Starting phenix.real_space_refine on Sun Mar 17 10:16:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v02_26927/03_2024/7v02_26927_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v02_26927/03_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_26927/03_2024/7v02_26927.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v02_26927/03_2024/7v02_26927.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v02_26927/03_2024/7v02_26927_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v02_26927/03_2024/7v02_26927_neut.pdb" } 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 Residue "A ARG 129": "NH1" <-> "NH2" Residue "A ARG 191": "NH1" <-> "NH2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B ARG 191": "NH1" <-> "NH2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C ARG 129": "NH1" <-> "NH2" Residue "C PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 159": "OE1" <-> "OE2" Residue "C ARG 191": "NH1" <-> "NH2" Residue "F GLU 250": "OE1" <-> "OE2" Residue "F GLU 355": "OE1" <-> "OE2" Residue "F GLU 446": "OE1" <-> "OE2" Residue "F GLU 610": "OE1" <-> "OE2" Residue "F GLU 673": "OE1" <-> "OE2" Residue "H TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 128": "OE1" <-> "OE2" Residue "K GLU 97": "OE1" <-> "OE2" Residue "K GLU 128": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 9.64, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 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: 7.18 Conformation dependent library (CDL) restraints added in 3.2 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: 5.25 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: 5.08 Time building geometry restraints manager: 7.76 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: 96.66 - 104.17: 234 104.17 - 111.67: 7893 111.67 - 119.17: 6644 119.17 - 126.67: 9093 126.67 - 134.17: 215 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 2.440 nonbonded pdb=" NH2 ARG A 129 " pdb=" OD1 ASN C 57 " model vdw 2.158 2.520 nonbonded pdb=" O PHE F 344 " pdb=" OG1 THR F 345 " model vdw 2.197 2.440 nonbonded pdb=" OH TYR F 499 " pdb=" O GLU F 574 " model vdw 2.265 2.440 ... (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 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: 0.490 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: 3.040 Check model and map are aligned: 0.240 Set scattering table: 0.160 Process input model: 50.200 Find NCS groups from input model: 0.600 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.740 ------------------------------------------------------------------------------- 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 : 1.909 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: 0.3763 time to fit residues: 157.9866 Evaluate side-chains 163 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 158 time to evaluate : 2.124 ------------------------------------------------------------------------------- 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: 0.9980 chunk 155 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 83 optimal weight: 0.0980 chunk 160 optimal weight: 6.9990 chunk 62 optimal weight: 0.0770 chunk 97 optimal weight: 0.9980 chunk 119 optimal weight: 4.9990 chunk 186 optimal weight: 7.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN E 316 ASN ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 HIS F 33 HIS ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 HIS ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 472 ASN F 474 ASN F 482 ASN ** F 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 708 ASN ** H 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN H 214 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 0.2446 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= 0.181 Angle : 0.646 10.025 24079 Z= 0.345 Chirality : 0.044 0.209 2651 Planarity : 0.003 0.033 2973 Dihedral : 13.685 174.243 2654 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.11 % Allowed : 2.43 % Favored : 97.46 % 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: -0.52 (0.18), residues: 2022 helix: 0.67 (0.17), residues: 910 sheet: -0.02 (0.26), residues: 377 loop : -1.79 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP F 339 HIS 0.018 0.001 HIS B 110 PHE 0.033 0.002 PHE I 85 TYR 0.020 0.002 TYR E 95 ARG 0.005 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 180 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 178 time to evaluate : 2.077 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: B 17 LEU cc_start: 0.8894 (tt) cc_final: 0.8244 (mp) REVERT: B 46 ILE cc_start: 0.8608 (tt) cc_final: 0.8373 (pt) REVERT: B 115 ASP cc_start: 0.8338 (t0) cc_final: 0.8119 (m-30) REVERT: C 55 MET cc_start: 0.7928 (tpt) cc_final: 0.7404 (tpt) REVERT: E 24 MET cc_start: 0.3869 (ttt) cc_final: 0.3340 (tmm) REVERT: E 49 PHE cc_start: 0.9013 (t80) cc_final: 0.8681 (t80) REVERT: E 87 SER cc_start: 0.9472 (m) cc_final: 0.9217 (p) REVERT: E 116 LEU cc_start: 0.7683 (tp) cc_final: 0.7200 (tp) REVERT: F 318 LEU cc_start: 0.9283 (tp) cc_final: 0.8849 (tp) REVERT: F 347 ASP cc_start: 0.6791 (t0) cc_final: 0.6366 (t70) REVERT: F 588 LEU cc_start: 0.8873 (tp) cc_final: 0.8557 (mm) REVERT: H 10 LEU cc_start: 0.8383 (mp) cc_final: 0.7958 (mt) REVERT: I 55 VAL cc_start: 0.9518 (p) cc_final: 0.9257 (p) REVERT: I 74 PHE cc_start: 0.9024 (t80) cc_final: 0.8783 (t80) REVERT: I 75 ILE cc_start: 0.9055 (mm) cc_final: 0.8794 (mm) REVERT: I 81 LEU cc_start: 0.9515 (tp) cc_final: 0.8947 (tt) REVERT: I 86 TYR cc_start: 0.7663 (m-80) cc_final: 0.7092 (m-80) REVERT: I 102 THR cc_start: 0.8934 (p) cc_final: 0.8702 (p) REVERT: I 107 ILE cc_start: 0.9420 (mt) cc_final: 0.8529 (tp) REVERT: K 127 PHE cc_start: 0.8730 (t80) cc_final: 0.8051 (t80) outliers start: 2 outliers final: 0 residues processed: 180 average time/residue: 0.3227 time to fit residues: 87.2745 Evaluate side-chains 132 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 2.169 ------------------------------------------------------------------------------- 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: 10.0000 chunk 57 optimal weight: 1.9990 chunk 154 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 chunk 186 optimal weight: 10.0000 chunk 201 optimal weight: 7.9990 chunk 166 optimal weight: 5.9990 chunk 184 optimal weight: 0.0270 chunk 63 optimal weight: 5.9990 chunk 149 optimal weight: 7.9990 overall best weight: 4.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN A 174 HIS B 114 ASN ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 ASN ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 170 ASN ** E 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 320 HIS ** 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 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 ASN F 169 HIS F 306 ASN F 334 ASN F 474 ASN ** F 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 549 ASN ** F 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 129 GLN H 177 ASN ** H 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 17801 Z= 0.392 Angle : 0.815 10.021 24079 Z= 0.435 Chirality : 0.045 0.238 2651 Planarity : 0.005 0.048 2973 Dihedral : 13.814 175.728 2654 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 25.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.11 % Allowed : 4.27 % Favored : 95.62 % 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: -0.85 (0.18), residues: 2022 helix: 0.23 (0.16), residues: 915 sheet: -0.08 (0.27), residues: 385 loop : -1.78 (0.21), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP F 339 HIS 0.029 0.003 HIS E 17 PHE 0.040 0.003 PHE I 85 TYR 0.029 0.003 TYR C 206 ARG 0.006 0.001 ARG I 57 *********************** 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 153 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 151 time to evaluate : 2.074 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: C 55 MET cc_start: 0.8294 (tpt) cc_final: 0.7766 (tpt) REVERT: E 24 MET cc_start: 0.5062 (ttt) cc_final: 0.4794 (ppp) REVERT: E 40 MET cc_start: 0.6617 (mmp) cc_final: 0.5284 (mmp) REVERT: E 49 PHE cc_start: 0.9094 (t80) cc_final: 0.8836 (t80) REVERT: E 51 LYS cc_start: 0.9525 (mmpt) cc_final: 0.9150 (mmmt) REVERT: E 87 SER cc_start: 0.9498 (m) cc_final: 0.8820 (p) REVERT: E 119 MET cc_start: 0.6573 (mmt) cc_final: 0.6203 (mmt) REVERT: E 327 MET cc_start: 0.7964 (ptp) cc_final: 0.7588 (ptm) REVERT: F 318 LEU cc_start: 0.8989 (tp) cc_final: 0.8745 (tp) REVERT: F 468 MET cc_start: 0.9028 (tmm) cc_final: 0.8680 (tmm) REVERT: F 588 LEU cc_start: 0.8988 (tp) cc_final: 0.8406 (mm) REVERT: F 589 PHE cc_start: 0.7737 (t80) cc_final: 0.7120 (t80) REVERT: F 624 MET cc_start: 0.7964 (tpt) cc_final: 0.7732 (tpt) REVERT: I 14 MET cc_start: 0.8828 (tmm) cc_final: 0.8588 (tmm) REVERT: I 69 GLN cc_start: 0.8026 (tp40) cc_final: 0.7738 (tp40) REVERT: I 74 PHE cc_start: 0.9109 (t80) cc_final: 0.8758 (t80) REVERT: I 75 ILE cc_start: 0.9243 (mm) cc_final: 0.8973 (mm) REVERT: I 86 TYR cc_start: 0.8115 (m-80) cc_final: 0.7546 (m-80) REVERT: I 107 ILE cc_start: 0.9386 (mt) cc_final: 0.8746 (tp) REVERT: K 54 GLN cc_start: 0.9704 (tp-100) cc_final: 0.9227 (tp-100) REVERT: K 123 TYR cc_start: 0.8473 (t80) cc_final: 0.8234 (t80) REVERT: K 127 PHE cc_start: 0.8731 (t80) cc_final: 0.8423 (t80) outliers start: 2 outliers final: 1 residues processed: 153 average time/residue: 0.3130 time to fit residues: 72.0467 Evaluate side-chains 117 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 116 time to evaluate : 2.152 ------------------------------------------------------------------------------- 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: 7.9990 chunk 140 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 89 optimal weight: 0.5980 chunk 125 optimal weight: 10.0000 chunk 187 optimal weight: 20.0000 chunk 198 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 177 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 ASN E 255 GLN E 324 GLN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 314 HIS ** F 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 207 GLN H 213 ASN K 41 ASN K 138 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.4796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17801 Z= 0.199 Angle : 0.577 8.113 24079 Z= 0.310 Chirality : 0.041 0.263 2651 Planarity : 0.003 0.039 2973 Dihedral : 13.557 176.210 2654 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.05 % Allowed : 1.73 % Favored : 98.22 % 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: -0.36 (0.18), residues: 2022 helix: 0.69 (0.17), residues: 909 sheet: 0.17 (0.28), residues: 351 loop : -1.54 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 339 HIS 0.009 0.001 HIS B 110 PHE 0.032 0.002 PHE I 85 TYR 0.030 0.002 TYR K 126 ARG 0.006 0.001 ARG E 64 *********************** 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 145 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 144 time to evaluate : 2.447 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: B 115 ASP cc_start: 0.9253 (m-30) cc_final: 0.8985 (m-30) REVERT: C 55 MET cc_start: 0.8199 (tpt) cc_final: 0.7533 (tpt) REVERT: E 49 PHE cc_start: 0.9131 (t80) cc_final: 0.8756 (t80) REVERT: E 51 LYS cc_start: 0.9428 (mmpt) cc_final: 0.8970 (mmmt) REVERT: E 119 MET cc_start: 0.6548 (mmt) cc_final: 0.5657 (mmm) REVERT: F 363 MET cc_start: 0.8464 (mmp) cc_final: 0.8092 (mmm) REVERT: F 588 LEU cc_start: 0.9132 (tp) cc_final: 0.8731 (mm) REVERT: F 589 PHE cc_start: 0.7691 (t80) cc_final: 0.7412 (t80) REVERT: I 14 MET cc_start: 0.8588 (tmm) cc_final: 0.8236 (tmm) REVERT: I 69 GLN cc_start: 0.8140 (tp40) cc_final: 0.7770 (tp40) REVERT: I 74 PHE cc_start: 0.8862 (t80) cc_final: 0.8602 (t80) REVERT: I 75 ILE cc_start: 0.9226 (mm) cc_final: 0.8930 (mm) REVERT: I 98 PHE cc_start: 0.9220 (t80) cc_final: 0.8821 (t80) REVERT: I 107 ILE cc_start: 0.9462 (mt) cc_final: 0.9061 (tp) REVERT: K 51 LEU cc_start: 0.9233 (mt) cc_final: 0.9014 (mt) REVERT: K 61 ILE cc_start: 0.9628 (mm) cc_final: 0.9414 (mm) REVERT: K 123 TYR cc_start: 0.8530 (t80) cc_final: 0.8296 (t80) REVERT: K 127 PHE cc_start: 0.8593 (t80) cc_final: 0.8169 (t80) outliers start: 1 outliers final: 0 residues processed: 145 average time/residue: 0.3240 time to fit residues: 71.0003 Evaluate side-chains 113 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 2.177 ------------------------------------------------------------------------------- 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: 0.8980 chunk 2 optimal weight: 9.9990 chunk 147 optimal weight: 9.9990 chunk 81 optimal weight: 5.9990 chunk 169 optimal weight: 0.8980 chunk 136 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 177 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 overall best weight: 3.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 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 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 192 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** H 251 GLN I 18 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.6083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 17801 Z= 0.320 Angle : 0.690 8.980 24079 Z= 0.376 Chirality : 0.043 0.216 2651 Planarity : 0.004 0.061 2973 Dihedral : 13.699 177.193 2654 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 27.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 2.97 % 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: -0.73 (0.18), residues: 2022 helix: 0.36 (0.16), residues: 912 sheet: -0.25 (0.28), residues: 362 loop : -1.57 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 339 HIS 0.007 0.002 HIS H 17 PHE 0.029 0.002 PHE I 85 TYR 0.021 0.002 TYR E 6 ARG 0.008 0.001 ARG I 110 *********************** 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 134 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 2.072 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: 0.8571 (tpt) cc_final: 0.7987 (tpt) REVERT: E 51 LYS cc_start: 0.9391 (mmpt) cc_final: 0.9076 (mmmt) REVERT: E 119 MET cc_start: 0.7279 (mmt) cc_final: 0.5649 (mmt) REVERT: F 318 LEU cc_start: 0.8551 (tp) cc_final: 0.8153 (tp) REVERT: F 588 LEU cc_start: 0.9097 (tp) cc_final: 0.8448 (mm) REVERT: F 589 PHE cc_start: 0.8198 (t80) cc_final: 0.7576 (t80) REVERT: I 14 MET cc_start: 0.8727 (tmm) cc_final: 0.8268 (tmm) REVERT: I 18 HIS cc_start: 0.8517 (t70) cc_final: 0.8312 (t70) REVERT: I 69 GLN cc_start: 0.7832 (tp40) cc_final: 0.7371 (tp40) REVERT: I 74 PHE cc_start: 0.8886 (t80) cc_final: 0.8547 (t80) REVERT: I 75 ILE cc_start: 0.9307 (mm) cc_final: 0.9011 (mm) REVERT: I 76 ASP cc_start: 0.9644 (t70) cc_final: 0.9435 (t0) REVERT: I 98 PHE cc_start: 0.9317 (t80) cc_final: 0.8993 (t80) REVERT: I 107 ILE cc_start: 0.9040 (mt) cc_final: 0.8769 (tp) REVERT: K 52 MET cc_start: 0.7631 (tpt) cc_final: 0.7207 (tpt) REVERT: K 54 GLN cc_start: 0.9616 (tp-100) cc_final: 0.9361 (tp-100) REVERT: K 127 PHE cc_start: 0.8735 (t80) cc_final: 0.8315 (t80) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.3180 time to fit residues: 64.0215 Evaluate side-chains 106 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 2.000 ------------------------------------------------------------------------------- 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: 0.0050 chunk 178 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 chunk 198 optimal weight: 10.0000 chunk 164 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 65 optimal weight: 0.4980 chunk 104 optimal weight: 4.9990 overall best weight: 1.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 HIS ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 324 GLN ** 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 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 251 GLN K 54 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.6128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17801 Z= 0.168 Angle : 0.551 8.219 24079 Z= 0.296 Chirality : 0.040 0.173 2651 Planarity : 0.003 0.039 2973 Dihedral : 13.561 176.061 2654 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.05 % Allowed : 1.68 % 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: -0.33 (0.18), residues: 2022 helix: 0.81 (0.17), residues: 914 sheet: -0.15 (0.28), residues: 366 loop : -1.50 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 339 HIS 0.011 0.001 HIS A 174 PHE 0.034 0.002 PHE I 85 TYR 0.025 0.002 TYR H 255 ARG 0.004 0.001 ARG A 37 *********************** 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 130 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 129 time to evaluate : 2.125 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: 0.8478 (tpt) cc_final: 0.7888 (tpt) REVERT: E 51 LYS cc_start: 0.9463 (mmpt) cc_final: 0.9206 (mmmt) REVERT: E 119 MET cc_start: 0.7619 (mmt) cc_final: 0.7221 (mmt) REVERT: E 327 MET cc_start: 0.7952 (ptp) cc_final: 0.7547 (ptp) REVERT: F 160 MET cc_start: 0.9625 (mpp) cc_final: 0.9425 (mpp) REVERT: F 189 TRP cc_start: 0.6756 (m-10) cc_final: 0.6355 (m-10) REVERT: F 318 LEU cc_start: 0.8665 (tp) cc_final: 0.8308 (tp) REVERT: F 496 MET cc_start: 0.0097 (pmm) cc_final: -0.0223 (pmm) REVERT: F 588 LEU cc_start: 0.8993 (tp) cc_final: 0.8699 (mm) REVERT: F 589 PHE cc_start: 0.7665 (t80) cc_final: 0.7333 (t80) REVERT: I 14 MET cc_start: 0.8499 (tmm) cc_final: 0.8097 (tmm) REVERT: I 69 GLN cc_start: 0.7985 (tp40) cc_final: 0.7545 (tp40) REVERT: I 74 PHE cc_start: 0.8882 (t80) cc_final: 0.8513 (t80) REVERT: I 75 ILE cc_start: 0.9294 (mm) cc_final: 0.8988 (mm) REVERT: I 76 ASP cc_start: 0.9590 (t70) cc_final: 0.9353 (t0) REVERT: I 86 TYR cc_start: 0.7434 (m-80) cc_final: 0.5695 (m-80) REVERT: I 98 PHE cc_start: 0.9278 (t80) cc_final: 0.8943 (t80) REVERT: I 107 ILE cc_start: 0.9537 (mt) cc_final: 0.9123 (tp) REVERT: K 127 PHE cc_start: 0.8638 (t80) cc_final: 0.8269 (t80) outliers start: 1 outliers final: 0 residues processed: 130 average time/residue: 0.3214 time to fit residues: 63.7420 Evaluate side-chains 104 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.876 ------------------------------------------------------------------------------- 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: 2.9990 chunk 22 optimal weight: 5.9990 chunk 113 optimal weight: 0.0060 chunk 144 optimal weight: 10.0000 chunk 112 optimal weight: 0.3980 chunk 166 optimal weight: 0.0370 chunk 110 optimal weight: 4.9990 chunk 197 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 120 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 overall best weight: 1.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 ASN ** F 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 681 GLN ** 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** H 251 GLN ** I 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.6325 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 : 0.543 7.053 24079 Z= 0.293 Chirality : 0.040 0.167 2651 Planarity : 0.003 0.040 2973 Dihedral : 13.496 176.334 2654 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 19.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.05 % Allowed : 1.03 % Favored : 98.92 % 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: -0.13 (0.18), residues: 2022 helix: 1.02 (0.17), residues: 914 sheet: -0.15 (0.28), residues: 366 loop : -1.41 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 339 HIS 0.005 0.001 HIS B 110 PHE 0.039 0.002 PHE I 85 TYR 0.025 0.001 TYR H 255 ARG 0.004 0.000 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: 1 poor density : 125 time to evaluate : 2.097 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: 0.8530 (tpt) cc_final: 0.7980 (tpt) REVERT: E 51 LYS cc_start: 0.9425 (mmpt) cc_final: 0.9221 (mmmt) REVERT: E 119 MET cc_start: 0.7742 (mmt) cc_final: 0.7450 (mmt) REVERT: F 160 MET cc_start: 0.9567 (mpp) cc_final: 0.9325 (mpp) REVERT: F 189 TRP cc_start: 0.6593 (m-10) cc_final: 0.6212 (m-10) REVERT: F 318 LEU cc_start: 0.8671 (tp) cc_final: 0.8375 (tp) REVERT: F 588 LEU cc_start: 0.9023 (tp) cc_final: 0.8697 (mm) REVERT: F 589 PHE cc_start: 0.7800 (t80) cc_final: 0.7363 (t80) REVERT: I 14 MET cc_start: 0.8871 (tmm) cc_final: 0.8219 (tmm) REVERT: I 69 GLN cc_start: 0.8164 (tp40) cc_final: 0.7747 (tp40) REVERT: I 74 PHE cc_start: 0.8927 (t80) cc_final: 0.8542 (t80) REVERT: I 75 ILE cc_start: 0.9312 (mm) cc_final: 0.9017 (mm) REVERT: I 76 ASP cc_start: 0.9579 (t70) cc_final: 0.9334 (t0) REVERT: I 86 TYR cc_start: 0.6174 (m-80) cc_final: 0.4519 (m-80) REVERT: I 98 PHE cc_start: 0.9297 (t80) cc_final: 0.8951 (t80) REVERT: I 107 ILE cc_start: 0.9468 (mt) cc_final: 0.8904 (tp) REVERT: K 52 MET cc_start: 0.7046 (tpt) cc_final: 0.6842 (tpt) REVERT: K 123 TYR cc_start: 0.8386 (t80) cc_final: 0.8070 (t80) REVERT: K 127 PHE cc_start: 0.8657 (t80) cc_final: 0.8242 (t80) outliers start: 1 outliers final: 0 residues processed: 126 average time/residue: 0.3299 time to fit residues: 62.7434 Evaluate side-chains 103 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.967 ------------------------------------------------------------------------------- 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: 10.0000 chunk 78 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 chunk 59 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 125 optimal weight: 10.0000 chunk 134 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 155 optimal weight: 9.9990 chunk 179 optimal weight: 0.7980 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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** B 161 GLN C 69 GLN C 72 HIS ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 475 GLN ** F 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 ASN H 137 GLN ** 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 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.7026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17801 Z= 0.263 Angle : 0.627 11.110 24079 Z= 0.338 Chirality : 0.042 0.348 2651 Planarity : 0.004 0.049 2973 Dihedral : 13.650 179.475 2654 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 27.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.05 % Allowed : 0.81 % Favored : 99.14 % 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: -0.42 (0.18), residues: 2022 helix: 0.72 (0.16), residues: 925 sheet: -0.31 (0.28), residues: 346 loop : -1.48 (0.21), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 339 HIS 0.012 0.002 HIS E 117 PHE 0.040 0.002 PHE K 85 TYR 0.023 0.002 TYR H 255 ARG 0.006 0.001 ARG K 91 *********************** 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 125 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 2.037 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: C 55 MET cc_start: 0.8692 (tpt) cc_final: 0.8253 (tpt) REVERT: E 51 LYS cc_start: 0.9309 (mmpt) cc_final: 0.9100 (mmmt) REVERT: E 62 PHE cc_start: 0.9008 (m-80) cc_final: 0.8283 (m-80) REVERT: E 327 MET cc_start: 0.7881 (ptp) cc_final: 0.7563 (ptp) REVERT: F 160 MET cc_start: 0.9593 (mpp) cc_final: 0.9267 (mpp) REVERT: F 588 LEU cc_start: 0.8950 (tp) cc_final: 0.8430 (mm) REVERT: F 589 PHE cc_start: 0.8029 (t80) cc_final: 0.7246 (t80) REVERT: I 69 GLN cc_start: 0.8275 (tp40) cc_final: 0.7787 (tp40) REVERT: I 74 PHE cc_start: 0.8969 (t80) cc_final: 0.8591 (t80) REVERT: I 75 ILE cc_start: 0.9342 (mm) cc_final: 0.9059 (mm) REVERT: I 86 TYR cc_start: 0.7308 (m-80) cc_final: 0.6978 (m-80) REVERT: I 107 ILE cc_start: 0.9523 (mt) cc_final: 0.8794 (tp) REVERT: K 123 TYR cc_start: 0.8280 (t80) cc_final: 0.8080 (t80) REVERT: K 127 PHE cc_start: 0.8654 (t80) cc_final: 0.8256 (t80) outliers start: 1 outliers final: 0 residues processed: 125 average time/residue: 0.3198 time to fit residues: 60.7599 Evaluate side-chains 96 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 2.278 ------------------------------------------------------------------------------- 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: 0.8980 chunk 172 optimal weight: 8.9990 chunk 184 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 144 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 166 optimal weight: 0.0570 chunk 174 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 120 optimal weight: 5.9990 overall best weight: 0.9302 ------------------------------------------------------------------------------- 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 324 GLN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.6908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17801 Z= 0.150 Angle : 0.546 9.382 24079 Z= 0.289 Chirality : 0.041 0.295 2651 Planarity : 0.003 0.042 2973 Dihedral : 13.470 175.849 2654 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.05 % Allowed : 0.76 % Favored : 99.19 % 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: -0.06 (0.19), residues: 2022 helix: 1.10 (0.17), residues: 924 sheet: -0.30 (0.28), residues: 361 loop : -1.31 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP H 52 HIS 0.010 0.001 HIS H 174 PHE 0.037 0.002 PHE I 85 TYR 0.017 0.001 TYR H 255 ARG 0.004 0.000 ARG K 91 *********************** 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 125 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 2.132 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: 0.8517 (tpt) cc_final: 0.8014 (tpt) REVERT: E 62 PHE cc_start: 0.8673 (m-80) cc_final: 0.8269 (m-80) REVERT: E 327 MET cc_start: 0.7821 (ptp) cc_final: 0.7469 (ptp) REVERT: F 1 MET cc_start: 0.6347 (tmm) cc_final: 0.5857 (tmm) REVERT: F 318 LEU cc_start: 0.8879 (tp) cc_final: 0.8603 (tp) REVERT: F 588 LEU cc_start: 0.9006 (tp) cc_final: 0.8689 (mm) REVERT: F 589 PHE cc_start: 0.7689 (t80) cc_final: 0.7087 (t80) REVERT: I 14 MET cc_start: 0.8770 (tmm) cc_final: 0.8116 (tmm) REVERT: I 18 HIS cc_start: 0.8512 (t-170) cc_final: 0.8098 (t-170) REVERT: I 69 GLN cc_start: 0.8324 (tp40) cc_final: 0.7931 (tp40) REVERT: I 74 PHE cc_start: 0.8912 (t80) cc_final: 0.8551 (t80) REVERT: I 75 ILE cc_start: 0.9321 (mm) cc_final: 0.9007 (mm) REVERT: I 107 ILE cc_start: 0.9516 (mt) cc_final: 0.8906 (tp) REVERT: K 56 ASN cc_start: 0.9152 (m110) cc_final: 0.8743 (m-40) REVERT: K 127 PHE cc_start: 0.8575 (t80) cc_final: 0.8215 (t80) outliers start: 1 outliers final: 0 residues processed: 125 average time/residue: 0.3174 time to fit residues: 60.7352 Evaluate side-chains 98 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 2.135 ------------------------------------------------------------------------------- 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: 0.2980 chunk 118 optimal weight: 0.0050 chunk 92 optimal weight: 4.9990 chunk 135 optimal weight: 7.9990 chunk 204 optimal weight: 0.9980 chunk 187 optimal weight: 30.0000 chunk 162 optimal weight: 7.9990 chunk 16 optimal weight: 0.7980 chunk 125 optimal weight: 0.3980 chunk 99 optimal weight: 6.9990 chunk 129 optimal weight: 9.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- 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 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 192 ASN ** H 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.6904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17801 Z= 0.136 Angle : 0.526 9.491 24079 Z= 0.278 Chirality : 0.041 0.294 2651 Planarity : 0.003 0.042 2973 Dihedral : 13.280 175.788 2654 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % 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: 0.07 (0.19), residues: 2022 helix: 1.20 (0.17), residues: 928 sheet: -0.17 (0.28), residues: 362 loop : -1.31 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 189 HIS 0.005 0.001 HIS B 110 PHE 0.018 0.001 PHE K 120 TYR 0.052 0.001 TYR E 95 ARG 0.006 0.000 ARG E 121 ********************** 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 124 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.951 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: C 55 MET cc_start: 0.8504 (tpt) cc_final: 0.8005 (tpt) REVERT: E 40 MET cc_start: 0.8825 (tpt) cc_final: 0.8438 (tpp) REVERT: E 62 PHE cc_start: 0.8632 (m-80) cc_final: 0.8306 (m-80) REVERT: F 1 MET cc_start: 0.6827 (tmm) cc_final: 0.6293 (tmm) REVERT: F 47 PHE cc_start: 0.5074 (m-80) cc_final: 0.4063 (m-80) REVERT: F 160 MET cc_start: 0.9331 (mpp) cc_final: 0.8974 (mpp) REVERT: F 318 LEU cc_start: 0.8896 (tp) cc_final: 0.8610 (tp) REVERT: F 496 MET cc_start: 0.0186 (pmm) cc_final: -0.0105 (pmm) REVERT: F 588 LEU cc_start: 0.8781 (tp) cc_final: 0.8453 (mm) REVERT: F 589 PHE cc_start: 0.7512 (t80) cc_final: 0.7066 (t80) REVERT: I 14 MET cc_start: 0.8673 (tmm) cc_final: 0.8049 (tmm) REVERT: I 18 HIS cc_start: 0.8487 (t-170) cc_final: 0.8044 (t-170) REVERT: I 49 ARG cc_start: 0.8754 (mtm180) cc_final: 0.8398 (ptt180) REVERT: I 54 GLN cc_start: 0.9309 (mp10) cc_final: 0.9085 (mp10) REVERT: I 69 GLN cc_start: 0.8316 (tp40) cc_final: 0.7914 (tp40) REVERT: I 74 PHE cc_start: 0.8918 (t80) cc_final: 0.8554 (t80) REVERT: I 75 ILE cc_start: 0.9326 (mm) cc_final: 0.9021 (mm) REVERT: I 76 ASP cc_start: 0.9565 (t70) cc_final: 0.9258 (t0) REVERT: I 86 TYR cc_start: 0.7417 (m-80) cc_final: 0.6268 (m-80) REVERT: I 107 ILE cc_start: 0.9513 (mt) cc_final: 0.8827 (tp) REVERT: K 56 ASN cc_start: 0.9067 (m110) cc_final: 0.8784 (m110) REVERT: K 127 PHE cc_start: 0.8515 (t80) cc_final: 0.8217 (t80) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.3056 time to fit residues: 58.8963 Evaluate side-chains 100 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 2.110 ------------------------------------------------------------------------------- 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: 6.9990 chunk 49 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 45 optimal weight: 0.3980 chunk 162 optimal weight: 0.0270 chunk 68 optimal weight: 2.9990 chunk 167 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 143 optimal weight: 0.8980 overall best weight: 1.4642 ------------------------------------------------------------------------------- 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 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 54 GLN ** 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 = 0.3061 r_free = 0.3061 target = 0.041739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.035004 restraints weight = 276957.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.035747 restraints weight = 169831.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.036245 restraints weight = 119007.827| |-----------------------------------------------------------------------------| r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.7093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17801 Z= 0.162 Angle : 0.520 8.720 24079 Z= 0.279 Chirality : 0.040 0.299 2651 Planarity : 0.003 0.049 2973 Dihedral : 13.207 176.424 2654 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % 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: 0.14 (0.19), residues: 2022 helix: 1.30 (0.17), residues: 923 sheet: -0.21 (0.28), residues: 362 loop : -1.26 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 52 HIS 0.011 0.001 HIS K 18 PHE 0.028 0.001 PHE K 85 TYR 0.037 0.001 TYR E 95 ARG 0.007 0.000 ARG I 91 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2862.66 seconds wall clock time: 54 minutes 11.90 seconds (3251.90 seconds total)