Starting phenix.real_space_refine on Sat Feb 17 11:44:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v01_26925/02_2024/7v01_26925_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v01_26925/02_2024/7v01_26925.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v01_26925/02_2024/7v01_26925.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v01_26925/02_2024/7v01_26925.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v01_26925/02_2024/7v01_26925_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v01_26925/02_2024/7v01_26925_neut_updated.pdb" } resolution = 3.67 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 61 5.49 5 S 51 5.16 5 C 11549 2.51 5 N 3112 2.21 5 O 3719 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 129": "NH1" <-> "NH2" Residue "A ARG 191": "NH1" <-> "NH2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B ARG 191": "NH1" <-> "NH2" Residue "C ARG 129": "NH1" <-> "NH2" Residue "C ARG 191": "NH1" <-> "NH2" Residue "F GLU 298": "OE1" <-> "OE2" Residue "F GLU 343": "OE1" <-> "OE2" Residue "F GLU 673": "OE1" <-> "OE2" Residue "I GLU 128": "OE1" <-> "OE2" Residue "K GLU 128": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18492 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1628 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 200} Chain breaks: 1 Chain: "B" Number of atoms: 1523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1523 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 187} Chain breaks: 2 Chain: "C" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1628 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 200} Chain breaks: 1 Chain: "E" Number of atoms: 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: 5636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 693, 5636 Classifications: {'peptide': 693} Link IDs: {'PTRANS': 7, 'TRANS': 685} Chain breaks: 3 Chain: "G" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 644 Classifications: {'RNA': 30} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 2, 'rna3p_pur': 11, 'rna3p_pyr': 9} Link IDs: {'rna2p': 10, 'rna3p': 19} Chain: "H" Number of atoms: 2386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2386 Classifications: {'peptide': 297} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 287} Chain breaks: 1 Chain: "I" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 995 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Chain: "K" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 995 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Chain: "U" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 522 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 8, 'rna3p_pur': 5, 'rna3p_pyr': 8} Link IDs: {'rna2p': 12, 'rna3p': 12} 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: 10.78, per 1000 atoms: 0.58 Number of scatterers: 18492 At special positions: 0 Unit cell: (96.21, 118.659, 186.006, 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 51 16.00 P 61 15.00 O 3719 8.00 N 3112 7.00 C 11549 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 410 " - pdb=" SG CYS F 426 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.80 Conformation dependent library (CDL) restraints added in 3.6 seconds 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3988 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 85 helices and 22 sheets defined 42.1% alpha, 13.0% beta 8 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 7.95 Creating SS restraints... Processing helix chain 'A' and resid 48 through 62 Processing helix chain 'A' and resid 67 through 72 removed outlier: 3.991A 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 113 Processing helix chain 'A' and resid 160 through 178 removed outlier: 4.160A pdb=" N GLU A 163 " --> pdb=" O SER A 160 " (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 62 Processing helix chain 'B' and resid 78 through 83 removed outlier: 3.537A pdb=" N PHE B 83 " --> pdb=" O VAL B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 114 Processing helix chain 'B' and resid 159 through 178 removed outlier: 3.623A pdb=" N VAL B 162 " --> pdb=" O GLU B 159 " (cutoff:3.500A) removed outlier: 5.609A 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 82 Processing helix chain 'C' and resid 105 through 114 Processing helix chain 'C' and resid 159 through 177 removed outlier: 3.920A pdb=" N VAL C 162 " --> pdb=" O GLU C 159 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N GLU C 163 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 3.700A 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 '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 230 Processing helix chain 'E' and resid 238 through 247 Processing helix chain 'E' and resid 249 through 254 removed outlier: 4.805A pdb=" N ASN E 254 " --> pdb=" O PRO E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 295 removed outlier: 3.762A pdb=" N ARG E 294 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 6.513A 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: 3.712A pdb=" N LEU F 13 " --> pdb=" O TYR F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 23 removed outlier: 3.704A pdb=" N ILE F 19 " --> pdb=" O ILE F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 30 removed outlier: 4.178A pdb=" N ARG F 30 " --> pdb=" O THR F 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 27 through 30' Processing helix chain 'F' and resid 33 through 43 Processing helix chain 'F' and resid 50 through 57 Processing helix chain 'F' and resid 61 through 66 removed outlier: 3.692A pdb=" N LYS F 66 " --> pdb=" O LYS F 62 " (cutoff:3.500A) 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 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 236 Processing helix chain 'F' and resid 240 through 248 Processing helix chain 'F' and resid 262 through 267 removed outlier: 4.086A pdb=" N TYR F 267 " --> pdb=" O GLN F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 299 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 362 No H-bonds generated for 'chain 'F' and resid 359 through 362' Processing helix chain 'F' and resid 368 through 383 Processing helix chain 'F' and resid 390 through 397 removed outlier: 3.508A pdb=" N ASN F 397 " --> pdb=" O ILE F 393 " (cutoff:3.500A) 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 575 removed outlier: 5.823A pdb=" N LEU F 569 " --> pdb=" O PHE F 565 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ASN F 570 " --> pdb=" O LYS F 566 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU F 574 " --> pdb=" O ASN F 570 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ASN F 575 " --> pdb=" O HIS F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 594 through 611 Processing helix chain 'F' and resid 631 through 635 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 734 Processing helix chain 'F' and resid 736 through 749 Processing helix chain 'H' and resid 32 through 46 Processing helix chain 'H' and resid 98 through 105 removed outlier: 5.296A pdb=" N ASN H 102 " --> pdb=" O HIS H 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 119 Processing helix chain 'H' and resid 137 through 139 No H-bonds generated for 'chain 'H' and resid 137 through 139' Processing helix chain 'H' and resid 169 through 184 removed outlier: 4.992A 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 24 Processing helix chain 'I' and resid 45 through 63 removed outlier: 4.965A 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 'K' and resid 16 through 24 Processing helix chain 'K' and resid 45 through 63 removed outlier: 4.964A pdb=" N ASN K 50 " --> pdb=" O LYS K 47 " (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 Processing sheet with id= B, first strand: chain 'A' and resid 119 through 124 removed outlier: 3.551A pdb=" N LYS A 122 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE A 139 " --> pdb=" O LYS A 122 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 4 through 8 removed outlier: 3.504A pdb=" N VAL A 203 " --> pdb=" O LYS A 4 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LYS A 6 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N THR A 201 " --> pdb=" O LYS A 6 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N SER A 8 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ILE A 199 " --> pdb=" O SER A 8 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 192 through 195 removed outlier: 4.434A pdb=" N SER B 3 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 156 " --> pdb=" O SER B 3 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 119 through 124 Processing sheet with id= F, first strand: chain 'B' and resid 4 through 8 removed outlier: 3.624A pdb=" N VAL B 203 " --> pdb=" O LYS B 4 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LYS B 6 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N THR B 201 " --> pdb=" O LYS B 6 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N SER B 8 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ILE B 199 " --> pdb=" O SER B 8 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 192 through 195 removed outlier: 4.281A pdb=" N SER C 3 " --> pdb=" O VAL C 156 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 119 through 124 removed outlier: 3.818A pdb=" N ARG C 141 " --> pdb=" O GLU C 120 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 4 through 8 removed outlier: 3.832A pdb=" N VAL C 203 " --> pdb=" O LYS C 4 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LYS C 6 " --> pdb=" O THR C 201 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N THR C 201 " --> pdb=" O LYS C 6 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N SER C 8 " --> pdb=" O ILE C 199 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N ILE C 199 " --> pdb=" O SER C 8 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 257 through 259 Processing sheet with id= K, first strand: chain 'E' and resid 171 through 175 Processing sheet with id= L, first strand: chain 'E' and resid 177 through 179 removed outlier: 3.722A pdb=" N THR E 321 " --> pdb=" O ASN E 316 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 38 through 41 removed outlier: 3.681A pdb=" N TYR E 95 " --> pdb=" O MET E 40 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 350 through 357 removed outlier: 3.516A pdb=" N LEU F 254 " --> pdb=" O GLU F 355 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY F 311 " --> pdb=" O HIS F 314 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR F 309 " --> pdb=" O TYR F 316 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N LEU F 318 " --> pdb=" O LEU F 307 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU F 307 " --> pdb=" O LEU F 318 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'F' and resid 441 through 445 removed outlier: 3.692A pdb=" N LYS F 456 " --> pdb=" O MET F 452 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 618 through 626 removed outlier: 3.650A pdb=" N ARG F 530 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY F 623 " --> pdb=" O VAL F 528 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL F 528 " --> pdb=" O GLY F 623 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE F 625 " --> pdb=" O LEU F 526 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR F 582 " --> pdb=" O PHE F 589 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ILE F 591 " --> pdb=" O ALA F 580 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ALA F 580 " --> pdb=" O ILE F 591 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'H' and resid 7 through 11 removed outlier: 3.825A pdb=" N VAL H 7 " --> pdb=" O ILE H 203 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE H 203 " --> pdb=" O VAL H 7 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'H' and resid 63 through 65 Processing sheet with id= S, first strand: chain 'H' and resid 71 through 73 Processing sheet with id= T, first strand: chain 'H' and resid 125 through 131 Processing sheet with id= U, first strand: chain 'H' and resid 243 through 246 Processing sheet with id= V, first strand: chain 'H' and resid 281 through 284 702 hydrogen bonds defined for protein. 1785 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 20 hydrogen bonds 40 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 5.71 Time building geometry restraints manager: 8.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3874 1.33 - 1.45: 4726 1.45 - 1.57: 10139 1.57 - 1.70: 118 1.70 - 1.82: 90 Bond restraints: 18947 Sorted by residual: bond pdb=" C4 ATP F 802 " pdb=" C5 ATP F 802 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 6.99e+01 bond pdb=" C5 ATP F 802 " pdb=" C6 ATP F 802 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.71e+01 bond pdb=" C5 ATP F 802 " pdb=" N7 ATP F 802 " ideal model delta sigma weight residual 1.387 1.333 0.054 1.00e-02 1.00e+04 2.97e+01 bond pdb=" C4 ATP F 802 " pdb=" N9 ATP F 802 " ideal model delta sigma weight residual 1.374 1.330 0.044 1.00e-02 1.00e+04 1.97e+01 bond pdb=" C8 ATP F 802 " pdb=" N7 ATP F 802 " ideal model delta sigma weight residual 1.310 1.352 -0.042 1.00e-02 1.00e+04 1.76e+01 ... (remaining 18942 not shown) Histogram of bond angle deviations from ideal: 97.13 - 105.00: 389 105.00 - 112.87: 10043 112.87 - 120.74: 9068 120.74 - 128.62: 6106 128.62 - 136.49: 143 Bond angle restraints: 25749 Sorted by residual: angle pdb=" PB ATP F 802 " pdb=" O3B ATP F 802 " pdb=" PG ATP F 802 " ideal model delta sigma weight residual 139.87 123.45 16.42 1.00e+00 1.00e+00 2.70e+02 angle pdb=" PA ATP F 802 " pdb=" O3A ATP F 802 " pdb=" PB ATP F 802 " ideal model delta sigma weight residual 136.83 121.94 14.89 1.00e+00 1.00e+00 2.22e+02 angle pdb=" CA PHE F 540 " pdb=" CB PHE F 540 " pdb=" CG PHE F 540 " ideal model delta sigma weight residual 113.80 99.01 14.79 1.00e+00 1.00e+00 2.19e+02 angle pdb=" C4' A U 25 " pdb=" C3' A U 25 " pdb=" O3' A U 25 " ideal model delta sigma weight residual 113.00 97.76 15.24 1.50e+00 4.44e-01 1.03e+02 angle pdb=" O3' U U 28 " pdb=" C3' U U 28 " pdb=" C2' U U 28 " ideal model delta sigma weight residual 109.50 124.01 -14.51 1.50e+00 4.44e-01 9.36e+01 ... (remaining 25744 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 11156 35.78 - 71.55: 277 71.55 - 107.33: 33 107.33 - 143.10: 3 143.10 - 178.88: 4 Dihedral angle restraints: 11473 sinusoidal: 5268 harmonic: 6205 Sorted by residual: dihedral pdb=" O4' U U 17 " pdb=" C1' U U 17 " pdb=" N1 U U 17 " pdb=" C2 U U 17 " ideal model delta sinusoidal sigma weight residual -128.00 48.98 -176.98 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U U 10 " pdb=" C1' U U 10 " pdb=" N1 U U 10 " pdb=" C2 U U 10 " ideal model delta sinusoidal sigma weight residual 232.00 75.77 156.23 1 1.70e+01 3.46e-03 6.36e+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 7.04 -135.04 1 1.70e+01 3.46e-03 5.67e+01 ... (remaining 11470 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2472 0.074 - 0.149: 337 0.149 - 0.223: 32 0.223 - 0.297: 6 0.297 - 0.371: 2 Chirality restraints: 2849 Sorted by residual: chirality pdb=" P G U 29 " pdb=" OP1 G U 29 " pdb=" OP2 G U 29 " pdb=" O5' G U 29 " both_signs ideal model delta sigma weight residual True 2.41 -2.78 -0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" C3' A U 25 " pdb=" C4' A U 25 " pdb=" O3' A U 25 " pdb=" C2' A U 25 " both_signs ideal model delta sigma weight residual False -2.48 -2.83 0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" C1' G G 21 " pdb=" O4' G G 21 " pdb=" C2' G G 21 " pdb=" N9 G G 21 " both_signs ideal model delta sigma weight residual False 2.44 2.16 0.28 2.00e-01 2.50e+01 1.93e+00 ... (remaining 2846 not shown) Planarity restraints: 3088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 540 " -0.061 2.00e-02 2.50e+03 4.57e-02 3.65e+01 pdb=" CG PHE F 540 " 0.102 2.00e-02 2.50e+03 pdb=" CD1 PHE F 540 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE F 540 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE F 540 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE F 540 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE F 540 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY E 14 " 0.063 5.00e-02 4.00e+02 9.41e-02 1.42e+01 pdb=" N PRO E 15 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO E 15 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO E 15 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 43 " 0.059 5.00e-02 4.00e+02 8.68e-02 1.20e+01 pdb=" N PRO A 44 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO A 44 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 44 " 0.048 5.00e-02 4.00e+02 ... (remaining 3085 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 70 2.44 - 3.05: 12413 3.05 - 3.67: 27375 3.67 - 4.28: 40878 4.28 - 4.90: 66003 Nonbonded interactions: 146739 Sorted by model distance: nonbonded pdb=" ND2 ASN B 57 " pdb=" O2 C G 8 " model vdw 1.822 2.520 nonbonded pdb=" OG SER B 86 " pdb=" O2' G G 5 " model vdw 2.070 2.440 nonbonded pdb=" OH TYR B 2 " pdb=" OE1 GLN H 45 " model vdw 2.177 2.440 nonbonded pdb=" OG SER I 46 " pdb=" OP2 U U 9 " model vdw 2.182 2.440 nonbonded pdb=" O2' G U 21 " pdb=" O5' C U 22 " model vdw 2.211 2.440 ... (remaining 146734 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 23 or resid 33 through 63 or resid 76 through 21 \ 4)) selection = chain 'B' selection = (chain 'C' and (resid 2 through 23 or resid 33 through 63 or resid 76 through 21 \ 4)) } ncs_group { reference = chain 'I' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 15.730 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 56.660 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 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 0.090 18947 Z= 0.357 Angle : 0.884 16.419 25749 Z= 0.535 Chirality : 0.052 0.371 2849 Planarity : 0.005 0.094 3088 Dihedral : 15.848 178.878 7482 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.47 % Allowed : 0.58 % Favored : 98.95 % 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: -1.18 (0.17), residues: 2086 helix: -0.01 (0.16), residues: 926 sheet: -0.42 (0.28), residues: 321 loop : -1.75 (0.19), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP F 339 HIS 0.007 0.001 HIS F 60 PHE 0.102 0.003 PHE F 540 TYR 0.055 0.002 TYR K 86 ARG 0.040 0.001 ARG C 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 375 time to evaluate : 2.322 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: C 137 ARG cc_start: 0.7021 (OUTLIER) cc_final: 0.6566 (ttm170) REVERT: E 119 MET cc_start: 0.7313 (tpp) cc_final: 0.6999 (tpp) REVERT: E 289 LEU cc_start: 0.7281 (mt) cc_final: 0.6794 (tt) REVERT: F 163 MET cc_start: 0.7443 (ptp) cc_final: 0.7050 (tpt) REVERT: F 588 LEU cc_start: 0.8293 (tp) cc_final: 0.8052 (tp) REVERT: F 697 MET cc_start: 0.7188 (mmm) cc_final: 0.6916 (mmm) REVERT: H 258 MET cc_start: -0.0037 (mmm) cc_final: -0.0583 (mmt) REVERT: I 43 LEU cc_start: 0.8394 (tp) cc_final: 0.8112 (tp) REVERT: I 58 LEU cc_start: 0.9499 (mt) cc_final: 0.9086 (mt) REVERT: I 81 LEU cc_start: 0.9526 (tp) cc_final: 0.9092 (tp) REVERT: I 84 LYS cc_start: 0.9569 (mmtm) cc_final: 0.9265 (mmmt) REVERT: I 120 PHE cc_start: 0.9357 (t80) cc_final: 0.9117 (t80) REVERT: K 75 ILE cc_start: 0.9334 (mm) cc_final: 0.8728 (mm) REVERT: K 77 GLU cc_start: 0.9211 (mm-30) cc_final: 0.9007 (mm-30) REVERT: K 87 TYR cc_start: 0.8289 (t80) cc_final: 0.6884 (t80) REVERT: K 137 TYR cc_start: 0.7843 (m-10) cc_final: 0.7469 (m-10) outliers start: 9 outliers final: 2 residues processed: 383 average time/residue: 0.4084 time to fit residues: 218.4343 Evaluate side-chains 168 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 165 time to evaluate : 2.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 137 ARG Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain F residue 384 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 0.4980 chunk 162 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 167 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 194 optimal weight: 0.0470 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 HIS ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 HIS C 168 ASN E 54 ASN ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 560 GLN ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN K 69 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18947 Z= 0.211 Angle : 0.720 11.824 25749 Z= 0.379 Chirality : 0.044 0.214 2849 Planarity : 0.005 0.066 3088 Dihedral : 17.153 179.143 3199 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.74 % Allowed : 10.00 % Favored : 88.26 % 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: -1.01 (0.18), residues: 2086 helix: 0.21 (0.17), residues: 932 sheet: -0.37 (0.27), residues: 364 loop : -1.83 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 339 HIS 0.005 0.001 HIS F 60 PHE 0.045 0.002 PHE I 85 TYR 0.023 0.002 TYR I 126 ARG 0.008 0.001 ARG H 22 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 185 time to evaluate : 2.377 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: E 186 MET cc_start: 0.5601 (mmt) cc_final: 0.5074 (mmt) REVERT: E 190 ARG cc_start: 0.7244 (mtm110) cc_final: 0.6772 (ttm110) REVERT: F 262 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8482 (mp) REVERT: F 588 LEU cc_start: 0.8410 (tp) cc_final: 0.8123 (tp) REVERT: F 624 MET cc_start: 0.4309 (tmm) cc_final: 0.3326 (tpp) REVERT: I 58 LEU cc_start: 0.9558 (mt) cc_final: 0.9291 (mt) REVERT: I 120 PHE cc_start: 0.9379 (t80) cc_final: 0.9110 (t80) REVERT: K 75 ILE cc_start: 0.9027 (mm) cc_final: 0.8791 (mm) REVERT: K 81 LEU cc_start: 0.9600 (tp) cc_final: 0.9395 (tt) REVERT: K 85 PHE cc_start: 0.8952 (m-80) cc_final: 0.8599 (m-80) REVERT: K 113 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8281 (pptt) REVERT: K 137 TYR cc_start: 0.8003 (m-10) cc_final: 0.7752 (m-80) outliers start: 33 outliers final: 12 residues processed: 209 average time/residue: 0.3396 time to fit residues: 104.9651 Evaluate side-chains 149 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 135 time to evaluate : 2.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 125 ASN Chi-restraints excluded: chain E residue 133 SER Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 347 ASP Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 113 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 108 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 161 optimal weight: 0.7980 chunk 132 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 194 optimal weight: 9.9990 chunk 210 optimal weight: 1.9990 chunk 173 optimal weight: 4.9990 chunk 193 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 156 optimal weight: 8.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 ASN ** F 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 549 ASN F 689 HIS ** F 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 206 GLN ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 18947 Z= 0.400 Angle : 0.787 11.850 25749 Z= 0.413 Chirality : 0.046 0.337 2849 Planarity : 0.005 0.069 3088 Dihedral : 16.904 178.897 3191 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 21.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.16 % Allowed : 11.26 % Favored : 85.58 % 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: -1.31 (0.17), residues: 2086 helix: -0.09 (0.16), residues: 928 sheet: -0.55 (0.26), residues: 360 loop : -1.87 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 89 HIS 0.009 0.002 HIS K 18 PHE 0.036 0.002 PHE F 693 TYR 0.029 0.002 TYR E 155 ARG 0.017 0.001 ARG E 242 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 148 time to evaluate : 2.368 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: E 113 LEU cc_start: 0.3182 (OUTLIER) cc_final: 0.2614 (mt) REVERT: E 186 MET cc_start: 0.5739 (mmt) cc_final: 0.5312 (mmt) REVERT: F 1 MET cc_start: 0.6448 (mmt) cc_final: 0.6054 (mmt) REVERT: F 163 MET cc_start: 0.6522 (tpt) cc_final: 0.6196 (tpt) REVERT: F 463 TYR cc_start: 0.7238 (OUTLIER) cc_final: 0.6624 (p90) REVERT: F 624 MET cc_start: 0.4105 (tmm) cc_final: 0.3711 (tpp) REVERT: H 187 LEU cc_start: 0.8374 (mt) cc_final: 0.7891 (tt) REVERT: I 120 PHE cc_start: 0.9411 (t80) cc_final: 0.8991 (t80) REVERT: K 50 ASN cc_start: 0.8722 (m-40) cc_final: 0.8032 (m110) REVERT: K 78 LEU cc_start: 0.9534 (OUTLIER) cc_final: 0.9230 (mm) REVERT: K 137 TYR cc_start: 0.8294 (m-10) cc_final: 0.7980 (m-80) outliers start: 60 outliers final: 37 residues processed: 197 average time/residue: 0.3419 time to fit residues: 100.7190 Evaluate side-chains 167 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 127 time to evaluate : 2.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 133 SER Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 347 ASP Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 463 TYR Chi-restraints excluded: chain F residue 499 TYR Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 570 ASN Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 228 LYS Chi-restraints excluded: chain I residue 16 PHE Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 71 ASN Chi-restraints excluded: chain I residue 73 GLU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 63 PHE Chi-restraints excluded: chain K residue 64 ASN Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 94 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 192 optimal weight: 0.8980 chunk 146 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 130 optimal weight: 0.7980 chunk 195 optimal weight: 3.9990 chunk 206 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 185 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 GLN ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 ASN F 165 HIS ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 ASN K 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18947 Z= 0.224 Angle : 0.645 11.792 25749 Z= 0.340 Chirality : 0.042 0.275 2849 Planarity : 0.004 0.053 3088 Dihedral : 16.693 179.488 3191 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.63 % Allowed : 13.53 % Favored : 83.84 % 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: -1.05 (0.18), residues: 2086 helix: 0.16 (0.17), residues: 928 sheet: -0.40 (0.27), residues: 357 loop : -1.80 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 339 HIS 0.007 0.001 HIS K 18 PHE 0.032 0.002 PHE F 693 TYR 0.020 0.001 TYR E 155 ARG 0.005 0.000 ARG K 91 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 147 time to evaluate : 2.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LYS cc_start: 0.7070 (OUTLIER) cc_final: 0.6830 (mmtt) REVERT: B 131 THR cc_start: 0.9191 (OUTLIER) cc_final: 0.8989 (m) REVERT: E 113 LEU cc_start: 0.3533 (tt) cc_final: 0.3054 (mt) REVERT: E 125 ASN cc_start: 0.8694 (OUTLIER) cc_final: 0.8275 (t0) REVERT: E 186 MET cc_start: 0.5889 (mmt) cc_final: 0.5483 (mmt) REVERT: E 300 MET cc_start: 0.2981 (ppp) cc_final: 0.2725 (ppp) REVERT: F 47 PHE cc_start: 0.6798 (m-80) cc_final: 0.6576 (m-80) REVERT: F 163 MET cc_start: 0.6718 (tpt) cc_final: 0.6270 (tpt) REVERT: F 624 MET cc_start: 0.3993 (tmm) cc_final: 0.3475 (tpp) REVERT: F 697 MET cc_start: 0.4920 (mmt) cc_final: 0.4665 (mmt) REVERT: I 96 ASP cc_start: 0.9070 (OUTLIER) cc_final: 0.8733 (m-30) REVERT: I 120 PHE cc_start: 0.9376 (t80) cc_final: 0.9034 (t80) REVERT: I 124 CYS cc_start: 0.8694 (m) cc_final: 0.8493 (m) outliers start: 50 outliers final: 34 residues processed: 190 average time/residue: 0.3316 time to fit residues: 94.4765 Evaluate side-chains 168 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 130 time to evaluate : 2.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain C residue 189 ASN Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain E residue 125 ASN Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain F residue 347 ASP Chi-restraints excluded: chain F residue 361 ASP Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 570 ASN Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 228 LYS Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 66 ASN Chi-restraints excluded: chain I residue 71 ASN Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 96 ASP Chi-restraints excluded: chain K residue 15 THR Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 63 PHE Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 94 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 172 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 3 optimal weight: 0.0020 chunk 154 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 176 optimal weight: 2.9990 chunk 142 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 105 optimal weight: 8.9990 chunk 185 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 overall best weight: 2.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN ** E 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 HIS ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 ASN F 155 ASN F 472 ASN ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 ASN ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.5203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 18947 Z= 0.312 Angle : 0.675 9.638 25749 Z= 0.359 Chirality : 0.043 0.287 2849 Planarity : 0.004 0.051 3088 Dihedral : 16.640 178.953 3191 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 19.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.63 % Allowed : 14.16 % Favored : 82.21 % 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: -1.06 (0.18), residues: 2086 helix: 0.24 (0.17), residues: 925 sheet: -0.49 (0.27), residues: 359 loop : -1.88 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP H 52 HIS 0.007 0.001 HIS K 18 PHE 0.033 0.002 PHE E 62 TYR 0.032 0.002 TYR I 126 ARG 0.009 0.001 ARG F 279 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 130 time to evaluate : 2.068 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 54 LYS cc_start: 0.7378 (OUTLIER) cc_final: 0.7087 (mmtt) REVERT: F 163 MET cc_start: 0.6901 (tpt) cc_final: 0.6576 (tpt) REVERT: F 463 TYR cc_start: 0.7287 (OUTLIER) cc_final: 0.6565 (p90) REVERT: F 624 MET cc_start: 0.4277 (tmm) cc_final: 0.4029 (tpp) REVERT: H 187 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7817 (tt) REVERT: I 96 ASP cc_start: 0.9107 (m-30) cc_final: 0.8725 (m-30) REVERT: I 120 PHE cc_start: 0.9367 (t80) cc_final: 0.9011 (t80) REVERT: I 124 CYS cc_start: 0.8723 (m) cc_final: 0.8520 (m) REVERT: K 56 ASN cc_start: 0.9008 (m110) cc_final: 0.8755 (m110) REVERT: K 137 TYR cc_start: 0.8204 (m-80) cc_final: 0.7979 (m-80) outliers start: 69 outliers final: 48 residues processed: 188 average time/residue: 0.3452 time to fit residues: 97.6318 Evaluate side-chains 171 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 120 time to evaluate : 2.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain C residue 106 LYS Chi-restraints excluded: chain C residue 189 ASN Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 155 ASN Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 243 THR Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain F residue 347 ASP Chi-restraints excluded: chain F residue 361 ASP Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 463 TYR Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain F residue 499 TYR Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 558 SER Chi-restraints excluded: chain F residue 570 ASN Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 228 LYS Chi-restraints excluded: chain I residue 16 PHE Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 66 ASN Chi-restraints excluded: chain I residue 71 ASN Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 50 ASN Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 63 PHE Chi-restraints excluded: chain K residue 64 ASN Chi-restraints excluded: chain K residue 71 ASN Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 94 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 69 optimal weight: 6.9990 chunk 186 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 207 optimal weight: 8.9990 chunk 171 optimal weight: 0.0050 chunk 95 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 overall best weight: 2.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN ** E 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 ASN F 155 ASN ** F 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 HIS ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 ASN K 37 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.5533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 18947 Z= 0.286 Angle : 0.658 12.106 25749 Z= 0.350 Chirality : 0.043 0.298 2849 Planarity : 0.004 0.093 3088 Dihedral : 16.603 179.281 3191 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.84 % Allowed : 15.42 % Favored : 80.74 % 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: -1.03 (0.18), residues: 2086 helix: 0.31 (0.17), residues: 917 sheet: -0.49 (0.27), residues: 359 loop : -1.89 (0.19), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP E 89 HIS 0.005 0.001 HIS B 110 PHE 0.062 0.002 PHE E 62 TYR 0.015 0.001 TYR E 155 ARG 0.007 0.001 ARG K 91 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 129 time to evaluate : 1.993 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 54 LYS cc_start: 0.7292 (OUTLIER) cc_final: 0.7052 (mmtt) REVERT: F 163 MET cc_start: 0.7102 (tpt) cc_final: 0.6877 (tpt) REVERT: F 352 MET cc_start: 0.7833 (mmm) cc_final: 0.6629 (mmm) REVERT: F 463 TYR cc_start: 0.7459 (OUTLIER) cc_final: 0.6691 (p90) REVERT: F 697 MET cc_start: 0.4519 (mmt) cc_final: 0.4317 (mmt) REVERT: H 187 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.7877 (tt) REVERT: I 96 ASP cc_start: 0.9122 (m-30) cc_final: 0.8747 (m-30) REVERT: I 120 PHE cc_start: 0.9348 (t80) cc_final: 0.8950 (t80) REVERT: I 124 CYS cc_start: 0.8749 (m) cc_final: 0.8515 (m) REVERT: K 14 MET cc_start: 0.6734 (ttt) cc_final: 0.6422 (ttt) REVERT: K 56 ASN cc_start: 0.9062 (m110) cc_final: 0.8776 (m110) outliers start: 73 outliers final: 50 residues processed: 189 average time/residue: 0.3174 time to fit residues: 91.3871 Evaluate side-chains 169 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 116 time to evaluate : 2.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 106 LYS Chi-restraints excluded: chain C residue 189 ASN Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 243 THR Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain F residue 347 ASP Chi-restraints excluded: chain F residue 361 ASP Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 463 TYR Chi-restraints excluded: chain F residue 478 ILE Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 558 SER Chi-restraints excluded: chain F residue 570 ASN Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 228 LYS Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 66 ASN Chi-restraints excluded: chain I residue 71 ASN Chi-restraints excluded: chain I residue 73 GLU Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 50 ASN Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 71 ASN Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 94 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 199 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 151 optimal weight: 8.9990 chunk 174 optimal weight: 8.9990 chunk 115 optimal weight: 0.9990 chunk 206 optimal weight: 0.6980 chunk 129 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 127 optimal weight: 0.6980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 HIS ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 ASN ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 ASN ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 ASN F 155 ASN ** F 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.5813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18947 Z= 0.237 Angle : 0.631 11.337 25749 Z= 0.336 Chirality : 0.042 0.291 2849 Planarity : 0.004 0.072 3088 Dihedral : 16.488 179.384 3191 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.79 % Allowed : 16.37 % Favored : 79.84 % 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: -0.93 (0.18), residues: 2086 helix: 0.38 (0.17), residues: 917 sheet: -0.48 (0.27), residues: 363 loop : -1.81 (0.19), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP E 89 HIS 0.004 0.001 HIS B 110 PHE 0.060 0.002 PHE E 62 TYR 0.018 0.001 TYR E 59 ARG 0.011 0.001 ARG E 190 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 123 time to evaluate : 2.255 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 54 LYS cc_start: 0.7316 (OUTLIER) cc_final: 0.7091 (mmtt) REVERT: E 125 ASN cc_start: 0.8827 (OUTLIER) cc_final: 0.8476 (t0) REVERT: F 463 TYR cc_start: 0.7459 (OUTLIER) cc_final: 0.6709 (p90) REVERT: F 697 MET cc_start: 0.4544 (mmt) cc_final: 0.4325 (mmt) REVERT: H 187 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.7996 (tt) REVERT: I 86 TYR cc_start: 0.9250 (m-10) cc_final: 0.8971 (m-10) REVERT: I 96 ASP cc_start: 0.9080 (m-30) cc_final: 0.8709 (m-30) REVERT: I 120 PHE cc_start: 0.9334 (t80) cc_final: 0.8959 (t80) REVERT: I 124 CYS cc_start: 0.8737 (m) cc_final: 0.8489 (m) REVERT: K 14 MET cc_start: 0.7100 (ttt) cc_final: 0.6727 (ttm) REVERT: K 56 ASN cc_start: 0.9010 (m110) cc_final: 0.8720 (m110) REVERT: K 78 LEU cc_start: 0.9571 (OUTLIER) cc_final: 0.9291 (mm) outliers start: 72 outliers final: 46 residues processed: 186 average time/residue: 0.3323 time to fit residues: 94.7139 Evaluate side-chains 163 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 112 time to evaluate : 2.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 189 ASN Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 ASN Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain F residue 155 ASN Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 347 ASP Chi-restraints excluded: chain F residue 361 ASP Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 463 TYR Chi-restraints excluded: chain F residue 478 ILE Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 558 SER Chi-restraints excluded: chain F residue 570 ASN Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 66 ASN Chi-restraints excluded: chain I residue 71 ASN Chi-restraints excluded: chain I residue 73 GLU Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 50 ASN Chi-restraints excluded: chain K residue 71 ASN Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 94 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 82 optimal weight: 0.1980 chunk 123 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 140 optimal weight: 0.0370 chunk 101 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 162 optimal weight: 4.9990 chunk 187 optimal weight: 0.7980 overall best weight: 0.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 ASN F 155 ASN ** F 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 87 HIS ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 ASN K 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.5976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18947 Z= 0.169 Angle : 0.632 12.216 25749 Z= 0.328 Chirality : 0.042 0.275 2849 Planarity : 0.004 0.065 3088 Dihedral : 16.396 179.036 3191 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.53 % Allowed : 17.58 % Favored : 79.89 % 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: -0.82 (0.18), residues: 2086 helix: 0.39 (0.17), residues: 923 sheet: -0.33 (0.28), residues: 363 loop : -1.70 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 89 HIS 0.005 0.001 HIS F 165 PHE 0.063 0.001 PHE E 62 TYR 0.032 0.001 TYR F 156 ARG 0.012 0.000 ARG K 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 126 time to evaluate : 2.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LYS cc_start: 0.7163 (OUTLIER) cc_final: 0.6962 (mmtt) REVERT: E 125 ASN cc_start: 0.8707 (OUTLIER) cc_final: 0.8377 (t0) REVERT: E 186 MET cc_start: 0.7092 (tpp) cc_final: 0.6756 (tpp) REVERT: F 155 ASN cc_start: 0.8769 (OUTLIER) cc_final: 0.8532 (t160) REVERT: F 463 TYR cc_start: 0.7375 (OUTLIER) cc_final: 0.6632 (p90) REVERT: F 624 MET cc_start: 0.4623 (OUTLIER) cc_final: 0.2260 (mpp) REVERT: H 187 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7978 (tt) REVERT: I 14 MET cc_start: 0.3679 (ppp) cc_final: 0.3407 (ppp) REVERT: I 86 TYR cc_start: 0.9170 (m-10) cc_final: 0.8930 (m-10) REVERT: I 96 ASP cc_start: 0.9023 (m-30) cc_final: 0.8676 (m-30) REVERT: I 120 PHE cc_start: 0.9294 (t80) cc_final: 0.8930 (t80) REVERT: I 124 CYS cc_start: 0.8700 (m) cc_final: 0.8448 (m) REVERT: K 14 MET cc_start: 0.7440 (ttt) cc_final: 0.7072 (ttm) REVERT: K 56 ASN cc_start: 0.8973 (m110) cc_final: 0.8657 (m110) outliers start: 48 outliers final: 34 residues processed: 166 average time/residue: 0.3218 time to fit residues: 80.9337 Evaluate side-chains 154 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 114 time to evaluate : 2.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain C residue 106 LYS Chi-restraints excluded: chain C residue 189 ASN Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 ASN Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain F residue 155 ASN Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain F residue 361 ASP Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 463 TYR Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 558 SER Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain F residue 624 MET Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 228 LYS Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 66 ASN Chi-restraints excluded: chain I residue 73 GLU Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 71 ASN Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 86 TYR Chi-restraints excluded: chain K residue 94 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 197 optimal weight: 0.4980 chunk 180 optimal weight: 0.7980 chunk 192 optimal weight: 7.9990 chunk 115 optimal weight: 0.9980 chunk 83 optimal weight: 0.4980 chunk 150 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 173 optimal weight: 0.8980 chunk 181 optimal weight: 0.7980 chunk 191 optimal weight: 8.9990 chunk 126 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN E 86 GLN ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 ASN F 155 ASN ** F 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 472 ASN ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 ASN K 37 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.6116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 18947 Z= 0.165 Angle : 0.643 13.643 25749 Z= 0.330 Chirality : 0.042 0.262 2849 Planarity : 0.004 0.060 3088 Dihedral : 16.307 178.863 3191 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.37 % Allowed : 17.89 % Favored : 79.74 % 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: -0.80 (0.18), residues: 2086 helix: 0.38 (0.17), residues: 937 sheet: -0.27 (0.28), residues: 359 loop : -1.72 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP E 89 HIS 0.009 0.001 HIS H 87 PHE 0.060 0.001 PHE E 62 TYR 0.037 0.001 TYR F 156 ARG 0.007 0.000 ARG K 91 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 123 time to evaluate : 2.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 125 ASN cc_start: 0.8662 (OUTLIER) cc_final: 0.8339 (t0) REVERT: E 186 MET cc_start: 0.7138 (tpp) cc_final: 0.6797 (tpp) REVERT: F 163 MET cc_start: 0.7469 (tpp) cc_final: 0.7051 (tpt) REVERT: F 463 TYR cc_start: 0.7364 (OUTLIER) cc_final: 0.6642 (p90) REVERT: F 624 MET cc_start: 0.4684 (OUTLIER) cc_final: 0.2679 (mpp) REVERT: H 187 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7922 (tt) REVERT: I 14 MET cc_start: 0.3754 (ppp) cc_final: 0.3479 (ppp) REVERT: I 86 TYR cc_start: 0.9172 (m-10) cc_final: 0.8938 (m-10) REVERT: I 96 ASP cc_start: 0.8918 (m-30) cc_final: 0.8606 (m-30) REVERT: I 120 PHE cc_start: 0.9286 (t80) cc_final: 0.8930 (t80) REVERT: I 124 CYS cc_start: 0.8673 (m) cc_final: 0.8420 (m) REVERT: K 14 MET cc_start: 0.7392 (ttt) cc_final: 0.7153 (ttm) REVERT: K 56 ASN cc_start: 0.8964 (m110) cc_final: 0.8609 (m110) outliers start: 45 outliers final: 34 residues processed: 160 average time/residue: 0.3230 time to fit residues: 79.4275 Evaluate side-chains 154 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 116 time to evaluate : 2.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain C residue 106 LYS Chi-restraints excluded: chain C residue 189 ASN Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 ASN Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 347 ASP Chi-restraints excluded: chain F residue 361 ASP Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 463 TYR Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 558 SER Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain F residue 624 MET Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 66 ASN Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 50 ASN Chi-restraints excluded: chain K residue 71 ASN Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 86 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 203 optimal weight: 0.0980 chunk 124 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 141 optimal weight: 0.7980 chunk 213 optimal weight: 9.9990 chunk 196 optimal weight: 4.9990 chunk 169 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 134 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN E 316 ASN ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 ASN F 155 ASN ** F 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 ASN K 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.6227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 18947 Z= 0.159 Angle : 0.637 13.135 25749 Z= 0.326 Chirality : 0.042 0.257 2849 Planarity : 0.004 0.056 3088 Dihedral : 16.240 178.951 3191 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.37 % Allowed : 17.89 % Favored : 79.74 % 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 (0.18), residues: 2086 helix: 0.47 (0.17), residues: 921 sheet: -0.14 (0.29), residues: 354 loop : -1.67 (0.20), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP E 89 HIS 0.004 0.001 HIS H 87 PHE 0.062 0.001 PHE E 62 TYR 0.028 0.001 TYR K 87 ARG 0.010 0.000 ARG K 91 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 115 time to evaluate : 2.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LYS cc_start: 0.7022 (OUTLIER) cc_final: 0.6780 (mmtt) REVERT: A 68 LYS cc_start: 0.7374 (OUTLIER) cc_final: 0.7040 (tmtt) REVERT: E 125 ASN cc_start: 0.8608 (OUTLIER) cc_final: 0.8286 (t0) REVERT: E 186 MET cc_start: 0.7087 (tpp) cc_final: 0.6861 (tpp) REVERT: F 163 MET cc_start: 0.7476 (tpp) cc_final: 0.6999 (tpt) REVERT: F 463 TYR cc_start: 0.7522 (OUTLIER) cc_final: 0.6773 (p90) REVERT: F 624 MET cc_start: 0.4455 (tpp) cc_final: 0.2507 (mpp) REVERT: H 187 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7880 (tt) REVERT: I 14 MET cc_start: 0.3861 (ppp) cc_final: 0.3576 (ppp) REVERT: I 86 TYR cc_start: 0.9152 (m-10) cc_final: 0.8927 (m-10) REVERT: I 96 ASP cc_start: 0.8911 (m-30) cc_final: 0.8585 (m-30) REVERT: I 120 PHE cc_start: 0.9268 (t80) cc_final: 0.8932 (t80) REVERT: I 124 CYS cc_start: 0.8662 (m) cc_final: 0.8369 (m) REVERT: K 14 MET cc_start: 0.7657 (ttt) cc_final: 0.7378 (ttm) REVERT: K 56 ASN cc_start: 0.8961 (m110) cc_final: 0.8626 (m110) REVERT: K 78 LEU cc_start: 0.9559 (OUTLIER) cc_final: 0.9281 (mm) REVERT: K 98 PHE cc_start: 0.8081 (t80) cc_final: 0.7479 (t80) REVERT: K 120 PHE cc_start: 0.8501 (t80) cc_final: 0.8252 (t80) outliers start: 45 outliers final: 30 residues processed: 154 average time/residue: 0.3440 time to fit residues: 83.0303 Evaluate side-chains 150 residues out of total 1900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 114 time to evaluate : 2.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain C residue 106 LYS Chi-restraints excluded: chain C residue 189 ASN Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain E residue 125 ASN Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain F residue 262 ILE Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 361 ASP Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 463 TYR Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 558 SER Chi-restraints excluded: chain F residue 601 SER Chi-restraints excluded: chain H residue 7 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 66 ASN Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 71 ASN Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 86 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 156 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 170 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 174 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 HIS ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 ASN ** E 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 316 ASN ** E 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 ASN ** F 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 ASN ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 ASN K 37 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.056225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.043344 restraints weight = 134600.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.044723 restraints weight = 78236.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.045570 restraints weight = 54631.824| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.6706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 18947 Z= 0.401 Angle : 0.788 15.284 25749 Z= 0.411 Chirality : 0.045 0.306 2849 Planarity : 0.005 0.056 3088 Dihedral : 16.519 177.871 3191 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 23.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 2.68 % Allowed : 17.58 % Favored : 79.74 % 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: -1.03 (0.18), residues: 2086 helix: 0.27 (0.17), residues: 916 sheet: -0.39 (0.28), residues: 339 loop : -1.85 (0.19), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP E 89 HIS 0.006 0.002 HIS H 218 PHE 0.077 0.002 PHE E 62 TYR 0.024 0.002 TYR I 126 ARG 0.012 0.001 ARG K 91 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3548.03 seconds wall clock time: 66 minutes 34.83 seconds (3994.83 seconds total)