc_start: 0.7457 (tp) cc_final: 0.7117 (tp) REVERT: I 85 ARG cc_start: 0.6724 (tpp-160) cc_final: 0.6436 (tpp-160) REVERT: I 101 PHE cc_start: 0.7721 (t80) cc_final: 0.7090 (t80) REVERT: I 126 GLU cc_start: 0.8390 (tt0) cc_final: 0.7630 (pt0) REVERT: J 31 CYS cc_start: 0.6875 (m) cc_final: 0.6532 (m) REVERT: J 81 THR cc_start: 0.7500 (t) cc_final: 0.7284 (t) REVERT: J 82 GLU cc_start: 0.8593 (pt0) cc_final: 0.7828 (tp30) REVERT: J 207 GLU cc_start: 0.1816 (tt0) cc_final: 0.0606 (mp0) REVERT: K 1 MET cc_start: 0.1516 (mtt) cc_final: 0.0504 (mtm) REVERT: K 70 MET cc_start: 0.1710 (mtm) cc_final: 0.1488 (mtp) REVERT: K 217 ASP cc_start: 0.4733 (t70) cc_final: 0.4412 (t0) REVERT: K 275 MET cc_start: 0.0683 (mmm) cc_final: 0.0192 (mmm) REVERT: K 417 MET cc_start: 0.3876 (mtm) cc_final: 0.3237 (mmt) REVERT: K 423 LYS cc_start: 0.7162 (tptp) cc_final: 0.6582 (mmtt) REVERT: K 438 ILE cc_start: 0.5302 (tp) cc_final: 0.4235 (tt) REVERT: K 442 ARG cc_start: 0.3839 (mmt180) cc_final: 0.2378 (ptt180) REVERT: K 637 MET cc_start: 0.0546 (tpp) cc_final: -0.0022 (tpp) REVERT: K 747 LYS cc_start: 0.4650 (mttp) cc_final: 0.4351 (tttm) REVERT: K 756 MET cc_start: -0.1669 (mmt) cc_final: -0.1974 (mmt) REVERT: K 774 ARG cc_start: 0.4660 (ptm-80) cc_final: 0.4018 (mmp80) REVERT: K 777 GLU cc_start: 0.4432 (mp0) cc_final: 0.3873 (tt0) REVERT: K 863 ARG cc_start: 0.3948 (mtt180) cc_final: 0.3596 (mmm160) REVERT: K 981 MET cc_start: 0.0511 (ttp) cc_final: 0.0303 (ttt) REVERT: K 990 MET cc_start: 0.3058 (mmp) cc_final: 0.1157 (mtm) REVERT: K 1021 MET cc_start: 0.6018 (mmm) cc_final: 0.5346 (mmt) outliers start: 2 outliers final: 1 residues processed: 467 average time/residue: 0.4999 time to fit residues: 389.2720 Evaluate side-chains 398 residues out of total 2610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 397 time to evaluate : 2.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 260 optimal weight: 8.9990 chunk 349 optimal weight: 9.9990 chunk 100 optimal weight: 9.9990 chunk 302 optimal weight: 10.0000 chunk 48 optimal weight: 0.5980 chunk 91 optimal weight: 30.0000 chunk 328 optimal weight: 10.0000 chunk 137 optimal weight: 10.0000 chunk 336 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 overall best weight: 5.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN E 131 ASN F 147 ASN F 177 ASN ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 231 ASN K 440 GLN ** K 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 725 GLN ** K 793 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.176149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.161024 restraints weight = 108810.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.161763 restraints weight = 121429.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.160599 restraints weight = 66826.995| |-----------------------------------------------------------------------------| r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.6356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 51840 Z= 0.350 Angle : 0.891 13.490 75674 Z= 0.448 Chirality : 0.047 0.277 9476 Planarity : 0.007 0.176 5341 Dihedral : 23.770 179.896 21038 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 20.57 Ramachandran Plot: Outliers : 0.67 % Allowed : 16.28 % Favored : 83.05 % Rotamer: Outliers : 0.04 % Allowed : 0.31 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % Cis-general : 0.28 % Twisted Proline : 4.62 % Twisted General : 0.07 % 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: -3.80 (0.14), residues: 3003 helix: -1.06 (0.19), residues: 685 sheet: -2.72 (0.26), residues: 324 loop : -3.25 (0.12), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP F 171 HIS 0.010 0.002 HIS K 334 PHE 0.026 0.003 PHE I 138 TYR 0.031 0.003 TYR K 862 ARG 0.017 0.001 ARG K 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7857.28 seconds wall clock time: 139 minutes 11.07 seconds (8351.07 seconds total)