Starting phenix.real_space_refine on Sat Sep 28 01:22:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v02_26927/09_2024/7v02_26927_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v02_26927/09_2024/7v02_26927.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v02_26927/09_2024/7v02_26927.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v02_26927/09_2024/7v02_26927.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v02_26927/09_2024/7v02_26927_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v02_26927/09_2024/7v02_26927_neut.cif" } resolution = 4.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.033 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 29 5.49 5 S 49 5.16 5 C 10999 2.51 5 N 2928 2.21 5 O 3412 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 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: 17417 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1628 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 200} Chain breaks: 1 Chain: "B" Number of atoms: 1523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1523 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 187} Chain breaks: 2 Chain: "C" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1628 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 200} Chain breaks: 1 Chain: "E" Number of atoms: 2354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2354 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 8, 'TRANS': 279} Chain breaks: 3 Chain: "F" Number of atoms: 5292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 5292 Classifications: {'peptide': 650} Link IDs: {'PTRANS': 7, 'TRANS': 642} Chain breaks: 6 Chain: "G" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 624 Classifications: {'RNA': 29} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 2, 'rna3p_pur': 11, 'rna3p_pyr': 8} Link IDs: {'rna2p': 10, 'rna3p': 18} Chain: "H" Number of atoms: 2378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2378 Classifications: {'peptide': 296} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 286} Chain breaks: 1 Chain: "I" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 995 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Chain: "K" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 995 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Time building chain proxies: 9.84, per 1000 atoms: 0.56 Number of scatterers: 17417 At special positions: 0 Unit cell: (96.219, 119.739, 186.023, 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 49 16.00 P 29 15.00 O 3412 8.00 N 2928 7.00 C 10999 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 410 " - pdb=" SG CYS F 426 " distance=2.03 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: 4.23 Conformation dependent library (CDL) restraints added in 2.1 seconds 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3886 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 24 sheets defined 47.7% alpha, 15.7% beta 0 base pairs and 5 stacking pairs defined. Time for finding SS restraints: 5.54 Creating SS restraints... Processing helix chain 'A' and resid 47 through 63 removed outlier: 3.695A pdb=" N ILE A 51 " --> pdb=" O PRO A 47 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 72 Processing helix chain 'A' and resid 76 through 84 Processing helix chain 'A' and resid 104 through 115 Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 161 through 178 removed outlier: 3.685A pdb=" N ASN A 178 " --> pdb=" O HIS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'B' and resid 47 through 62 Processing helix chain 'B' and resid 77 through 84 Processing helix chain 'B' and resid 104 through 114 Processing helix chain 'B' and resid 158 through 160 No H-bonds generated for 'chain 'B' and resid 158 through 160' Processing helix chain 'B' and resid 161 through 178 removed outlier: 3.564A pdb=" N ASN B 178 " --> pdb=" O HIS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 188 Processing helix chain 'C' and resid 47 through 63 removed outlier: 3.558A pdb=" N ILE C 51 " --> pdb=" O PRO C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 72 removed outlier: 3.687A pdb=" N HIS C 72 " --> pdb=" O LYS C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 84 Processing helix chain 'C' and resid 104 through 115 Processing helix chain 'C' and resid 158 through 160 No H-bonds generated for 'chain 'C' and resid 158 through 160' Processing helix chain 'C' and resid 161 through 178 Processing helix chain 'E' and resid 42 through 53 Processing helix chain 'E' and resid 55 through 65 Processing helix chain 'E' and resid 69 through 73 Processing helix chain 'E' and resid 75 through 82 removed outlier: 3.670A pdb=" N GLN E 82 " --> pdb=" O TYR E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 92 Processing helix chain 'E' and resid 130 through 147 removed outlier: 3.679A pdb=" N ILE E 134 " --> pdb=" O PRO E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 156 removed outlier: 4.191A pdb=" N SER E 156 " --> pdb=" O LYS E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 169 No H-bonds generated for 'chain 'E' and resid 167 through 169' Processing helix chain 'E' and resid 211 through 230 Processing helix chain 'E' and resid 237 through 247 Processing helix chain 'E' and resid 248 through 253 Processing helix chain 'E' and resid 278 through 290 Processing helix chain 'F' and resid 2 through 12 Processing helix chain 'F' and resid 13 through 15 No H-bonds generated for 'chain 'F' and resid 13 through 15' Processing helix chain 'F' and resid 16 through 24 removed outlier: 3.872A pdb=" N ILE F 20 " --> pdb=" O ILE F 16 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY F 24 " --> pdb=" O ILE F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 42 Processing helix chain 'F' and resid 49 through 58 removed outlier: 3.653A pdb=" N LEU F 53 " --> pdb=" O ASP F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 67 removed outlier: 4.096A pdb=" N LYS F 66 " --> pdb=" O LYS F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 86 Processing helix chain 'F' and resid 152 through 170 removed outlier: 4.245A pdb=" N TYR F 156 " --> pdb=" O SER F 152 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR F 157 " --> pdb=" O SER F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 190 removed outlier: 3.900A pdb=" N GLN F 190 " --> pdb=" O GLU F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 227 Processing helix chain 'F' and resid 231 through 236 Processing helix chain 'F' and resid 239 through 249 Processing helix chain 'F' and resid 261 through 267 Processing helix chain 'F' and resid 273 through 300 removed outlier: 3.597A pdb=" N SER F 280 " --> pdb=" O LYS F 276 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE F 283 " --> pdb=" O ARG F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 305 No H-bonds generated for 'chain 'F' and resid 303 through 305' Processing helix chain 'F' and resid 322 through 344 Processing helix chain 'F' and resid 358 through 363 removed outlier: 3.611A pdb=" N LEU F 362 " --> pdb=" O SER F 358 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET F 363 " --> pdb=" O GLY F 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 358 through 363' Processing helix chain 'F' and resid 367 through 384 removed outlier: 3.774A pdb=" N THR F 371 " --> pdb=" O GLY F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 398 Processing helix chain 'F' and resid 419 through 421 No H-bonds generated for 'chain 'F' and resid 419 through 421' Processing helix chain 'F' and resid 424 through 437 removed outlier: 4.530A pdb=" N ARG F 437 " --> pdb=" O SER F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 472 Processing helix chain 'F' and resid 536 through 542 Processing helix chain 'F' and resid 550 through 573 removed outlier: 3.625A pdb=" N THR F 554 " --> pdb=" O SER F 550 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LEU F 569 " --> pdb=" O PHE F 565 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ASN F 570 " --> pdb=" O LYS F 566 " (cutoff:3.500A) Processing helix chain 'F' and resid 593 through 612 Processing helix chain 'F' and resid 630 through 638 removed outlier: 3.990A pdb=" N PHE F 636 " --> pdb=" O SER F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 665 through 670 Processing helix chain 'F' and resid 674 through 686 Processing helix chain 'F' and resid 690 through 703 removed outlier: 4.005A pdb=" N ASN F 703 " --> pdb=" O ALA F 699 " (cutoff:3.500A) Processing helix chain 'F' and resid 705 through 719 Processing helix chain 'F' and resid 722 through 734 Processing helix chain 'F' and resid 735 through 750 Processing helix chain 'H' and resid 31 through 47 Processing helix chain 'H' and resid 100 through 106 Processing helix chain 'H' and resid 110 through 120 Processing helix chain 'H' and resid 168 through 183 Processing helix chain 'H' and resid 190 through 194 Processing helix chain 'H' and resid 205 through 213 Processing helix chain 'H' and resid 231 through 236 Processing helix chain 'I' and resid 15 through 24 removed outlier: 3.907A pdb=" N GLU I 19 " --> pdb=" O THR I 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 47 Processing helix chain 'I' and resid 48 through 65 Processing helix chain 'I' and resid 71 through 92 Processing helix chain 'I' and resid 92 through 102 Processing helix chain 'I' and resid 103 through 115 Processing helix chain 'I' and resid 116 through 137 Processing helix chain 'K' and resid 15 through 24 removed outlier: 5.084A pdb=" N VAL K 21 " --> pdb=" O ALA K 17 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N LYS K 22 " --> pdb=" O HIS K 18 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER K 23 " --> pdb=" O GLU K 19 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 47 Processing helix chain 'K' and resid 48 through 65 Processing helix chain 'K' and resid 71 through 92 Processing helix chain 'K' and resid 92 through 102 Processing helix chain 'K' and resid 103 through 115 Processing helix chain 'K' and resid 116 through 137 removed outlier: 3.888A pdb=" N TYR K 137 " --> pdb=" O TYR K 133 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 103 removed outlier: 5.574A pdb=" N VAL A 151 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ALA A 101 " --> pdb=" O ASP A 149 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ASP A 149 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N PHE A 103 " --> pdb=" O GLU A 147 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N GLU A 147 " --> pdb=" O PHE A 103 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY A 9 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LYS A 4 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N THR A 201 " --> pdb=" O LYS A 4 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LYS A 6 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ILE A 199 " --> pdb=" O LYS A 6 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N SER A 8 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N THR A 197 " --> pdb=" O SER A 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 124 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.511A pdb=" N PHE B 102 " --> pdb=" O ASP B 149 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 96 through 98 removed outlier: 4.472A pdb=" N SER B 3 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LYS B 4 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N THR B 201 " --> pdb=" O LYS B 4 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LYS B 6 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ILE B 199 " --> pdb=" O LYS B 6 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N SER B 8 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N THR B 197 " --> pdb=" O SER B 8 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 119 through 127 Processing sheet with id=AA6, first strand: chain 'C' and resid 45 through 46 removed outlier: 3.571A pdb=" N PHE C 102 " --> pdb=" O ASP C 149 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP C 149 " --> pdb=" O PHE C 102 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 45 through 46 removed outlier: 3.571A pdb=" N PHE C 102 " --> pdb=" O ASP C 149 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP C 149 " --> pdb=" O PHE C 102 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LYS C 4 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N THR C 10 " --> pdb=" O ASP C 196 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ASP C 196 " --> pdb=" O THR C 10 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLU C 12 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N PHE C 194 " --> pdb=" O GLU C 12 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 119 through 127 Processing sheet with id=AA9, first strand: chain 'E' and resid 158 through 160 Processing sheet with id=AB1, first strand: chain 'E' and resid 19 through 24 removed outlier: 4.938A pdb=" N GLN E 22 " --> pdb=" O LEU E 118 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 38 through 41 Processing sheet with id=AB3, first strand: chain 'E' and resid 184 through 193 removed outlier: 7.186A pdb=" N MET E 186 " --> pdb=" O ASP E 178 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ASP E 178 " --> pdb=" O MET E 186 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU E 188 " --> pdb=" O LYS E 176 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N GLN E 175 " --> pdb=" O THR E 315 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR E 315 " --> pdb=" O GLN E 175 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 307 through 311 removed outlier: 6.570A pdb=" N TYR F 316 " --> pdb=" O LEU F 308 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N THR F 310 " --> pdb=" O HIS F 314 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N HIS F 314 " --> pdb=" O THR F 310 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA F 315 " --> pdb=" O MET F 257 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 417 through 418 Processing sheet with id=AB6, first strand: chain 'F' and resid 450 through 452 removed outlier: 4.168A pdb=" N LYS F 456 " --> pdb=" O MET F 452 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE F 461 " --> pdb=" O PHE F 441 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE F 441 " --> pdb=" O ILE F 461 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE F 478 " --> pdb=" O THR F 492 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 578 through 584 removed outlier: 5.725A pdb=" N ALA F 580 " --> pdb=" O ILE F 591 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ILE F 591 " --> pdb=" O ALA F 580 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL F 528 " --> pdb=" O GLY F 623 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 63 through 65 removed outlier: 3.519A pdb=" N GLY H 160 " --> pdb=" O TYR H 65 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 58 through 59 Processing sheet with id=AC1, first strand: chain 'H' and resid 71 through 73 Processing sheet with id=AC2, first strand: chain 'H' and resid 125 through 131 Processing sheet with id=AC3, first strand: chain 'H' and resid 273 through 274 Processing sheet with id=AC4, first strand: chain 'H' and resid 243 through 246 removed outlier: 3.693A pdb=" N SER H 267 " --> pdb=" O THR H 244 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 283 through 284 Processing sheet with id=AC6, first strand: chain 'I' and resid 25 through 26 removed outlier: 3.552A pdb=" N LYS I 26 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL I 38 " --> pdb=" O LYS I 26 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 804 hydrogen bonds defined for protein. 2325 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 5 stacking parallelities Total time for adding SS restraints: 5.81 Time building geometry restraints manager: 4.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5494 1.34 - 1.46: 4089 1.46 - 1.58: 8075 1.58 - 1.70: 57 1.70 - 1.82: 86 Bond restraints: 17801 Sorted by residual: bond pdb=" O3' U G 22 " pdb=" P A G 23 " ideal model delta sigma weight residual 1.607 1.658 -0.051 1.50e-02 4.44e+03 1.17e+01 bond pdb=" C3' U G 24 " pdb=" O3' U G 24 " ideal model delta sigma weight residual 1.417 1.466 -0.049 1.50e-02 4.44e+03 1.07e+01 bond pdb=" N ILE F 120 " pdb=" CA ILE F 120 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.04e+01 bond pdb=" N ILE A 91 " pdb=" CA ILE A 91 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.10e-02 8.26e+03 9.65e+00 bond pdb=" N ASP E 122 " pdb=" CA ASP E 122 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.14e-02 7.69e+03 9.46e+00 ... (remaining 17796 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 23405 2.54 - 5.08: 580 5.08 - 7.61: 80 7.61 - 10.15: 10 10.15 - 12.69: 4 Bond angle restraints: 24079 Sorted by residual: angle pdb=" C4' A G 27 " pdb=" C3' A G 27 " pdb=" O3' A G 27 " ideal model delta sigma weight residual 109.40 96.71 12.69 1.50e+00 4.44e-01 7.16e+01 angle pdb=" C3' C G 8 " pdb=" O3' C G 8 " pdb=" P A G 9 " ideal model delta sigma weight residual 120.20 130.50 -10.30 1.50e+00 4.44e-01 4.71e+01 angle pdb=" CA ASP E 122 " pdb=" CB ASP E 122 " pdb=" CG ASP E 122 " ideal model delta sigma weight residual 112.60 118.19 -5.59 1.00e+00 1.00e+00 3.12e+01 angle pdb=" C4' A G 19 " pdb=" C3' A G 19 " pdb=" O3' A G 19 " ideal model delta sigma weight residual 113.00 121.30 -8.30 1.50e+00 4.44e-01 3.06e+01 angle pdb=" C4' U G 26 " pdb=" C3' U G 26 " pdb=" O3' U G 26 " ideal model delta sigma weight residual 109.40 117.20 -7.80 1.50e+00 4.44e-01 2.71e+01 ... (remaining 24074 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 10487 35.89 - 71.79: 195 71.79 - 107.68: 20 107.68 - 143.58: 2 143.58 - 179.47: 2 Dihedral angle restraints: 10706 sinusoidal: 4667 harmonic: 6039 Sorted by residual: dihedral pdb=" O4' C G 10 " pdb=" C1' C G 10 " pdb=" N1 C G 10 " pdb=" C2 C G 10 " ideal model delta sinusoidal sigma weight residual -160.00 -2.54 -157.46 1 1.50e+01 4.44e-03 8.21e+01 dihedral pdb=" CB CYS F 410 " pdb=" SG CYS F 410 " pdb=" SG CYS F 426 " pdb=" CB CYS F 426 " ideal model delta sinusoidal sigma weight residual -86.00 -158.19 72.19 1 1.00e+01 1.00e-02 6.66e+01 dihedral pdb=" O4' C G 2 " pdb=" C1' C G 2 " pdb=" N1 C G 2 " pdb=" C2 C G 2 " ideal model delta sinusoidal sigma weight residual 232.00 52.53 179.47 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 10703 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2093 0.066 - 0.132: 466 0.132 - 0.198: 67 0.198 - 0.264: 19 0.264 - 0.330: 6 Chirality restraints: 2651 Sorted by residual: chirality pdb=" CG LEU A 58 " pdb=" CB LEU A 58 " pdb=" CD1 LEU A 58 " pdb=" CD2 LEU A 58 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" P G G 5 " pdb=" OP1 G G 5 " pdb=" OP2 G G 5 " pdb=" O5' G G 5 " both_signs ideal model delta sigma weight residual True 2.41 -2.71 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CB ILE C 91 " pdb=" CA ILE C 91 " pdb=" CG1 ILE C 91 " pdb=" CG2 ILE C 91 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 2648 not shown) Planarity restraints: 2973 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 339 " -0.031 2.00e-02 2.50e+03 3.09e-02 2.39e+01 pdb=" CG TRP F 339 " 0.079 2.00e-02 2.50e+03 pdb=" CD1 TRP F 339 " -0.046 2.00e-02 2.50e+03 pdb=" CD2 TRP F 339 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP F 339 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP F 339 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP F 339 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 339 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 339 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP F 339 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE I 85 " -0.022 2.00e-02 2.50e+03 2.21e-02 8.51e+00 pdb=" CG PHE I 85 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE I 85 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE I 85 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE I 85 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE I 85 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE I 85 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP F 72 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.70e+00 pdb=" CG ASP F 72 " 0.041 2.00e-02 2.50e+03 pdb=" OD1 ASP F 72 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP F 72 " -0.014 2.00e-02 2.50e+03 ... (remaining 2970 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 152 2.62 - 3.19: 15977 3.19 - 3.76: 25525 3.76 - 4.33: 36218 4.33 - 4.90: 58169 Nonbonded interactions: 136041 Sorted by model distance: nonbonded pdb=" O ARG A 144 " pdb=" OE1 GLN C 40 " model vdw 2.048 3.040 nonbonded pdb=" O LEU E 55 " pdb=" OG1 THR E 58 " model vdw 2.098 3.040 nonbonded pdb=" NH2 ARG A 129 " pdb=" OD1 ASN C 57 " model vdw 2.158 3.120 nonbonded pdb=" O PHE F 344 " pdb=" OG1 THR F 345 " model vdw 2.197 3.040 nonbonded pdb=" OH TYR F 499 " pdb=" O GLU F 574 " model vdw 2.265 3.040 ... (remaining 136036 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 23 or resid 33 through 63 or resid 76 through 21 \ 4)) selection = chain 'B' selection = (chain 'C' and (resid 2 through 23 or resid 33 through 63 or resid 76 through 21 \ 4)) } ncs_group { reference = chain 'I' selection = chain 'K' } 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: 0.740 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: 0.010 Extract box with map and model: 0.630 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 42.060 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6594 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 : 0.006 0.052 17801 Z= 0.392 Angle : 0.931 12.691 24079 Z= 0.551 Chirality : 0.058 0.330 2651 Planarity : 0.004 0.041 2973 Dihedral : 14.119 179.472 6817 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.85 % Favored : 95.10 % Rotamer: Outliers : 0.65 % Allowed : 0.76 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.17), residues: 2022 helix: 0.01 (0.17), residues: 878 sheet: -0.02 (0.28), residues: 336 loop : -1.86 (0.19), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.004 TRP F 339 HIS 0.007 0.002 HIS I 18 PHE 0.051 0.003 PHE I 85 TYR 0.024 0.002 TYR E 189 ARG 0.019 0.002 ARG A 137 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 287 time to evaluate : 2.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LEU cc_start: 0.8201 (tp) cc_final: 0.7857 (mp) REVERT: B 17 LEU cc_start: 0.9298 (tt) cc_final: 0.8437 (mt) REVERT: B 46 ILE cc_start: 0.8693 (tt) cc_final: 0.8450 (pt) REVERT: B 115 ASP cc_start: 0.8646 (t0) cc_final: 0.8183 (m-30) REVERT: E 66 PRO cc_start: 0.8088 (Cg_exo) cc_final: 0.7559 (Cg_endo) REVERT: F 13 LEU cc_start: 0.9263 (mt) cc_final: 0.8989 (mp) REVERT: F 588 LEU cc_start: 0.8993 (tp) cc_final: 0.8437 (mm) REVERT: F 669 LYS cc_start: 0.9187 (mttt) cc_final: 0.8687 (pttp) REVERT: H 10 LEU cc_start: 0.8266 (mp) cc_final: 0.7779 (mt) REVERT: I 18 HIS cc_start: 0.8633 (t70) cc_final: 0.8236 (t-170) REVERT: I 74 PHE cc_start: 0.9166 (t80) cc_final: 0.8894 (t80) REVERT: I 75 ILE cc_start: 0.9155 (mm) cc_final: 0.8635 (mm) REVERT: I 102 THR cc_start: 0.9069 (p) cc_final: 0.8726 (p) REVERT: I 107 ILE cc_start: 0.8904 (mt) cc_final: 0.8421 (tp) REVERT: K 127 PHE cc_start: 0.8674 (t80) cc_final: 0.8474 (t80) outliers start: 12 outliers final: 5 residues processed: 296 average time/residue: 0.3616 time to fit residues: 151.0334 Evaluate side-chains 163 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 158 time to evaluate : 2.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 86 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 104 optimal weight: 6.9990 chunk 83 optimal weight: 0.0470 chunk 160 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 186 optimal weight: 9.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN B 174 HIS C 155 ASN E 27 GLN E 255 GLN E 316 ASN ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 HIS F 26 HIS F 33 HIS F 43 GLN F 60 HIS ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 ASN F 472 ASN F 482 ASN ** F 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 681 GLN F 708 ASN H 17 HIS ** H 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 214 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17801 Z= 0.179 Angle : 0.654 9.481 24079 Z= 0.349 Chirality : 0.045 0.216 2651 Planarity : 0.004 0.032 2973 Dihedral : 13.623 173.787 2654 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.11 % Allowed : 2.81 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.18), residues: 2022 helix: 0.71 (0.17), residues: 912 sheet: -0.01 (0.27), residues: 377 loop : -1.78 (0.21), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP F 339 HIS 0.020 0.001 HIS B 110 PHE 0.032 0.002 PHE I 85 TYR 0.023 0.002 TYR E 95 ARG 0.007 0.001 ARG E 190 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 180 time to evaluate : 2.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 LEU cc_start: 0.8869 (tt) cc_final: 0.8238 (mt) REVERT: B 46 ILE cc_start: 0.8632 (tt) cc_final: 0.8383 (pt) REVERT: B 115 ASP cc_start: 0.8145 (t0) cc_final: 0.7744 (m-30) REVERT: C 55 MET cc_start: 0.7970 (tpt) cc_final: 0.7400 (tpt) REVERT: E 24 MET cc_start: 0.3943 (ttt) cc_final: 0.3496 (tmm) REVERT: E 49 PHE cc_start: 0.8995 (t80) cc_final: 0.8709 (t80) REVERT: E 87 SER cc_start: 0.9529 (m) cc_final: 0.9235 (p) REVERT: E 116 LEU cc_start: 0.7775 (tp) cc_final: 0.7222 (tp) REVERT: F 318 LEU cc_start: 0.9285 (tp) cc_final: 0.8844 (tp) REVERT: F 588 LEU cc_start: 0.8896 (tp) cc_final: 0.8573 (mm) REVERT: H 10 LEU cc_start: 0.8400 (mp) cc_final: 0.7986 (mt) REVERT: I 55 VAL cc_start: 0.9515 (p) cc_final: 0.9233 (p) REVERT: I 74 PHE cc_start: 0.9026 (t80) cc_final: 0.8789 (t80) REVERT: I 75 ILE cc_start: 0.9061 (mm) cc_final: 0.8806 (mm) REVERT: I 81 LEU cc_start: 0.9516 (tp) cc_final: 0.8933 (tt) REVERT: I 86 TYR cc_start: 0.7643 (m-80) cc_final: 0.7095 (m-80) REVERT: I 102 THR cc_start: 0.8950 (p) cc_final: 0.8724 (p) REVERT: I 107 ILE cc_start: 0.9418 (mt) cc_final: 0.8571 (tp) REVERT: K 127 PHE cc_start: 0.8725 (t80) cc_final: 0.8070 (t80) outliers start: 2 outliers final: 0 residues processed: 182 average time/residue: 0.3057 time to fit residues: 84.5020 Evaluate side-chains 130 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 103 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 154 optimal weight: 9.9990 chunk 126 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 186 optimal weight: 9.9990 chunk 201 optimal weight: 3.9990 chunk 166 optimal weight: 7.9990 chunk 184 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 149 optimal weight: 0.4980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 HIS E 324 GLN F 43 GLN ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 ASN ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 17801 Z= 0.185 Angle : 0.586 7.520 24079 Z= 0.313 Chirality : 0.042 0.262 2651 Planarity : 0.003 0.033 2973 Dihedral : 13.414 173.893 2654 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.16 % Allowed : 2.81 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.18), residues: 2022 helix: 0.89 (0.17), residues: 914 sheet: 0.15 (0.27), residues: 369 loop : -1.60 (0.21), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 339 HIS 0.013 0.001 HIS B 110 PHE 0.056 0.002 PHE I 85 TYR 0.027 0.002 TYR E 57 ARG 0.005 0.001 ARG E 190 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 154 time to evaluate : 1.934 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: A 17 LEU cc_start: 0.8487 (tp) cc_final: 0.7609 (mp) REVERT: B 17 LEU cc_start: 0.8957 (tt) cc_final: 0.8346 (mt) REVERT: B 46 ILE cc_start: 0.8885 (tt) cc_final: 0.8650 (pt) REVERT: B 115 ASP cc_start: 0.8263 (t0) cc_final: 0.7899 (m-30) REVERT: C 55 MET cc_start: 0.8031 (tpt) cc_final: 0.7376 (tpt) REVERT: E 49 PHE cc_start: 0.9039 (t80) cc_final: 0.8631 (t80) REVERT: E 51 LYS cc_start: 0.9679 (mmpt) cc_final: 0.9271 (mmmt) REVERT: E 327 MET cc_start: 0.7857 (ptp) cc_final: 0.7546 (ptp) REVERT: F 47 PHE cc_start: 0.4304 (m-80) cc_final: 0.3896 (m-80) REVERT: F 182 LEU cc_start: 0.9382 (tt) cc_final: 0.9110 (mt) REVERT: F 318 LEU cc_start: 0.9291 (tp) cc_final: 0.8304 (pp) REVERT: F 468 MET cc_start: 0.8927 (tmm) cc_final: 0.8571 (tmm) REVERT: F 588 LEU cc_start: 0.8708 (tp) cc_final: 0.8205 (mm) REVERT: H 10 LEU cc_start: 0.8442 (mp) cc_final: 0.8055 (mt) REVERT: I 55 VAL cc_start: 0.9282 (p) cc_final: 0.9079 (p) REVERT: I 74 PHE cc_start: 0.9066 (t80) cc_final: 0.8806 (t80) REVERT: I 75 ILE cc_start: 0.9143 (mm) cc_final: 0.8867 (mm) REVERT: I 107 ILE cc_start: 0.9447 (mt) cc_final: 0.8764 (tp) REVERT: K 51 LEU cc_start: 0.9301 (mt) cc_final: 0.9098 (mt) REVERT: K 123 TYR cc_start: 0.8473 (t80) cc_final: 0.8236 (t80) REVERT: K 127 PHE cc_start: 0.8547 (t80) cc_final: 0.7974 (t80) outliers start: 3 outliers final: 1 residues processed: 157 average time/residue: 0.3060 time to fit residues: 73.0238 Evaluate side-chains 125 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 2.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 184 optimal weight: 0.2980 chunk 140 optimal weight: 0.9990 chunk 96 optimal weight: 0.0050 chunk 20 optimal weight: 10.0000 chunk 89 optimal weight: 7.9990 chunk 125 optimal weight: 4.9990 chunk 187 optimal weight: 0.9990 chunk 198 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 177 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 306 ASN H 207 GLN I 18 HIS I 54 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 17801 Z= 0.142 Angle : 0.546 7.966 24079 Z= 0.290 Chirality : 0.041 0.256 2651 Planarity : 0.003 0.074 2973 Dihedral : 13.248 174.201 2654 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.19), residues: 2022 helix: 1.14 (0.17), residues: 903 sheet: 0.21 (0.27), residues: 374 loop : -1.45 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 339 HIS 0.007 0.001 HIS F 60 PHE 0.031 0.001 PHE I 85 TYR 0.024 0.001 TYR K 80 ARG 0.012 0.000 ARG F 405 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 2.622 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: A 17 LEU cc_start: 0.8496 (tp) cc_final: 0.7611 (mp) REVERT: B 17 LEU cc_start: 0.8977 (tt) cc_final: 0.8327 (mt) REVERT: B 115 ASP cc_start: 0.8169 (t0) cc_final: 0.7797 (m-30) REVERT: C 55 MET cc_start: 0.7938 (tpt) cc_final: 0.7315 (tpt) REVERT: E 49 PHE cc_start: 0.8964 (t80) cc_final: 0.8672 (t80) REVERT: E 51 LYS cc_start: 0.9573 (mmmt) cc_final: 0.9286 (mmmt) REVERT: E 116 LEU cc_start: 0.8395 (tp) cc_final: 0.6223 (tp) REVERT: F 47 PHE cc_start: 0.4167 (m-80) cc_final: 0.3601 (m-80) REVERT: F 182 LEU cc_start: 0.9384 (tt) cc_final: 0.9118 (mt) REVERT: F 363 MET cc_start: 0.7813 (mmp) cc_final: 0.7593 (mmm) REVERT: F 496 MET cc_start: 0.2924 (pmm) cc_final: 0.2589 (pmm) REVERT: F 588 LEU cc_start: 0.8863 (tp) cc_final: 0.8449 (mm) REVERT: H 10 LEU cc_start: 0.8385 (mp) cc_final: 0.8175 (mt) REVERT: I 55 VAL cc_start: 0.9240 (p) cc_final: 0.9026 (p) REVERT: I 74 PHE cc_start: 0.8827 (t80) cc_final: 0.8624 (t80) REVERT: I 75 ILE cc_start: 0.9160 (mm) cc_final: 0.8901 (mm) REVERT: I 87 TYR cc_start: 0.6397 (t80) cc_final: 0.6191 (t80) REVERT: I 107 ILE cc_start: 0.9475 (mt) cc_final: 0.8886 (tp) REVERT: K 51 LEU cc_start: 0.9348 (mt) cc_final: 0.8993 (mt) REVERT: K 56 ASN cc_start: 0.9008 (m110) cc_final: 0.8422 (m110) REVERT: K 80 TYR cc_start: 0.9274 (t80) cc_final: 0.8612 (t80) REVERT: K 83 ILE cc_start: 0.8651 (tp) cc_final: 0.8163 (pt) REVERT: K 127 PHE cc_start: 0.8498 (t80) cc_final: 0.7977 (t80) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.3145 time to fit residues: 74.5758 Evaluate side-chains 120 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 2.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 165 optimal weight: 10.0000 chunk 112 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 147 optimal weight: 9.9990 chunk 81 optimal weight: 8.9990 chunk 169 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 101 optimal weight: 9.9990 chunk 177 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 HIS ** C 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 320 HIS E 324 GLN ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 ASN F 169 HIS F 549 ASN H 177 ASN I 24 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17801 Z= 0.220 Angle : 0.594 8.635 24079 Z= 0.318 Chirality : 0.041 0.211 2651 Planarity : 0.003 0.041 2973 Dihedral : 13.126 175.637 2654 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.16 % Allowed : 1.73 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.18), residues: 2022 helix: 1.09 (0.17), residues: 906 sheet: 0.21 (0.28), residues: 366 loop : -1.42 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 339 HIS 0.005 0.001 HIS K 18 PHE 0.037 0.002 PHE K 85 TYR 0.037 0.002 TYR K 126 ARG 0.004 0.001 ARG E 64 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 145 time to evaluate : 2.273 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: C 55 MET cc_start: 0.7964 (tpt) cc_final: 0.7512 (tpt) REVERT: E 49 PHE cc_start: 0.8943 (t80) cc_final: 0.8685 (t80) REVERT: E 56 LEU cc_start: 0.8066 (mt) cc_final: 0.7808 (mt) REVERT: E 327 MET cc_start: 0.7533 (ptp) cc_final: 0.7134 (ptp) REVERT: F 47 PHE cc_start: 0.4523 (m-80) cc_final: 0.3998 (m-80) REVERT: F 363 MET cc_start: 0.8270 (mmp) cc_final: 0.8039 (mmm) REVERT: F 588 LEU cc_start: 0.9103 (tp) cc_final: 0.8754 (mm) REVERT: F 589 PHE cc_start: 0.7331 (t80) cc_final: 0.7002 (t80) REVERT: I 55 VAL cc_start: 0.9228 (p) cc_final: 0.8982 (p) REVERT: I 69 GLN cc_start: 0.7805 (tp40) cc_final: 0.7554 (tp40) REVERT: I 74 PHE cc_start: 0.8886 (t80) cc_final: 0.8650 (t80) REVERT: I 75 ILE cc_start: 0.9237 (mm) cc_final: 0.8973 (mm) REVERT: I 76 ASP cc_start: 0.9606 (t70) cc_final: 0.9344 (t0) REVERT: I 107 ILE cc_start: 0.9414 (mt) cc_final: 0.9208 (mm) REVERT: K 127 PHE cc_start: 0.8524 (t80) cc_final: 0.8079 (t80) outliers start: 3 outliers final: 0 residues processed: 148 average time/residue: 0.3214 time to fit residues: 71.4911 Evaluate side-chains 113 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 2.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 66 optimal weight: 3.9990 chunk 178 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 198 optimal weight: 10.0000 chunk 164 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 65 optimal weight: 8.9990 chunk 104 optimal weight: 9.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN A 178 ASN C 168 ASN ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 314 HIS ** H 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 HIS I 54 GLN ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.5163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17801 Z= 0.244 Angle : 0.591 7.370 24079 Z= 0.319 Chirality : 0.041 0.201 2651 Planarity : 0.004 0.079 2973 Dihedral : 13.148 176.482 2654 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.05 % Allowed : 1.62 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.18), residues: 2022 helix: 0.98 (0.17), residues: 903 sheet: 0.28 (0.29), residues: 352 loop : -1.39 (0.21), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 339 HIS 0.006 0.001 HIS F 169 PHE 0.021 0.002 PHE K 85 TYR 0.022 0.002 TYR E 57 ARG 0.017 0.001 ARG I 110 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 131 time to evaluate : 2.682 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: C 55 MET cc_start: 0.7972 (tpt) cc_final: 0.7571 (tpt) REVERT: E 51 LYS cc_start: 0.9586 (mmpt) cc_final: 0.9244 (mmmt) REVERT: E 62 PHE cc_start: 0.9248 (m-10) cc_final: 0.8361 (m-10) REVERT: F 318 LEU cc_start: 0.8599 (tp) cc_final: 0.8064 (tp) REVERT: F 588 LEU cc_start: 0.8830 (tp) cc_final: 0.8396 (mm) REVERT: F 589 PHE cc_start: 0.7515 (t80) cc_final: 0.7095 (t80) REVERT: H 187 LEU cc_start: 0.8681 (mt) cc_final: 0.8406 (pp) REVERT: I 18 HIS cc_start: 0.8772 (t70) cc_final: 0.8548 (t-170) REVERT: I 54 GLN cc_start: 0.9076 (mp10) cc_final: 0.8841 (mp10) REVERT: I 69 GLN cc_start: 0.8179 (tp40) cc_final: 0.7823 (tp40) REVERT: I 74 PHE cc_start: 0.8922 (t80) cc_final: 0.8614 (t80) REVERT: I 75 ILE cc_start: 0.9308 (mm) cc_final: 0.9001 (mm) REVERT: I 76 ASP cc_start: 0.9600 (t70) cc_final: 0.9361 (t0) REVERT: I 86 TYR cc_start: 0.8219 (m-80) cc_final: 0.7368 (m-80) REVERT: I 107 ILE cc_start: 0.9430 (mt) cc_final: 0.8998 (tp) REVERT: K 56 ASN cc_start: 0.9154 (m110) cc_final: 0.8708 (m110) REVERT: K 127 PHE cc_start: 0.8545 (t80) cc_final: 0.8142 (t80) outliers start: 1 outliers final: 0 residues processed: 132 average time/residue: 0.3901 time to fit residues: 78.1790 Evaluate side-chains 103 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 2.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 191 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 chunk 112 optimal weight: 0.2980 chunk 166 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 197 optimal weight: 6.9990 chunk 123 optimal weight: 0.9980 chunk 120 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.5670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 17801 Z= 0.221 Angle : 0.588 12.172 24079 Z= 0.314 Chirality : 0.041 0.319 2651 Planarity : 0.003 0.046 2973 Dihedral : 13.131 175.611 2654 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.18), residues: 2022 helix: 0.99 (0.17), residues: 906 sheet: 0.12 (0.28), residues: 365 loop : -1.39 (0.21), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 339 HIS 0.005 0.001 HIS F 169 PHE 0.028 0.002 PHE K 85 TYR 0.025 0.002 TYR E 57 ARG 0.010 0.001 ARG I 110 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 2.334 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: C 55 MET cc_start: 0.7984 (tpt) cc_final: 0.7542 (tpt) REVERT: E 62 PHE cc_start: 0.9212 (m-10) cc_final: 0.8233 (m-10) REVERT: E 327 MET cc_start: 0.7734 (ptp) cc_final: 0.7439 (ptp) REVERT: F 318 LEU cc_start: 0.8682 (tp) cc_final: 0.8269 (tp) REVERT: F 588 LEU cc_start: 0.8833 (tp) cc_final: 0.8417 (mm) REVERT: F 589 PHE cc_start: 0.7502 (t80) cc_final: 0.7054 (t80) REVERT: F 624 MET cc_start: 0.5808 (mmp) cc_final: 0.5365 (mmm) REVERT: F 634 MET cc_start: 0.8161 (mmm) cc_final: 0.7604 (mmm) REVERT: H 187 LEU cc_start: 0.8751 (mt) cc_final: 0.8438 (pp) REVERT: I 14 MET cc_start: 0.8810 (tmm) cc_final: 0.8596 (tmm) REVERT: I 69 GLN cc_start: 0.8353 (tp40) cc_final: 0.7928 (tp40) REVERT: I 74 PHE cc_start: 0.8871 (t80) cc_final: 0.8580 (t80) REVERT: I 75 ILE cc_start: 0.9336 (mm) cc_final: 0.9021 (mm) REVERT: I 76 ASP cc_start: 0.9597 (t70) cc_final: 0.9331 (t0) REVERT: I 85 PHE cc_start: 0.8815 (m-10) cc_final: 0.8609 (m-10) REVERT: I 107 ILE cc_start: 0.9437 (mt) cc_final: 0.8931 (tp) REVERT: K 56 ASN cc_start: 0.9199 (m110) cc_final: 0.8792 (m110) REVERT: K 127 PHE cc_start: 0.8545 (t80) cc_final: 0.8181 (t80) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.3230 time to fit residues: 61.8059 Evaluate side-chains 101 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 2.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 122 optimal weight: 9.9990 chunk 78 optimal weight: 0.0040 chunk 118 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 125 optimal weight: 0.0870 chunk 134 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 155 optimal weight: 10.0000 chunk 179 optimal weight: 0.7980 overall best weight: 1.1774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 324 GLN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 ASN ** H 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.5810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 17801 Z= 0.156 Angle : 0.530 7.713 24079 Z= 0.281 Chirality : 0.040 0.271 2651 Planarity : 0.003 0.042 2973 Dihedral : 12.944 174.898 2654 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.11 % Allowed : 1.08 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.19), residues: 2022 helix: 1.17 (0.17), residues: 906 sheet: 0.10 (0.28), residues: 368 loop : -1.35 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 339 HIS 0.003 0.001 HIS K 18 PHE 0.019 0.001 PHE E 49 TYR 0.024 0.001 TYR E 57 ARG 0.007 0.000 ARG I 110 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 125 time to evaluate : 2.066 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: C 55 MET cc_start: 0.7916 (tpt) cc_final: 0.7484 (tpt) REVERT: E 62 PHE cc_start: 0.9217 (m-10) cc_final: 0.8132 (m-80) REVERT: F 318 LEU cc_start: 0.8674 (tp) cc_final: 0.8353 (tp) REVERT: F 496 MET cc_start: 0.0251 (pmm) cc_final: -0.0108 (pmm) REVERT: F 588 LEU cc_start: 0.8893 (tp) cc_final: 0.8591 (mm) REVERT: F 589 PHE cc_start: 0.7324 (t80) cc_final: 0.6979 (t80) REVERT: F 624 MET cc_start: 0.6130 (mmp) cc_final: 0.5811 (mmm) REVERT: H 187 LEU cc_start: 0.8649 (mt) cc_final: 0.8384 (pp) REVERT: I 18 HIS cc_start: 0.8521 (t-170) cc_final: 0.8190 (t-170) REVERT: I 49 ARG cc_start: 0.8747 (mtm180) cc_final: 0.8404 (ptt180) REVERT: I 69 GLN cc_start: 0.8323 (tp40) cc_final: 0.7908 (tp40) REVERT: I 74 PHE cc_start: 0.8906 (t80) cc_final: 0.8582 (t80) REVERT: I 75 ILE cc_start: 0.9351 (mm) cc_final: 0.9037 (mm) REVERT: I 76 ASP cc_start: 0.9561 (t70) cc_final: 0.9288 (t0) REVERT: I 107 ILE cc_start: 0.9434 (mt) cc_final: 0.9010 (tp) REVERT: K 56 ASN cc_start: 0.9142 (m110) cc_final: 0.8654 (m110) REVERT: K 127 PHE cc_start: 0.8489 (t80) cc_final: 0.8131 (t80) outliers start: 2 outliers final: 0 residues processed: 127 average time/residue: 0.3218 time to fit residues: 61.9923 Evaluate side-chains 106 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 2.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 189 optimal weight: 5.9990 chunk 172 optimal weight: 8.9990 chunk 184 optimal weight: 9.9990 chunk 110 optimal weight: 7.9990 chunk 80 optimal weight: 7.9990 chunk 144 optimal weight: 1.9990 chunk 56 optimal weight: 8.9990 chunk 166 optimal weight: 7.9990 chunk 174 optimal weight: 5.9990 chunk 183 optimal weight: 9.9990 chunk 120 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 GLN ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 ASN C 72 HIS ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 ASN E 220 GLN ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 334 ASN ** F 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 704 ASN F 722 ASN H 106 ASN ** H 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 HIS ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.7301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 17801 Z= 0.468 Angle : 0.912 11.685 24079 Z= 0.493 Chirality : 0.050 0.318 2651 Planarity : 0.006 0.082 2973 Dihedral : 13.594 178.456 2654 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 33.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.19 % Favored : 94.76 % Rotamer: Outliers : 0.05 % Allowed : 0.65 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.17), residues: 2022 helix: -0.44 (0.15), residues: 921 sheet: -0.60 (0.28), residues: 321 loop : -1.63 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP F 339 HIS 0.019 0.003 HIS H 17 PHE 0.031 0.004 PHE H 283 TYR 0.042 0.004 TYR I 86 ARG 0.010 0.001 ARG B 187 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 118 time to evaluate : 2.303 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: C 55 MET cc_start: 0.8455 (tpt) cc_final: 0.8061 (tpt) REVERT: E 62 PHE cc_start: 0.8859 (m-10) cc_final: 0.8650 (m-80) REVERT: F 588 LEU cc_start: 0.9157 (tp) cc_final: 0.8571 (mm) REVERT: F 589 PHE cc_start: 0.8304 (t80) cc_final: 0.7395 (t80) REVERT: H 258 MET cc_start: 0.6148 (mmp) cc_final: 0.5943 (mmp) REVERT: I 18 HIS cc_start: 0.8891 (t70) cc_final: 0.8664 (t70) REVERT: I 49 ARG cc_start: 0.8982 (mtm180) cc_final: 0.8400 (ptt180) REVERT: I 69 GLN cc_start: 0.8425 (tp40) cc_final: 0.8089 (tp40) REVERT: I 74 PHE cc_start: 0.8975 (t80) cc_final: 0.8592 (t80) REVERT: I 75 ILE cc_start: 0.9307 (mm) cc_final: 0.8850 (mm) REVERT: I 107 ILE cc_start: 0.9476 (mt) cc_final: 0.9183 (tp) REVERT: K 14 MET cc_start: 0.7660 (mmt) cc_final: 0.6664 (mmt) REVERT: K 56 ASN cc_start: 0.9145 (m110) cc_final: 0.8823 (m110) REVERT: K 76 ASP cc_start: 0.9525 (m-30) cc_final: 0.9280 (m-30) REVERT: K 80 TYR cc_start: 0.9134 (t80) cc_final: 0.8903 (t80) outliers start: 1 outliers final: 0 residues processed: 119 average time/residue: 0.3230 time to fit residues: 58.1088 Evaluate side-chains 95 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 2.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 194 optimal weight: 8.9990 chunk 118 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 135 optimal weight: 0.9980 chunk 204 optimal weight: 10.0000 chunk 187 optimal weight: 20.0000 chunk 162 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 125 optimal weight: 0.5980 chunk 99 optimal weight: 0.0170 chunk 129 optimal weight: 8.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 GLN ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 704 ASN H 106 ASN ** H 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 214 GLN ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 54 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.6835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17801 Z= 0.168 Angle : 0.583 8.726 24079 Z= 0.308 Chirality : 0.042 0.255 2651 Planarity : 0.003 0.058 2973 Dihedral : 13.199 174.023 2654 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.18), residues: 2022 helix: 0.69 (0.17), residues: 920 sheet: -0.34 (0.27), residues: 362 loop : -1.45 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 594 HIS 0.007 0.001 HIS A 72 PHE 0.050 0.002 PHE I 85 TYR 0.027 0.002 TYR K 126 ARG 0.008 0.001 ARG K 91 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 2.146 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: B 115 ASP cc_start: 0.7827 (m-30) cc_final: 0.7595 (m-30) REVERT: C 55 MET cc_start: 0.8296 (tpt) cc_final: 0.7825 (tpt) REVERT: E 62 PHE cc_start: 0.9270 (m-10) cc_final: 0.8965 (m-80) REVERT: F 588 LEU cc_start: 0.9210 (tp) cc_final: 0.8887 (mm) REVERT: F 589 PHE cc_start: 0.7602 (t80) cc_final: 0.6973 (t80) REVERT: H 187 LEU cc_start: 0.8815 (mt) cc_final: 0.8571 (pp) REVERT: I 49 ARG cc_start: 0.8912 (mtm180) cc_final: 0.8051 (ptt180) REVERT: I 54 GLN cc_start: 0.9126 (mp10) cc_final: 0.8856 (mp10) REVERT: I 69 GLN cc_start: 0.8365 (tp40) cc_final: 0.7980 (tp40) REVERT: I 74 PHE cc_start: 0.8881 (t80) cc_final: 0.8578 (t80) REVERT: I 75 ILE cc_start: 0.9404 (mm) cc_final: 0.9107 (mm) REVERT: I 107 ILE cc_start: 0.9420 (mt) cc_final: 0.9203 (tp) REVERT: K 14 MET cc_start: 0.7698 (mmt) cc_final: 0.6609 (mmt) REVERT: K 56 ASN cc_start: 0.9165 (m110) cc_final: 0.8823 (m110) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.3137 time to fit residues: 57.3477 Evaluate side-chains 99 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 2.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 149 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 45 optimal weight: 0.9980 chunk 162 optimal weight: 9.9990 chunk 68 optimal weight: 20.0000 chunk 167 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 143 optimal weight: 0.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.042206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.035365 restraints weight = 273635.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.036073 restraints weight = 169753.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.036570 restraints weight = 120042.603| |-----------------------------------------------------------------------------| r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.6996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17801 Z= 0.177 Angle : 0.570 8.892 24079 Z= 0.303 Chirality : 0.041 0.261 2651 Planarity : 0.003 0.055 2973 Dihedral : 13.078 173.297 2654 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.18), residues: 2022 helix: 0.84 (0.17), residues: 920 sheet: -0.35 (0.27), residues: 366 loop : -1.34 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 594 HIS 0.004 0.001 HIS H 17 PHE 0.040 0.002 PHE I 85 TYR 0.052 0.002 TYR E 95 ARG 0.007 0.001 ARG K 91 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2866.48 seconds wall clock time: 53 minutes 29.83 seconds (3209.83 seconds total)