Starting phenix.real_space_refine on Sun Feb 18 02:00:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v00_26924/02_2024/7v00_26924_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v00_26924/02_2024/7v00_26924.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v00_26924/02_2024/7v00_26924.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v00_26924/02_2024/7v00_26924.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v00_26924/02_2024/7v00_26924_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v00_26924/02_2024/7v00_26924_neut_updated.pdb" } resolution = 3.87 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= 0.030 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 36 5.49 5 S 56 5.16 5 C 12877 2.51 5 N 3440 2.21 5 O 4011 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 GLU 87": "OE1" <-> "OE2" 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 "D GLU 124": "OE1" <-> "OE2" Residue "D ARG 129": "NH1" <-> "NH2" Residue "D ARG 191": "NH1" <-> "NH2" Residue "E TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 250": "OE1" <-> "OE2" Residue "F GLU 355": "OE1" <-> "OE2" Residue "F GLU 446": "OE1" <-> "OE2" Residue "F GLU 521": "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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20420 Number of models: 1 Model: "" Number of chains: 12 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: "D" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1578 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 4, 'TRANS': 194} Chain breaks: 1 Chain: "E" Number of atoms: 2473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2473 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 8, 'TRANS': 293} Chain breaks: 3 Chain: "F" Number of atoms: 5652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 695, 5652 Classifications: {'peptide': 695} Link IDs: {'PTRANS': 7, 'TRANS': 687} Chain breaks: 3 Chain: "G" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 637 Classifications: {'RNA': 30} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 6, 'rna3p_pur': 11, 'rna3p_pyr': 8} Link IDs: {'rna2p': 10, 'rna3p': 19} 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: "J" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 871 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain breaks: 2 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 Chain: "F" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 11.46, per 1000 atoms: 0.56 Number of scatterers: 20420 At special positions: 0 Unit cell: (93.003, 120.797, 209.524, 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 56 16.00 P 36 15.00 O 4011 8.00 N 3440 7.00 C 12877 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: 9.31 Conformation dependent library (CDL) restraints added in 3.6 seconds 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4550 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 94 helices and 27 sheets defined 41.7% alpha, 13.5% beta 0 base pairs and 6 stacking pairs defined. Time for finding SS restraints: 9.30 Creating SS restraints... Processing helix chain 'A' and resid 48 through 62 Processing helix chain 'A' and resid 67 through 72 removed outlier: 3.771A pdb=" N HIS A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 83 Processing helix chain 'A' and resid 105 through 114 Processing helix chain 'A' and resid 159 through 178 removed outlier: 4.728A pdb=" N GLU A 163 " --> pdb=" O SER A 160 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP A 164 " --> pdb=" O GLN A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 187 No H-bonds generated for 'chain 'A' and resid 185 through 187' Processing helix chain 'B' and resid 48 through 61 Processing helix chain 'B' and resid 77 through 82 Processing helix chain 'B' and resid 105 through 113 Processing helix chain 'B' and resid 159 through 178 removed outlier: 3.587A pdb=" N VAL B 162 " --> pdb=" O GLU B 159 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N GLU B 163 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 187 No H-bonds generated for 'chain 'B' and resid 185 through 187' Processing helix chain 'C' and resid 48 through 62 Processing helix chain 'C' and resid 67 through 71 Processing helix chain 'C' and resid 77 through 83 Processing helix chain 'C' and resid 105 through 114 Processing helix chain 'C' and resid 159 through 177 removed outlier: 3.740A pdb=" N VAL C 162 " --> pdb=" O GLU C 159 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N GLU C 163 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP C 164 " --> pdb=" O GLN C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 187 No H-bonds generated for 'chain 'C' and resid 185 through 187' Processing helix chain 'D' and resid 48 through 62 Processing helix chain 'D' and resid 67 through 72 Processing helix chain 'D' and resid 77 through 83 Processing helix chain 'D' and resid 105 through 113 Processing helix chain 'D' and resid 162 through 178 Processing helix chain 'E' and resid 43 through 52 Processing helix chain 'E' and resid 56 through 64 Processing helix chain 'E' and resid 70 through 72 No H-bonds generated for 'chain 'E' and resid 70 through 72' Processing helix chain 'E' and resid 76 through 81 Processing helix chain 'E' and resid 86 through 91 Processing helix chain 'E' and resid 131 through 146 Processing helix chain 'E' and resid 151 through 155 Processing helix chain 'E' and resid 168 through 170 No H-bonds generated for 'chain 'E' and resid 168 through 170' Processing helix chain 'E' and resid 212 through 229 Processing helix chain 'E' and resid 238 through 246 Processing helix chain 'E' and resid 249 through 254 removed outlier: 4.909A pdb=" N ASN E 254 " --> pdb=" O PRO E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 295 removed outlier: 3.809A pdb=" N ARG E 294 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLY E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 302 Processing helix chain 'F' and resid 3 through 13 removed outlier: 4.274A pdb=" N LEU F 13 " --> pdb=" O TYR F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 21 Processing helix chain 'F' and resid 33 through 43 removed outlier: 4.420A pdb=" N GLN F 43 " --> pdb=" O GLN F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 58 Processing helix chain 'F' and resid 61 through 65 Processing helix chain 'F' and resid 74 through 85 Processing helix chain 'F' and resid 117 through 121 Processing helix chain 'F' and resid 153 through 169 removed outlier: 3.547A pdb=" N THR F 157 " --> pdb=" O SER F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 189 Processing helix chain 'F' and resid 206 through 226 Processing helix chain 'F' and resid 232 through 235 No H-bonds generated for 'chain 'F' and resid 232 through 235' Processing helix chain 'F' and resid 240 through 248 Processing helix chain 'F' and resid 262 through 266 Processing helix chain 'F' and resid 274 through 299 removed outlier: 3.596A 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 304 through 306 No H-bonds generated for 'chain 'F' and resid 304 through 306' Processing helix chain 'F' and resid 323 through 343 Processing helix chain 'F' and resid 359 through 363 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 359 through 363' Processing helix chain 'F' and resid 368 through 383 Processing helix chain 'F' and resid 390 through 397 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 436 Processing helix chain 'F' and resid 463 through 471 Processing helix chain 'F' and resid 501 through 504 Processing helix chain 'F' and resid 513 through 517 Processing helix chain 'F' and resid 537 through 541 Processing helix chain 'F' and resid 551 through 572 removed outlier: 4.896A 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 594 through 611 Processing helix chain 'F' and resid 631 through 637 removed outlier: 3.990A pdb=" N PHE F 636 " --> pdb=" O SER F 632 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU F 637 " --> pdb=" O LYS F 633 " (cutoff:3.500A) Processing helix chain 'F' and resid 665 through 669 Processing helix chain 'F' and resid 675 through 685 Processing helix chain 'F' and resid 691 through 702 Processing helix chain 'F' and resid 706 through 718 Processing helix chain 'F' and resid 723 through 733 Processing helix chain 'F' and resid 736 through 749 Processing helix chain 'H' and resid 32 through 46 Processing helix chain 'H' and resid 101 through 105 Processing helix chain 'H' and resid 111 through 119 Processing helix chain 'H' and resid 169 through 184 removed outlier: 4.584A pdb=" N TYR H 184 " --> pdb=" O THR H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 193 No H-bonds generated for 'chain 'H' and resid 191 through 193' Processing helix chain 'H' and resid 206 through 212 Processing helix chain 'H' and resid 232 through 235 No H-bonds generated for 'chain 'H' and resid 232 through 235' Processing helix chain 'I' and resid 16 through 23 Processing helix chain 'I' and resid 45 through 64 removed outlier: 3.836A pdb=" N ARG I 49 " --> pdb=" O SER I 46 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ASN I 50 " --> pdb=" O LYS I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 91 Processing helix chain 'I' and resid 93 through 101 Processing helix chain 'I' and resid 104 through 114 Processing helix chain 'I' and resid 117 through 136 Processing helix chain 'J' and resid 18 through 23 Processing helix chain 'J' and resid 45 through 60 removed outlier: 3.603A pdb=" N ARG J 49 " --> pdb=" O SER J 46 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ASN J 50 " --> pdb=" O LYS J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 91 Processing helix chain 'J' and resid 93 through 101 Processing helix chain 'J' and resid 104 through 114 Processing helix chain 'J' and resid 117 through 136 Processing helix chain 'K' and resid 16 through 24 removed outlier: 5.083A pdb=" N VAL K 21 " --> pdb=" O ALA K 17 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LYS K 22 " --> pdb=" O HIS K 18 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER K 23 " --> pdb=" O GLU K 19 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 64 removed outlier: 3.590A pdb=" N ARG K 49 " --> pdb=" O SER K 46 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ASN K 50 " --> pdb=" O LYS K 47 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN K 64 " --> pdb=" O ILE K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 91 Processing helix chain 'K' and resid 93 through 101 Processing helix chain 'K' and resid 104 through 114 Processing helix chain 'K' and resid 117 through 136 Processing sheet with id= A, first strand: chain 'A' and resid 192 through 195 removed outlier: 3.568A pdb=" N GLY A 9 " --> pdb=" O PHE A 150 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 101 through 103 Processing sheet with id= C, first strand: chain 'A' and resid 119 through 124 Processing sheet with id= D, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.592A pdb=" N LYS A 6 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N THR A 201 " --> pdb=" O LYS A 6 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N SER A 8 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ILE A 199 " --> pdb=" O SER A 8 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 192 through 195 removed outlier: 4.471A pdb=" N SER B 3 " --> pdb=" O VAL B 156 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 101 through 103 removed outlier: 3.511A pdb=" N PHE B 102 " --> pdb=" O ASP B 149 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 119 through 127 Processing sheet with id= H, first strand: chain 'B' and resid 4 through 8 removed outlier: 3.622A pdb=" N VAL B 203 " --> pdb=" O LYS B 4 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LYS B 6 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N THR B 201 " --> pdb=" O LYS B 6 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N SER B 8 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE B 199 " --> pdb=" O SER B 8 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 192 through 195 Processing sheet with id= J, first strand: chain 'C' and resid 119 through 127 Processing sheet with id= K, first strand: chain 'C' and resid 4 through 8 removed outlier: 3.658A pdb=" N VAL C 203 " --> pdb=" O LYS C 4 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LYS C 6 " --> pdb=" O THR C 201 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N THR C 201 " --> pdb=" O LYS C 6 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N SER C 8 " --> pdb=" O ILE C 199 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ILE C 199 " --> pdb=" O SER C 8 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 192 through 195 removed outlier: 4.274A pdb=" N SER D 3 " --> pdb=" O VAL D 156 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY D 9 " --> pdb=" O PHE D 150 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 101 through 103 Processing sheet with id= N, first strand: chain 'D' and resid 119 through 124 Processing sheet with id= O, first strand: chain 'D' and resid 4 through 8 removed outlier: 3.783A pdb=" N VAL D 203 " --> pdb=" O LYS D 4 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LYS D 6 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N THR D 201 " --> pdb=" O LYS D 6 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N SER D 8 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N ILE D 199 " --> pdb=" O SER D 8 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 257 through 259 Processing sheet with id= Q, first strand: chain 'E' and resid 171 through 175 Processing sheet with id= R, first strand: chain 'E' and resid 313 through 315 Processing sheet with id= S, first strand: chain 'E' and resid 38 through 41 Processing sheet with id= T, first strand: chain 'F' and resid 350 through 357 removed outlier: 3.697A pdb=" N ALA F 315 " --> pdb=" O MET F 257 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR F 309 " --> pdb=" O TYR F 316 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU F 318 " --> pdb=" O LEU F 307 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N LEU F 307 " --> pdb=" O LEU F 318 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 441 through 445 removed outlier: 3.862A pdb=" N PHE F 441 " --> pdb=" O ILE F 461 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE F 461 " --> pdb=" O PHE F 441 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS F 456 " --> pdb=" O MET F 452 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 618 through 626 removed outlier: 3.622A pdb=" N VAL F 528 " --> pdb=" O GLY F 623 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ILE F 591 " --> pdb=" O ALA F 580 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ALA F 580 " --> pdb=" O ILE F 591 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ALA F 593 " --> pdb=" O ILE F 578 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ILE F 578 " --> pdb=" O ALA F 593 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 8 through 11 Processing sheet with id= X, first strand: chain 'H' and resid 63 through 65 removed outlier: 3.518A pdb=" N GLY H 160 " --> pdb=" O TYR H 65 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'H' and resid 71 through 73 Processing sheet with id= Z, first strand: chain 'H' and resid 125 through 131 Processing sheet with id= AA, 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) 804 hydrogen bonds defined for protein. 2064 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 6 stacking parallelities Total time for adding SS restraints: 6.50 Time building geometry restraints manager: 9.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6038 1.33 - 1.46: 4261 1.46 - 1.58: 10386 1.58 - 1.70: 70 1.70 - 1.82: 99 Bond restraints: 20854 Sorted by residual: bond pdb=" C1' A G 17 " pdb=" N9 A G 17 " ideal model delta sigma weight residual 1.475 1.386 0.089 1.50e-02 4.44e+03 3.50e+01 bond pdb=" C1' U G 19 " pdb=" N1 U G 19 " ideal model delta sigma weight residual 1.480 1.567 -0.087 1.50e-02 4.44e+03 3.33e+01 bond pdb=" C1' C G 28 " pdb=" N1 C G 28 " ideal model delta sigma weight residual 1.480 1.565 -0.085 1.50e-02 4.44e+03 3.19e+01 bond pdb=" C1' A G 16 " pdb=" N9 A G 16 " ideal model delta sigma weight residual 1.475 1.402 0.073 1.50e-02 4.44e+03 2.38e+01 bond pdb=" C1' U G 9 " pdb=" N1 U G 9 " ideal model delta sigma weight residual 1.470 1.540 -0.070 1.50e-02 4.44e+03 2.16e+01 ... (remaining 20849 not shown) Histogram of bond angle deviations from ideal: 95.53 - 103.69: 222 103.69 - 111.85: 9632 111.85 - 120.01: 9202 120.01 - 128.17: 8982 128.17 - 136.33: 143 Bond angle restraints: 28181 Sorted by residual: angle pdb=" PB ATP F 801 " pdb=" O3B ATP F 801 " pdb=" PG ATP F 801 " ideal model delta sigma weight residual 139.87 130.39 9.48 1.00e+00 1.00e+00 8.99e+01 angle pdb=" CA PHE F 540 " pdb=" CB PHE F 540 " pdb=" CG PHE F 540 " ideal model delta sigma weight residual 113.80 107.01 6.79 1.00e+00 1.00e+00 4.61e+01 angle pdb=" C THR F 539 " pdb=" N PHE F 540 " pdb=" CA PHE F 540 " ideal model delta sigma weight residual 120.31 111.85 8.46 1.52e+00 4.33e-01 3.10e+01 angle pdb=" C5' ATP F 801 " pdb=" O5' ATP F 801 " pdb=" PA ATP F 801 " ideal model delta sigma weight residual 121.27 116.99 4.28 1.00e+00 1.00e+00 1.83e+01 angle pdb=" N MET E 186 " pdb=" CA MET E 186 " pdb=" C MET E 186 " ideal model delta sigma weight residual 110.07 104.81 5.26 1.26e+00 6.30e-01 1.74e+01 ... (remaining 28176 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.68: 12230 31.68 - 63.35: 327 63.35 - 95.03: 42 95.03 - 126.70: 4 126.70 - 158.37: 3 Dihedral angle restraints: 12606 sinusoidal: 5528 harmonic: 7078 Sorted by residual: dihedral pdb=" O4' C G 28 " pdb=" C1' C G 28 " pdb=" N1 C G 28 " pdb=" C2 C G 28 " ideal model delta sinusoidal sigma weight residual 200.00 50.60 149.40 1 1.50e+01 4.44e-03 7.94e+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 -158.23 72.23 1 1.00e+01 1.00e-02 6.67e+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 -128.00 30.37 -158.37 1 1.70e+01 3.46e-03 6.41e+01 ... (remaining 12603 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2509 0.066 - 0.132: 516 0.132 - 0.198: 53 0.198 - 0.264: 8 0.264 - 0.330: 3 Chirality restraints: 3089 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 2.73e+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 2.34 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CB ILE D 46 " pdb=" CA ILE D 46 " pdb=" CG1 ILE D 46 " pdb=" CG2 ILE D 46 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 3086 not shown) Planarity restraints: 3493 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 339 " -0.031 2.00e-02 2.50e+03 3.08e-02 2.38e+01 pdb=" CG TRP F 339 " 0.079 2.00e-02 2.50e+03 pdb=" CD1 TRP F 339 " -0.045 2.00e-02 2.50e+03 pdb=" CD2 TRP F 339 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP F 339 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP F 339 " 0.003 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 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP F 339 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR F 129 " -0.020 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C THR F 129 " 0.067 2.00e-02 2.50e+03 pdb=" O THR F 129 " -0.024 2.00e-02 2.50e+03 pdb=" N ASN F 130 " -0.023 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 2.20e-02 8.49e+00 pdb=" CG PHE I 85 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE I 85 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE I 85 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE I 85 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE I 85 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE I 85 " -0.001 2.00e-02 2.50e+03 ... (remaining 3490 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 164 2.57 - 3.15: 17608 3.15 - 3.73: 30177 3.73 - 4.32: 42895 4.32 - 4.90: 69417 Nonbonded interactions: 160261 Sorted by model distance: nonbonded pdb=" ND2 ASN B 57 " pdb=" O2 C G 8 " model vdw 1.987 2.520 nonbonded pdb=" O TYR H 71 " pdb=" OH TYR H 162 " model vdw 2.035 2.440 nonbonded pdb=" OG1 THR C 126 " pdb=" O2' U G 25 " model vdw 2.056 2.440 nonbonded pdb=" NH1 ARG C 129 " pdb=" OD1 ASN D 57 " model vdw 2.057 2.520 nonbonded pdb=" O LEU E 55 " pdb=" OG1 THR E 58 " model vdw 2.118 2.440 ... (remaining 160256 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 20 \ 8)) selection = (chain 'B' and resid 2 through 208) selection = (chain 'C' and (resid 2 through 23 or resid 33 through 63 or resid 76 through 20 \ 8)) selection = (chain 'D' and (resid 2 through 23 or resid 33 through 63 or resid 76 through 20 \ 8)) } ncs_group { reference = (chain 'I' and (resid 17 through 61 or resid 74 through 139)) selection = chain 'J' selection = (chain 'K' and (resid 17 through 61 or resid 74 through 139)) } 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: 4.130 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: 0.020 Extract box with map and model: 15.730 Check model and map are aligned: 0.330 Set scattering table: 0.180 Process input model: 61.860 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.100 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 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 0.092 20854 Z= 0.377 Angle : 0.862 10.663 28181 Z= 0.497 Chirality : 0.053 0.330 3089 Planarity : 0.004 0.065 3493 Dihedral : 14.507 158.375 8053 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.67 % Favored : 95.29 % Rotamer: Outliers : 0.32 % Allowed : 0.69 % Favored : 98.99 % 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: -1.00 (0.16), residues: 2378 helix: 0.09 (0.15), residues: 1038 sheet: 0.13 (0.26), residues: 387 loop : -1.82 (0.18), residues: 953 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 0.030 0.002 TYR F 582 ARG 0.019 0.002 ARG A 137 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 444 time to evaluate : 2.403 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: D 110 HIS cc_start: 0.8270 (t-90) cc_final: 0.7697 (t-170) REVERT: D 131 THR cc_start: 0.8024 (p) cc_final: 0.7390 (p) REVERT: E 28 ASP cc_start: 0.8385 (m-30) cc_final: 0.7785 (m-30) REVERT: E 33 PHE cc_start: 0.8218 (m-10) cc_final: 0.7706 (m-80) REVERT: E 41 ILE cc_start: 0.8233 (mm) cc_final: 0.8017 (mp) REVERT: F 222 ASP cc_start: 0.8014 (m-30) cc_final: 0.7805 (m-30) REVERT: F 624 MET cc_start: 0.7867 (ttm) cc_final: 0.7514 (tpt) REVERT: I 85 PHE cc_start: 0.8837 (m-80) cc_final: 0.8540 (m-80) REVERT: I 104 MET cc_start: 0.8553 (mmm) cc_final: 0.8349 (tmm) REVERT: I 119 PHE cc_start: 0.9040 (t80) cc_final: 0.8747 (t80) REVERT: J 18 HIS cc_start: 0.7377 (t-170) cc_final: 0.6669 (t70) REVERT: J 126 TYR cc_start: 0.8998 (t80) cc_final: 0.8745 (t80) REVERT: K 50 ASN cc_start: 0.8962 (m-40) cc_final: 0.8045 (m110) outliers start: 7 outliers final: 0 residues processed: 449 average time/residue: 0.4285 time to fit residues: 273.8940 Evaluate side-chains 230 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 2.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 203 optimal weight: 6.9990 chunk 182 optimal weight: 2.9990 chunk 101 optimal weight: 0.0050 chunk 62 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 188 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 218 optimal weight: 0.9990 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 HIS ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 HIS D 178 ASN E 60 GLN E 316 ASN F 14 HIS ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 472 ASN F 474 ASN F 482 ASN F 560 GLN ** F 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 708 ASN F 740 ASN ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 251 GLN K 24 ASN ** K 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20854 Z= 0.237 Angle : 0.699 11.300 28181 Z= 0.373 Chirality : 0.045 0.278 3089 Planarity : 0.004 0.039 3493 Dihedral : 13.801 161.774 3140 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.38 % Allowed : 9.73 % Favored : 88.88 % 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: -0.70 (0.16), residues: 2378 helix: 0.22 (0.15), residues: 1054 sheet: 0.40 (0.26), residues: 386 loop : -1.58 (0.18), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F 339 HIS 0.010 0.001 HIS K 18 PHE 0.032 0.002 PHE K 85 TYR 0.033 0.002 TYR J 86 ARG 0.008 0.001 ARG D 191 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 233 time to evaluate : 2.690 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: D 131 THR cc_start: 0.7494 (p) cc_final: 0.7024 (p) REVERT: F 184 TRP cc_start: 0.4317 (m100) cc_final: 0.4116 (m100) REVERT: F 540 PHE cc_start: 0.8204 (OUTLIER) cc_final: 0.7861 (t80) REVERT: F 695 TYR cc_start: 0.6359 (OUTLIER) cc_final: 0.5217 (m-80) REVERT: H 13 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8215 (ptpp) REVERT: I 71 ASN cc_start: 0.8781 (OUTLIER) cc_final: 0.7801 (p0) REVERT: I 85 PHE cc_start: 0.8881 (m-80) cc_final: 0.8644 (m-80) REVERT: I 127 PHE cc_start: 0.9316 (t80) cc_final: 0.9116 (t80) outliers start: 30 outliers final: 16 residues processed: 255 average time/residue: 0.3704 time to fit residues: 140.1163 Evaluate side-chains 211 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 191 time to evaluate : 2.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain D residue 195 LYS Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 322 SER Chi-restraints excluded: chain E residue 325 GLN Chi-restraints excluded: chain E residue 327 MET Chi-restraints excluded: chain F residue 175 GLU Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 540 PHE Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 695 TYR Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain I residue 68 ASP Chi-restraints excluded: chain I residue 71 ASN Chi-restraints excluded: chain K residue 124 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 121 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 182 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 219 optimal weight: 2.9990 chunk 236 optimal weight: 7.9990 chunk 195 optimal weight: 3.9990 chunk 217 optimal weight: 6.9990 chunk 74 optimal weight: 0.5980 chunk 175 optimal weight: 1.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 GLN C 193 GLN D 110 HIS ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 ASN E 320 HIS F 39 GLN ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 HIS ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 472 ASN ** F 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 20854 Z= 0.291 Angle : 0.657 10.105 28181 Z= 0.350 Chirality : 0.043 0.184 3089 Planarity : 0.004 0.034 3493 Dihedral : 13.706 165.595 3140 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.89 % Allowed : 11.44 % Favored : 86.67 % 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: -0.63 (0.16), residues: 2378 helix: 0.24 (0.15), residues: 1058 sheet: 0.34 (0.26), residues: 403 loop : -1.49 (0.19), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 339 HIS 0.010 0.002 HIS F 26 PHE 0.057 0.002 PHE J 85 TYR 0.024 0.002 TYR I 126 ARG 0.006 0.001 ARG E 190 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 191 time to evaluate : 2.524 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: F 540 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.7885 (t80) REVERT: F 624 MET cc_start: 0.7975 (tpp) cc_final: 0.7642 (tpt) REVERT: F 695 TYR cc_start: 0.5947 (OUTLIER) cc_final: 0.4818 (m-80) REVERT: H 13 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8205 (ptpp) REVERT: I 14 MET cc_start: 0.6678 (ttt) cc_final: 0.4435 (tmm) REVERT: I 71 ASN cc_start: 0.8717 (OUTLIER) cc_final: 0.8467 (p0) REVERT: I 72 GLU cc_start: 0.8781 (pp20) cc_final: 0.8517 (pp20) REVERT: I 86 TYR cc_start: 0.8364 (m-80) cc_final: 0.7705 (m-80) REVERT: I 119 PHE cc_start: 0.9048 (t80) cc_final: 0.8788 (t80) REVERT: J 18 HIS cc_start: 0.7729 (t70) cc_final: 0.7181 (t70) REVERT: J 87 TYR cc_start: 0.7582 (t80) cc_final: 0.6248 (t80) outliers start: 41 outliers final: 26 residues processed: 218 average time/residue: 0.3615 time to fit residues: 119.2609 Evaluate side-chains 204 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 174 time to evaluate : 2.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain D residue 110 HIS Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 195 LYS Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 322 SER Chi-restraints excluded: chain E residue 325 GLN Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 175 GLU Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 463 TYR Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 540 PHE Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain F residue 695 TYR Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain I residue 23 SER Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 68 ASP Chi-restraints excluded: chain I residue 71 ASN Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 109 ASP Chi-restraints excluded: chain K residue 50 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 216 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 104 optimal weight: 9.9990 chunk 147 optimal weight: 6.9990 chunk 220 optimal weight: 0.0170 chunk 232 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 overall best weight: 2.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 HIS D 113 GLN D 155 ASN ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 ASN ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 549 ASN ** F 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 GLN ** K 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20854 Z= 0.249 Angle : 0.600 9.901 28181 Z= 0.322 Chirality : 0.042 0.172 3089 Planarity : 0.004 0.048 3493 Dihedral : 13.614 167.418 3140 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.03 % Allowed : 12.36 % Favored : 85.61 % 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: -0.60 (0.17), residues: 2378 helix: 0.32 (0.16), residues: 1057 sheet: 0.24 (0.25), residues: 412 loop : -1.49 (0.19), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 339 HIS 0.014 0.001 HIS F 26 PHE 0.050 0.002 PHE J 85 TYR 0.019 0.002 TYR I 126 ARG 0.009 0.001 ARG E 190 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 187 time to evaluate : 2.413 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: E 186 MET cc_start: 0.8346 (mmm) cc_final: 0.7928 (mpp) REVERT: F 496 MET cc_start: 0.7095 (pmm) cc_final: 0.6687 (pmm) REVERT: F 624 MET cc_start: 0.8019 (tpp) cc_final: 0.7714 (tpt) REVERT: F 695 TYR cc_start: 0.5856 (OUTLIER) cc_final: 0.4813 (m-80) REVERT: I 72 GLU cc_start: 0.8888 (pp20) cc_final: 0.8626 (pp20) REVERT: I 77 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8831 (mm-30) REVERT: I 86 TYR cc_start: 0.8229 (m-80) cc_final: 0.7930 (m-80) REVERT: I 119 PHE cc_start: 0.9058 (t80) cc_final: 0.8849 (t80) REVERT: J 74 PHE cc_start: 0.6673 (p90) cc_final: 0.6321 (p90) REVERT: K 14 MET cc_start: 0.4352 (mtm) cc_final: 0.3997 (mtm) REVERT: K 85 PHE cc_start: 0.8950 (m-80) cc_final: 0.8656 (m-80) outliers start: 44 outliers final: 28 residues processed: 216 average time/residue: 0.3369 time to fit residues: 110.6264 Evaluate side-chains 200 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 171 time to evaluate : 2.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 195 LYS Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 181 LYS Chi-restraints excluded: chain E residue 318 SER Chi-restraints excluded: chain E residue 322 SER Chi-restraints excluded: chain F residue 175 GLU Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 393 ILE Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 695 TYR Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain I residue 68 ASP Chi-restraints excluded: chain I residue 80 TYR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 83 ILE Chi-restraints excluded: chain J residue 109 ASP Chi-restraints excluded: chain J residue 138 GLN Chi-restraints excluded: chain K residue 50 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 194 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 173 optimal weight: 0.8980 chunk 96 optimal weight: 7.9990 chunk 198 optimal weight: 5.9990 chunk 161 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 209 optimal weight: 8.9990 chunk 58 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 GLN ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 GLN ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.4949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20854 Z= 0.265 Angle : 0.607 10.070 28181 Z= 0.324 Chirality : 0.041 0.186 3089 Planarity : 0.004 0.031 3493 Dihedral : 13.583 168.860 3140 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.12 % Allowed : 13.75 % Favored : 84.13 % 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: -0.55 (0.17), residues: 2378 helix: 0.36 (0.16), residues: 1041 sheet: 0.17 (0.25), residues: 416 loop : -1.39 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 594 HIS 0.008 0.001 HIS K 18 PHE 0.045 0.002 PHE I 85 TYR 0.023 0.002 TYR K 80 ARG 0.004 0.001 ARG E 121 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 178 time to evaluate : 2.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 LYS cc_start: 0.9500 (OUTLIER) cc_final: 0.9228 (ttpp) REVERT: E 40 MET cc_start: 0.7803 (ptp) cc_final: 0.7564 (ppp) REVERT: E 41 ILE cc_start: 0.6970 (mm) cc_final: 0.6676 (mp) REVERT: E 186 MET cc_start: 0.8413 (mmm) cc_final: 0.8042 (mpp) REVERT: F 1 MET cc_start: 0.6812 (mmt) cc_final: 0.6392 (tpp) REVERT: F 184 TRP cc_start: 0.4620 (m100) cc_final: 0.4387 (m100) REVERT: F 496 MET cc_start: 0.7351 (pmm) cc_final: 0.7026 (pmm) REVERT: F 624 MET cc_start: 0.8110 (tpp) cc_final: 0.7794 (tpt) REVERT: F 695 TYR cc_start: 0.5909 (OUTLIER) cc_final: 0.4880 (m-80) REVERT: F 721 MET cc_start: 0.6690 (mtt) cc_final: 0.6002 (ttt) REVERT: I 72 GLU cc_start: 0.8912 (pp20) cc_final: 0.8592 (pp20) REVERT: I 77 GLU cc_start: 0.9122 (mm-30) cc_final: 0.8832 (mm-30) REVERT: I 86 TYR cc_start: 0.8127 (m-80) cc_final: 0.7882 (m-80) REVERT: I 119 PHE cc_start: 0.9113 (t80) cc_final: 0.8877 (t80) REVERT: J 53 GLU cc_start: 0.8988 (tm-30) cc_final: 0.8743 (tm-30) outliers start: 46 outliers final: 32 residues processed: 215 average time/residue: 0.3426 time to fit residues: 111.4836 Evaluate side-chains 201 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 167 time to evaluate : 2.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 195 LYS Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 181 LYS Chi-restraints excluded: chain E residue 322 SER Chi-restraints excluded: chain F residue 33 HIS Chi-restraints excluded: chain F residue 175 GLU Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 393 ILE Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 695 TYR Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 140 ASP Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain I residue 68 ASP Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 83 ILE Chi-restraints excluded: chain J residue 109 ASP Chi-restraints excluded: chain K residue 50 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 78 optimal weight: 10.0000 chunk 209 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 136 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 233 optimal weight: 0.7980 chunk 193 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.7980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 670 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.5264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20854 Z= 0.232 Angle : 0.605 10.270 28181 Z= 0.320 Chirality : 0.041 0.197 3089 Planarity : 0.003 0.032 3493 Dihedral : 13.509 169.333 3140 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.12 % Allowed : 14.58 % Favored : 83.30 % 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: -0.50 (0.17), residues: 2378 helix: 0.40 (0.16), residues: 1049 sheet: 0.20 (0.25), residues: 411 loop : -1.36 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 594 HIS 0.007 0.001 HIS E 17 PHE 0.050 0.002 PHE I 85 TYR 0.028 0.001 TYR J 126 ARG 0.003 0.000 ARG J 57 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 176 time to evaluate : 2.558 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: A 171 LYS cc_start: 0.9469 (OUTLIER) cc_final: 0.9205 (ttpp) REVERT: B 120 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7168 (pp20) REVERT: D 66 LYS cc_start: 0.7838 (ttpp) cc_final: 0.7069 (mmtm) REVERT: E 40 MET cc_start: 0.7814 (ptp) cc_final: 0.7501 (ppp) REVERT: E 41 ILE cc_start: 0.6890 (mm) cc_final: 0.6677 (mp) REVERT: E 186 MET cc_start: 0.8491 (mmm) cc_final: 0.8166 (mpp) REVERT: F 1 MET cc_start: 0.6920 (mmt) cc_final: 0.6454 (tpp) REVERT: F 496 MET cc_start: 0.7467 (pmm) cc_final: 0.7133 (pmm) REVERT: F 624 MET cc_start: 0.8001 (tpp) cc_final: 0.7690 (tpt) REVERT: F 695 TYR cc_start: 0.6107 (OUTLIER) cc_final: 0.5104 (m-80) REVERT: F 721 MET cc_start: 0.6729 (mtt) cc_final: 0.6065 (ttt) REVERT: I 77 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8889 (mm-30) REVERT: J 107 ILE cc_start: 0.8394 (mm) cc_final: 0.8141 (mt) outliers start: 46 outliers final: 32 residues processed: 208 average time/residue: 0.3503 time to fit residues: 110.8412 Evaluate side-chains 200 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 165 time to evaluate : 2.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 195 LYS Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 181 LYS Chi-restraints excluded: chain E residue 318 SER Chi-restraints excluded: chain E residue 322 SER Chi-restraints excluded: chain F residue 33 HIS Chi-restraints excluded: chain F residue 175 GLU Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 393 ILE Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 565 PHE Chi-restraints excluded: chain F residue 695 TYR Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 140 ASP Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain I residue 68 ASP Chi-restraints excluded: chain I residue 122 ASP Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 83 ILE Chi-restraints excluded: chain J residue 109 ASP Chi-restraints excluded: chain K residue 50 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 224 optimal weight: 1.9990 chunk 26 optimal weight: 0.0070 chunk 132 optimal weight: 7.9990 chunk 170 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 196 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 232 optimal weight: 0.1980 chunk 145 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 107 optimal weight: 8.9990 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 GLN ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 504 GLN F 505 ASN F 670 ASN I 18 HIS ** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.5495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20854 Z= 0.162 Angle : 0.586 10.949 28181 Z= 0.310 Chirality : 0.041 0.231 3089 Planarity : 0.003 0.033 3493 Dihedral : 13.362 169.285 3140 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.75 % Allowed : 15.41 % Favored : 82.84 % 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: -0.38 (0.17), residues: 2378 helix: 0.47 (0.16), residues: 1054 sheet: 0.28 (0.25), residues: 415 loop : -1.30 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP H 52 HIS 0.006 0.001 HIS K 18 PHE 0.043 0.001 PHE J 85 TYR 0.026 0.001 TYR K 80 ARG 0.006 0.000 ARG F 477 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 171 time to evaluate : 2.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 LYS cc_start: 0.9434 (OUTLIER) cc_final: 0.9222 (ttpp) REVERT: D 113 GLN cc_start: 0.8013 (pp30) cc_final: 0.7149 (pp30) REVERT: E 51 LYS cc_start: 0.9269 (mmmt) cc_final: 0.9059 (mmmt) REVERT: E 186 MET cc_start: 0.8421 (mmm) cc_final: 0.7986 (mpp) REVERT: F 1 MET cc_start: 0.6842 (mmt) cc_final: 0.6415 (tpp) REVERT: F 8 MET cc_start: 0.8065 (mmp) cc_final: 0.7776 (mmp) REVERT: F 47 PHE cc_start: 0.6911 (OUTLIER) cc_final: 0.6402 (t80) REVERT: F 496 MET cc_start: 0.7471 (pmm) cc_final: 0.7089 (pmm) REVERT: F 624 MET cc_start: 0.8009 (tpp) cc_final: 0.7705 (tpt) REVERT: F 695 TYR cc_start: 0.6037 (OUTLIER) cc_final: 0.5115 (m-80) REVERT: F 721 MET cc_start: 0.6898 (mtt) cc_final: 0.5962 (ttt) REVERT: I 52 MET cc_start: 0.8047 (tmm) cc_final: 0.7747 (tmm) REVERT: I 77 GLU cc_start: 0.9101 (mm-30) cc_final: 0.8900 (mm-30) REVERT: I 105 PHE cc_start: 0.8852 (m-80) cc_final: 0.8557 (m-80) REVERT: J 104 MET cc_start: 0.8745 (mmm) cc_final: 0.8506 (tpt) REVERT: J 107 ILE cc_start: 0.8374 (mm) cc_final: 0.8163 (mt) REVERT: K 123 TYR cc_start: 0.8260 (t80) cc_final: 0.7969 (t80) outliers start: 38 outliers final: 24 residues processed: 200 average time/residue: 0.3457 time to fit residues: 105.1932 Evaluate side-chains 187 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 160 time to evaluate : 2.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain D residue 195 LYS Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 181 LYS Chi-restraints excluded: chain F residue 33 HIS Chi-restraints excluded: chain F residue 47 PHE Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 175 GLU Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 393 ILE Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain F residue 695 TYR Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 140 ASP Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 83 ILE Chi-restraints excluded: chain J residue 109 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 143 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 45 optimal weight: 9.9990 chunk 147 optimal weight: 7.9990 chunk 158 optimal weight: 5.9990 chunk 114 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 182 optimal weight: 6.9990 chunk 211 optimal weight: 7.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 ASN ** C 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 HIS ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 475 GLN ** F 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 177 ASN I 18 HIS I 27 ASN ** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.6050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 20854 Z= 0.387 Angle : 0.739 11.530 28181 Z= 0.388 Chirality : 0.044 0.251 3089 Planarity : 0.004 0.039 3493 Dihedral : 13.639 172.066 3140 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 21.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.08 % Allowed : 15.68 % Favored : 82.24 % 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: -0.74 (0.17), residues: 2378 helix: 0.10 (0.16), residues: 1046 sheet: 0.16 (0.26), residues: 407 loop : -1.39 (0.19), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 52 HIS 0.007 0.002 HIS A 174 PHE 0.038 0.002 PHE J 85 TYR 0.037 0.002 TYR J 137 ARG 0.006 0.001 ARG C 93 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 169 time to evaluate : 2.751 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: A 171 LYS cc_start: 0.9431 (OUTLIER) cc_final: 0.9119 (ttpp) REVERT: B 120 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7275 (pp20) REVERT: D 113 GLN cc_start: 0.8167 (pp30) cc_final: 0.7194 (pp30) REVERT: E 186 MET cc_start: 0.8603 (mmm) cc_final: 0.8006 (mpp) REVERT: F 1 MET cc_start: 0.7095 (mmt) cc_final: 0.6588 (tpp) REVERT: F 624 MET cc_start: 0.8056 (tpp) cc_final: 0.7636 (tpt) REVERT: F 695 TYR cc_start: 0.5859 (OUTLIER) cc_final: 0.5066 (m-80) REVERT: F 721 MET cc_start: 0.7096 (mtt) cc_final: 0.6200 (ttt) REVERT: I 14 MET cc_start: 0.7649 (ttt) cc_final: 0.7377 (ttm) REVERT: I 52 MET cc_start: 0.8013 (tmm) cc_final: 0.7700 (tmm) REVERT: I 76 ASP cc_start: 0.9106 (p0) cc_final: 0.8881 (p0) REVERT: I 77 GLU cc_start: 0.9182 (mm-30) cc_final: 0.8974 (mm-30) REVERT: J 49 ARG cc_start: 0.8073 (ttm-80) cc_final: 0.7425 (tmm-80) REVERT: J 104 MET cc_start: 0.8824 (mmm) cc_final: 0.8595 (mmm) REVERT: J 107 ILE cc_start: 0.8388 (mm) cc_final: 0.8149 (mt) REVERT: K 123 TYR cc_start: 0.8359 (t80) cc_final: 0.8036 (t80) outliers start: 45 outliers final: 37 residues processed: 201 average time/residue: 0.3534 time to fit residues: 109.3718 Evaluate side-chains 196 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 156 time to evaluate : 2.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain D residue 195 LYS Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 145 LYS Chi-restraints excluded: chain E residue 181 LYS Chi-restraints excluded: chain E residue 259 PHE Chi-restraints excluded: chain F residue 33 HIS Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 175 GLU Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 393 ILE Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 565 PHE Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain F residue 695 TYR Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 140 ASP Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain I residue 68 ASP Chi-restraints excluded: chain I residue 80 TYR Chi-restraints excluded: chain I residue 122 ASP Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 56 ASN Chi-restraints excluded: chain J residue 83 ILE Chi-restraints excluded: chain J residue 109 ASP Chi-restraints excluded: chain J residue 121 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 222 optimal weight: 0.9990 chunk 203 optimal weight: 5.9990 chunk 216 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 169 optimal weight: 0.1980 chunk 66 optimal weight: 10.0000 chunk 195 optimal weight: 0.8980 chunk 204 optimal weight: 0.6980 chunk 215 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS D 72 HIS D 168 ASN ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 670 ASN I 18 HIS ** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.6100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20854 Z= 0.171 Angle : 0.633 11.451 28181 Z= 0.331 Chirality : 0.042 0.265 3089 Planarity : 0.003 0.028 3493 Dihedral : 13.485 169.873 3140 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.66 % Allowed : 16.79 % Favored : 81.55 % 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: -0.47 (0.17), residues: 2378 helix: 0.33 (0.16), residues: 1050 sheet: 0.22 (0.25), residues: 415 loop : -1.24 (0.20), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP H 52 HIS 0.012 0.001 HIS D 72 PHE 0.049 0.002 PHE J 85 TYR 0.033 0.001 TYR I 86 ARG 0.007 0.000 ARG F 477 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 169 time to evaluate : 2.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 LYS cc_start: 0.9375 (OUTLIER) cc_final: 0.9148 (ttpp) REVERT: B 120 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7186 (pp20) REVERT: D 113 GLN cc_start: 0.8073 (pp30) cc_final: 0.7254 (pp30) REVERT: E 181 LYS cc_start: 0.7371 (OUTLIER) cc_final: 0.7028 (mmmt) REVERT: E 186 MET cc_start: 0.8502 (mmm) cc_final: 0.8145 (mpp) REVERT: F 1 MET cc_start: 0.6963 (mmt) cc_final: 0.6509 (tpp) REVERT: F 8 MET cc_start: 0.8013 (mmp) cc_final: 0.7660 (mmp) REVERT: F 47 PHE cc_start: 0.7056 (OUTLIER) cc_final: 0.6528 (t80) REVERT: F 496 MET cc_start: 0.7802 (pmm) cc_final: 0.7117 (pmm) REVERT: F 624 MET cc_start: 0.8002 (tpp) cc_final: 0.7665 (tpt) REVERT: F 695 TYR cc_start: 0.5742 (OUTLIER) cc_final: 0.4759 (m-80) REVERT: F 721 MET cc_start: 0.6902 (mtt) cc_final: 0.5957 (ttt) REVERT: I 52 MET cc_start: 0.7964 (tmm) cc_final: 0.7644 (tmm) REVERT: I 76 ASP cc_start: 0.9110 (p0) cc_final: 0.8692 (p0) REVERT: I 77 GLU cc_start: 0.9163 (mm-30) cc_final: 0.8936 (mm-30) REVERT: J 49 ARG cc_start: 0.8030 (ttm-80) cc_final: 0.7369 (tmm-80) REVERT: J 104 MET cc_start: 0.8738 (mmm) cc_final: 0.8482 (mmm) REVERT: J 107 ILE cc_start: 0.8340 (mm) cc_final: 0.8140 (mt) outliers start: 36 outliers final: 30 residues processed: 196 average time/residue: 0.3409 time to fit residues: 102.0647 Evaluate side-chains 192 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 157 time to evaluate : 2.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 195 LYS Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 145 LYS Chi-restraints excluded: chain E residue 181 LYS Chi-restraints excluded: chain F residue 33 HIS Chi-restraints excluded: chain F residue 47 PHE Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 175 GLU Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 565 PHE Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain F residue 695 TYR Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 137 GLN Chi-restraints excluded: chain H residue 140 ASP Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain I residue 80 TYR Chi-restraints excluded: chain J residue 54 GLN Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 109 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 228 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 159 optimal weight: 0.6980 chunk 240 optimal weight: 0.9990 chunk 220 optimal weight: 8.9990 chunk 191 optimal weight: 0.0040 chunk 19 optimal weight: 7.9990 chunk 147 optimal weight: 2.9990 chunk 117 optimal weight: 7.9990 chunk 151 optimal weight: 5.9990 overall best weight: 1.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 670 ASN H 17 HIS I 18 HIS I 69 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.6210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20854 Z= 0.201 Angle : 0.635 12.951 28181 Z= 0.333 Chirality : 0.042 0.277 3089 Planarity : 0.003 0.028 3493 Dihedral : 13.417 170.624 3140 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.61 % Allowed : 17.07 % Favored : 81.32 % 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: -0.49 (0.17), residues: 2378 helix: 0.29 (0.16), residues: 1059 sheet: 0.21 (0.25), residues: 415 loop : -1.23 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 52 HIS 0.008 0.001 HIS D 72 PHE 0.036 0.002 PHE J 85 TYR 0.016 0.001 TYR K 123 ARG 0.006 0.000 ARG F 477 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 161 time to evaluate : 3.024 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: D 113 GLN cc_start: 0.8079 (pp30) cc_final: 0.7266 (pp30) REVERT: E 181 LYS cc_start: 0.7505 (OUTLIER) cc_final: 0.7206 (mmmt) REVERT: E 186 MET cc_start: 0.8566 (mmm) cc_final: 0.8176 (mpp) REVERT: F 1 MET cc_start: 0.6995 (mmt) cc_final: 0.6524 (tpp) REVERT: F 8 MET cc_start: 0.8001 (mmp) cc_final: 0.7693 (mmp) REVERT: F 47 PHE cc_start: 0.7104 (OUTLIER) cc_final: 0.6517 (t80) REVERT: F 452 MET cc_start: 0.7769 (mmm) cc_final: 0.7485 (mmm) REVERT: F 496 MET cc_start: 0.7745 (pmm) cc_final: 0.7213 (pmm) REVERT: F 624 MET cc_start: 0.8018 (tpp) cc_final: 0.7673 (tpt) REVERT: F 695 TYR cc_start: 0.5733 (OUTLIER) cc_final: 0.4710 (m-80) REVERT: F 721 MET cc_start: 0.6953 (mtt) cc_final: 0.5992 (ttt) REVERT: I 14 MET cc_start: 0.7355 (ttt) cc_final: 0.7058 (ttm) REVERT: I 52 MET cc_start: 0.8012 (tmm) cc_final: 0.7665 (tmm) REVERT: I 77 GLU cc_start: 0.9168 (mm-30) cc_final: 0.8947 (mm-30) REVERT: J 49 ARG cc_start: 0.8045 (ttm-80) cc_final: 0.7382 (tmm-80) REVERT: J 107 ILE cc_start: 0.8356 (mm) cc_final: 0.8149 (mt) outliers start: 35 outliers final: 29 residues processed: 188 average time/residue: 0.3407 time to fit residues: 98.6386 Evaluate side-chains 190 residues out of total 2168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 158 time to evaluate : 2.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 195 LYS Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 145 LYS Chi-restraints excluded: chain E residue 181 LYS Chi-restraints excluded: chain F residue 33 HIS Chi-restraints excluded: chain F residue 47 PHE Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 175 GLU Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 565 PHE Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain F residue 695 TYR Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 137 GLN Chi-restraints excluded: chain H residue 140 ASP Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain I residue 80 TYR Chi-restraints excluded: chain J residue 54 GLN Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 56 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 203 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 176 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 191 optimal weight: 6.9990 chunk 80 optimal weight: 20.0000 chunk 196 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 168 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 HIS ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 670 ASN I 18 HIS I 69 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.056608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.043271 restraints weight = 152549.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.044437 restraints weight = 86434.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.045152 restraints weight = 58403.429| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.6308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20854 Z= 0.169 Angle : 0.624 13.341 28181 Z= 0.327 Chirality : 0.042 0.278 3089 Planarity : 0.003 0.027 3493 Dihedral : 13.311 170.783 3140 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.52 % Allowed : 17.11 % Favored : 81.37 % 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 (0.17), residues: 2378 helix: 0.32 (0.16), residues: 1070 sheet: 0.28 (0.26), residues: 411 loop : -1.22 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 52 HIS 0.007 0.001 HIS D 72 PHE 0.032 0.001 PHE J 85 TYR 0.021 0.001 TYR I 123 ARG 0.007 0.000 ARG F 477 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3932.35 seconds wall clock time: 73 minutes 26.15 seconds (4406.15 seconds total)