Starting phenix.real_space_refine on Sat Feb 17 13:11:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6loe_0937/02_2024/6loe_0937_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6loe_0937/02_2024/6loe_0937.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6loe_0937/02_2024/6loe_0937.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6loe_0937/02_2024/6loe_0937.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6loe_0937/02_2024/6loe_0937_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6loe_0937/02_2024/6loe_0937_updated.pdb" } resolution = 3.5 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= 0.000 sd= 0.008 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 Fe 21 7.16 5 S 106 5.16 5 C 12235 2.51 5 N 3163 2.21 5 O 3260 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 104": "NH1" <-> "NH2" Residue "A GLU 211": "OE1" <-> "OE2" Residue "A GLU 217": "OE1" <-> "OE2" Residue "B GLU 98": "OE1" <-> "OE2" Residue "B GLU 133": "OE1" <-> "OE2" Residue "B GLU 228": "OE1" <-> "OE2" Residue "B ARG 232": "NH1" <-> "NH2" Residue "B ARG 240": "NH1" <-> "NH2" Residue "B GLU 399": "OE1" <-> "OE2" Residue "B ARG 540": "NH1" <-> "NH2" Residue "B ARG 560": "NH1" <-> "NH2" Residue "B ARG 719": "NH1" <-> "NH2" Residue "B GLU 734": "OE1" <-> "OE2" Residue "B GLU 742": "OE1" <-> "OE2" Residue "B GLU 752": "OE1" <-> "OE2" Residue "B ARG 803": "NH1" <-> "NH2" Residue "B GLU 1006": "OE1" <-> "OE2" Residue "C GLU 16": "OE1" <-> "OE2" Residue "C ARG 116": "NH1" <-> "NH2" Residue "C ARG 165": "NH1" <-> "NH2" Residue "C GLU 325": "OE1" <-> "OE2" Residue "C ARG 371": "NH1" <-> "NH2" Residue "C PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 449": "OE1" <-> "OE2" Residue "C GLU 458": "OE1" <-> "OE2" Residue "D GLU 31": "OE1" <-> "OE2" Residue "D GLU 49": "OE1" <-> "OE2" Residue "D ARG 66": "NH1" <-> "NH2" Residue "D GLU 171": "OE1" <-> "OE2" Residue "D ARG 176": "NH1" <-> "NH2" Residue "E GLU 103": "OE1" <-> "OE2" Residue "E GLU 150": "OE1" <-> "OE2" Residue "E TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 184": "OE1" <-> "OE2" Residue "F GLU 5": "OE1" <-> "OE2" Residue "F ARG 15": "NH1" <-> "NH2" Residue "F ARG 79": "NH1" <-> "NH2" Residue "F GLU 102": "OE1" <-> "OE2" Residue "F GLU 117": "OE1" <-> "OE2" Residue "F GLU 123": "OE1" <-> "OE2" Residue "F ARG 156": "NH1" <-> "NH2" Residue "F GLU 162": "OE1" <-> "OE2" Residue "F ARG 172": "NH1" <-> "NH2" Residue "F GLU 204": "OE1" <-> "OE2" Residue "F GLU 294": "OE1" <-> "OE2" Residue "F ARG 320": "NH1" <-> "NH2" Residue "F ARG 379": "NH1" <-> "NH2" Residue "F ARG 389": "NH1" <-> "NH2" Residue "F ARG 394": "NH1" <-> "NH2" Residue "F GLU 397": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18785 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1763 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "B" Number of atoms: 7176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 929, 7176 Classifications: {'peptide': 929} Link IDs: {'PTRANS': 54, 'TRANS': 874} Chain: "C" Number of atoms: 3728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3728 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 22, 'TRANS': 433} Chain: "D" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1348 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 13, 'TRANS': 160} Chain: "E" Number of atoms: 1253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1253 Unusual residues: {'ACE': 1} Classifications: {'peptide': 157, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 11, 'TRANS': 145} Chain: "F" Number of atoms: 3159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3159 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 21, 'TRANS': 373} Chain: "A" Number of atoms: 215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 215 Unusual residues: {'HEC': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {'EL6': 1, 'F3S': 1, 'SF4': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "E" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'EL6': 1, 'HEC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7079 SG CYS B 772 44.642 62.351 45.588 1.00 5.32 S ATOM 8511 SG CYS B 952 44.756 61.852 50.721 1.00 6.62 S ATOM 7098 SG CYS B 775 49.722 62.205 47.271 1.00 5.50 S ATOM 7059 SG CYS B 769 47.536 57.136 48.142 1.00 6.47 S ATOM 8265 SG CYS B 921 55.418 69.826 53.259 1.00 5.04 S ATOM 8241 SG CYS B 918 57.887 64.114 52.522 1.00 6.02 S ATOM 7123 SG CYS B 779 56.767 67.351 48.402 1.00 5.35 S ATOM 8480 SG CYS B 948 52.480 64.905 52.339 1.00 5.40 S ATOM 7499 SG CYS B 824 63.216 61.122 54.019 1.00 5.24 S ATOM 7560 SG CYS B 832 68.738 59.364 54.348 1.00 3.74 S ATOM 7813 SG CYS B 866 66.309 56.854 50.988 1.00 5.53 S ATOM 7523 SG CYS B 827 64.450 56.126 56.803 1.00 4.46 S ATOM 7785 SG CYS B 862 72.524 61.822 49.307 1.00 5.33 S ATOM 7740 SG CYS B 856 73.695 67.329 47.823 1.00 5.51 S ATOM 7590 SG CYS B 836 76.283 64.552 52.718 1.00 5.66 S Time building chain proxies: 10.44, per 1000 atoms: 0.56 Number of scatterers: 18785 At special positions: 0 Unit cell: (161.2, 131.04, 95.68, 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) Fe 21 26.01 S 106 16.00 O 3260 8.00 N 3163 7.00 C 12235 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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=21, symmetry=0 Number of additional bonds: simple=21, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.54 Conformation dependent library (CDL) restraints added in 3.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S B1104 " pdb="FE1 F3S B1104 " - pdb=" SG CYS B 862 " pdb="FE3 F3S B1104 " - pdb=" SG CYS B 856 " pdb="FE4 F3S B1104 " - pdb=" SG CYS B 836 " pdb=" SF4 B1101 " pdb="FE2 SF4 B1101 " - pdb=" SG CYS B 952 " pdb="FE3 SF4 B1101 " - pdb=" SG CYS B 775 " pdb="FE1 SF4 B1101 " - pdb=" SG CYS B 772 " pdb="FE4 SF4 B1101 " - pdb=" SG CYS B 769 " pdb=" SF4 B1102 " pdb="FE3 SF4 B1102 " - pdb=" SG CYS B 779 " pdb="FE2 SF4 B1102 " - pdb=" SG CYS B 918 " pdb="FE1 SF4 B1102 " - pdb=" SG CYS B 921 " pdb="FE4 SF4 B1102 " - pdb=" SG CYS B 948 " pdb=" SF4 B1103 " pdb="FE2 SF4 B1103 " - pdb=" SG CYS B 832 " pdb="FE4 SF4 B1103 " - pdb=" SG CYS B 827 " pdb="FE3 SF4 B1103 " - pdb=" SG CYS B 866 " pdb="FE1 SF4 B1103 " - pdb=" SG CYS B 824 " Number of angles added : 45 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4306 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 95 helices and 7 sheets defined 41.9% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.03 Creating SS restraints... Processing helix chain 'A' and resid 13 through 24 removed outlier: 3.563A pdb=" N THR A 17 " --> pdb=" O ARG A 14 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU A 18 " --> pdb=" O ALA A 15 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N VAL A 21 " --> pdb=" O LEU A 18 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N SER A 22 " --> pdb=" O ALA A 19 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE A 23 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N PHE A 24 " --> pdb=" O VAL A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 42 removed outlier: 3.544A pdb=" N LEU A 40 " --> pdb=" O GLY A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 69 removed outlier: 3.807A pdb=" N LEU A 69 " --> pdb=" O LEU A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 98 removed outlier: 3.968A pdb=" N CYS A 97 " --> pdb=" O THR A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 115 Processing helix chain 'A' and resid 154 through 156 No H-bonds generated for 'chain 'A' and resid 154 through 156' Processing helix chain 'A' and resid 171 through 175 Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 203 through 210 removed outlier: 3.817A pdb=" N GLN A 208 " --> pdb=" O ARG A 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 156 removed outlier: 4.021A pdb=" N THR B 155 " --> pdb=" O MET B 152 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N MET B 156 " --> pdb=" O ILE B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 187 removed outlier: 3.511A pdb=" N ALA B 179 " --> pdb=" O ASP B 175 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA B 183 " --> pdb=" O ALA B 179 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA B 184 " --> pdb=" O ALA B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 218 Processing helix chain 'B' and resid 235 through 243 removed outlier: 3.679A pdb=" N ARG B 240 " --> pdb=" O ASN B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 281 removed outlier: 3.707A pdb=" N LEU B 280 " --> pdb=" O MET B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 331 removed outlier: 4.492A pdb=" N ARG B 326 " --> pdb=" O GLU B 322 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA B 327 " --> pdb=" O HIS B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 359 Processing helix chain 'B' and resid 375 through 385 Processing helix chain 'B' and resid 409 through 422 removed outlier: 3.508A pdb=" N GLU B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ALA B 421 " --> pdb=" O GLN B 417 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLY B 422 " --> pdb=" O GLU B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 437 No H-bonds generated for 'chain 'B' and resid 434 through 437' Processing helix chain 'B' and resid 444 through 447 No H-bonds generated for 'chain 'B' and resid 444 through 447' Processing helix chain 'B' and resid 487 through 489 No H-bonds generated for 'chain 'B' and resid 487 through 489' Processing helix chain 'B' and resid 507 through 515 removed outlier: 4.232A pdb=" N VAL B 513 " --> pdb=" O GLU B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 533 removed outlier: 4.583A pdb=" N THR B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 548 removed outlier: 3.515A pdb=" N ASN B 544 " --> pdb=" O ARG B 540 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR B 545 " --> pdb=" O VAL B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 603 No H-bonds generated for 'chain 'B' and resid 600 through 603' Processing helix chain 'B' and resid 622 through 625 No H-bonds generated for 'chain 'B' and resid 622 through 625' Processing helix chain 'B' and resid 681 through 684 removed outlier: 3.552A pdb=" N LEU B 684 " --> pdb=" O ALA B 681 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 681 through 684' Processing helix chain 'B' and resid 766 through 768 No H-bonds generated for 'chain 'B' and resid 766 through 768' Processing helix chain 'B' and resid 774 through 783 Processing helix chain 'B' and resid 790 through 793 No H-bonds generated for 'chain 'B' and resid 790 through 793' Processing helix chain 'B' and resid 861 through 865 Processing helix chain 'B' and resid 899 through 901 No H-bonds generated for 'chain 'B' and resid 899 through 901' Processing helix chain 'B' and resid 922 through 934 removed outlier: 3.907A pdb=" N GLU B 927 " --> pdb=" O GLN B 923 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN B 931 " --> pdb=" O GLU B 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 1002 through 1005 No H-bonds generated for 'chain 'B' and resid 1002 through 1005' Processing helix chain 'C' and resid 12 through 15 No H-bonds generated for 'chain 'C' and resid 12 through 15' Processing helix chain 'C' and resid 25 through 35 removed outlier: 3.505A pdb=" N ILE C 32 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE C 35 " --> pdb=" O THR C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 71 removed outlier: 4.431A pdb=" N ILE C 53 " --> pdb=" O VAL C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'C' and resid 86 through 105 removed outlier: 3.630A pdb=" N PHE C 91 " --> pdb=" O ASP C 87 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HIS C 99 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ALA C 100 " --> pdb=" O GLY C 96 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY C 101 " --> pdb=" O ILE C 97 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR C 102 " --> pdb=" O GLY C 98 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE C 104 " --> pdb=" O ALA C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 110 No H-bonds generated for 'chain 'C' and resid 107 through 110' Processing helix chain 'C' and resid 121 through 132 removed outlier: 4.115A pdb=" N MET C 126 " --> pdb=" O ALA C 122 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE C 128 " --> pdb=" O GLU C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 140 No H-bonds generated for 'chain 'C' and resid 137 through 140' Processing helix chain 'C' and resid 145 through 147 No H-bonds generated for 'chain 'C' and resid 145 through 147' Processing helix chain 'C' and resid 149 through 151 No H-bonds generated for 'chain 'C' and resid 149 through 151' Processing helix chain 'C' and resid 167 through 182 removed outlier: 3.668A pdb=" N VAL C 172 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE C 173 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER C 176 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR C 177 " --> pdb=" O PHE C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 199 Proline residue: C 192 - end of helix Processing helix chain 'C' and resid 207 through 213 Processing helix chain 'C' and resid 221 through 254 removed outlier: 3.555A pdb=" N ASN C 225 " --> pdb=" O ALA C 221 " (cutoff:3.500A) Proline residue: C 240 - end of helix removed outlier: 3.781A pdb=" N HIS C 246 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER C 247 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE C 253 " --> pdb=" O ILE C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 291 Proline residue: C 267 - end of helix removed outlier: 3.641A pdb=" N PHE C 270 " --> pdb=" O PRO C 267 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N VAL C 271 " --> pdb=" O PRO C 268 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA C 272 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL C 275 " --> pdb=" O ALA C 272 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N CYS C 277 " --> pdb=" O ALA C 274 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY C 278 " --> pdb=" O VAL C 275 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE C 279 " --> pdb=" O TYR C 276 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N VAL C 287 " --> pdb=" O LEU C 284 " (cutoff:3.500A) Proline residue: C 288 - end of helix Processing helix chain 'C' and resid 301 through 321 removed outlier: 3.995A pdb=" N VAL C 317 " --> pdb=" O ALA C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 331 Processing helix chain 'C' and resid 335 through 344 removed outlier: 3.557A pdb=" N LEU C 340 " --> pdb=" O TYR C 336 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 360 removed outlier: 4.236A pdb=" N LEU C 359 " --> pdb=" O ALA C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 368 removed outlier: 3.616A pdb=" N LEU C 367 " --> pdb=" O PRO C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 372 No H-bonds generated for 'chain 'C' and resid 370 through 372' Processing helix chain 'C' and resid 376 through 402 removed outlier: 3.684A pdb=" N ARG C 394 " --> pdb=" O MET C 390 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU C 400 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER C 401 " --> pdb=" O ILE C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 410 No H-bonds generated for 'chain 'C' and resid 408 through 410' Processing helix chain 'C' and resid 418 through 441 removed outlier: 3.587A pdb=" N LEU C 423 " --> pdb=" O TRP C 419 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY C 426 " --> pdb=" O SER C 422 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLY C 429 " --> pdb=" O ALA C 425 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU C 434 " --> pdb=" O TRP C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 451 No H-bonds generated for 'chain 'C' and resid 448 through 451' Processing helix chain 'C' and resid 455 through 463 removed outlier: 4.028A pdb=" N LEU C 463 " --> pdb=" O THR C 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 38 Processing helix chain 'D' and resid 70 through 82 Processing helix chain 'D' and resid 86 through 94 Processing helix chain 'D' and resid 101 through 103 No H-bonds generated for 'chain 'D' and resid 101 through 103' Processing helix chain 'D' and resid 113 through 117 Processing helix chain 'D' and resid 120 through 133 removed outlier: 3.595A pdb=" N MET D 132 " --> pdb=" O ALA D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 153 No H-bonds generated for 'chain 'D' and resid 151 through 153' Processing helix chain 'D' and resid 174 through 181 Processing helix chain 'E' and resid 99 through 111 removed outlier: 3.927A pdb=" N GLU E 103 " --> pdb=" O PRO E 99 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG E 104 " --> pdb=" O GLU E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 117 removed outlier: 4.085A pdb=" N HIS E 117 " --> pdb=" O ALA E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 130 No H-bonds generated for 'chain 'E' and resid 128 through 130' Processing helix chain 'E' and resid 141 through 144 No H-bonds generated for 'chain 'E' and resid 141 through 144' Processing helix chain 'E' and resid 148 through 157 removed outlier: 3.614A pdb=" N LEU E 155 " --> pdb=" O TYR E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 187 removed outlier: 3.658A pdb=" N VAL E 179 " --> pdb=" O ARG E 175 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LYS E 187 " --> pdb=" O ARG E 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 35 removed outlier: 3.886A pdb=" N MET F 28 " --> pdb=" O GLY F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 57 removed outlier: 4.175A pdb=" N PHE F 43 " --> pdb=" O ALA F 39 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE F 48 " --> pdb=" O HIS F 44 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TRP F 53 " --> pdb=" O ALA F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 69 Processing helix chain 'F' and resid 73 through 76 No H-bonds generated for 'chain 'F' and resid 73 through 76' Processing helix chain 'F' and resid 79 through 95 removed outlier: 3.536A pdb=" N GLU F 83 " --> pdb=" O ARG F 79 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA F 85 " --> pdb=" O LEU F 81 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N LEU F 89 " --> pdb=" O ALA F 85 " (cutoff:3.500A) Proline residue: F 90 - end of helix removed outlier: 3.889A pdb=" N ILE F 94 " --> pdb=" O PRO F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 104 Processing helix chain 'F' and resid 112 through 114 No H-bonds generated for 'chain 'F' and resid 112 through 114' Processing helix chain 'F' and resid 118 through 121 No H-bonds generated for 'chain 'F' and resid 118 through 121' Processing helix chain 'F' and resid 134 through 164 removed outlier: 4.185A pdb=" N ILE F 149 " --> pdb=" O PHE F 145 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG F 156 " --> pdb=" O ALA F 152 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER F 159 " --> pdb=" O LEU F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 191 Proline residue: F 181 - end of helix removed outlier: 3.791A pdb=" N VAL F 184 " --> pdb=" O GLY F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 202 No H-bonds generated for 'chain 'F' and resid 200 through 202' Processing helix chain 'F' and resid 210 through 235 removed outlier: 3.741A pdb=" N TYR F 214 " --> pdb=" O TYR F 210 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE F 215 " --> pdb=" O PRO F 211 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER F 217 " --> pdb=" O THR F 213 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE F 220 " --> pdb=" O ALA F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 275 removed outlier: 3.515A pdb=" N HIS F 249 " --> pdb=" O VAL F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 287 Processing helix chain 'F' and resid 293 through 302 removed outlier: 3.614A pdb=" N MET F 300 " --> pdb=" O LEU F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 313 removed outlier: 3.664A pdb=" N LEU F 312 " --> pdb=" O PRO F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 346 removed outlier: 3.723A pdb=" N ALA F 326 " --> pdb=" O ALA F 322 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE F 327 " --> pdb=" O ASN F 323 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL F 337 " --> pdb=" O LEU F 333 " (cutoff:3.500A) Proline residue: F 345 - end of helix Processing helix chain 'F' and resid 357 through 360 No H-bonds generated for 'chain 'F' and resid 357 through 360' Processing helix chain 'F' and resid 362 through 378 Processing helix chain 'F' and resid 390 through 394 Processing sheet with id= A, first strand: chain 'B' and resid 248 through 251 Processing sheet with id= B, first strand: chain 'B' and resid 426 through 429 removed outlier: 7.132A pdb=" N LEU B 453 " --> pdb=" O LEU B 427 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N MET B 429 " --> pdb=" O LEU B 453 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N MET B 455 " --> pdb=" O MET B 429 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 581 through 586 Processing sheet with id= D, first strand: chain 'B' and resid 616 through 619 removed outlier: 7.727A pdb=" N MET B 619 " --> pdb=" O PRO B 647 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N TRP B 649 " --> pdb=" O MET B 619 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 760 through 764 Processing sheet with id= F, first strand: chain 'B' and resid 120 through 124 removed outlier: 3.721A pdb=" N LYS B 131 " --> pdb=" O GLU B 123 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 159 through 164 removed outlier: 6.978A pdb=" N VAL D 190 " --> pdb=" O TYR D 21 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU D 23 " --> pdb=" O SER D 188 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N SER D 188 " --> pdb=" O LEU D 23 " (cutoff:3.500A) 523 hydrogen bonds defined for protein. 1509 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.25 Time building geometry restraints manager: 8.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.79: 19210 1.79 - 2.40: 161 2.40 - 3.01: 0 3.01 - 3.61: 0 3.61 - 4.22: 3 Bond restraints: 19374 Sorted by residual: bond pdb=" S4 F3S B1104 " pdb="FE1 F3S B1104 " ideal model delta sigma weight residual 2.233 4.217 -1.984 2.00e-02 2.50e+03 9.84e+03 bond pdb=" S1 F3S B1104 " pdb="FE4 F3S B1104 " ideal model delta sigma weight residual 2.258 4.212 -1.954 2.00e-02 2.50e+03 9.55e+03 bond pdb=" S2 F3S B1104 " pdb="FE3 F3S B1104 " ideal model delta sigma weight residual 2.300 4.221 -1.921 2.00e-02 2.50e+03 9.23e+03 bond pdb=" S2 F3S B1104 " pdb="FE4 F3S B1104 " ideal model delta sigma weight residual 2.317 2.205 0.112 2.00e-02 2.50e+03 3.13e+01 bond pdb=" S3 F3S B1104 " pdb="FE1 F3S B1104 " ideal model delta sigma weight residual 2.296 2.193 0.103 2.00e-02 2.50e+03 2.66e+01 ... (remaining 19369 not shown) Histogram of bond angle deviations from ideal: 40.58 - 68.16: 6 68.16 - 95.74: 69 95.74 - 123.32: 25244 123.32 - 150.90: 1191 150.90 - 178.48: 12 Bond angle restraints: 26522 Sorted by residual: angle pdb=" S1 F3S B1104 " pdb="FE4 F3S B1104 " pdb=" S3 F3S B1104 " ideal model delta sigma weight residual 114.75 40.58 74.17 3.00e+00 1.11e-01 6.11e+02 angle pdb=" S3 F3S B1104 " pdb="FE1 F3S B1104 " pdb=" S4 F3S B1104 " ideal model delta sigma weight residual 112.59 40.74 71.85 3.00e+00 1.11e-01 5.74e+02 angle pdb=" S1 F3S B1104 " pdb="FE3 F3S B1104 " pdb=" S4 F3S B1104 " ideal model delta sigma weight residual 112.54 145.94 -33.40 3.00e+00 1.11e-01 1.24e+02 angle pdb="FE1 F3S B1104 " pdb=" S4 F3S B1104 " pdb="FE3 F3S B1104 " ideal model delta sigma weight residual 74.86 44.67 30.19 3.00e+00 1.11e-01 1.01e+02 angle pdb=" S1 F3S B1104 " pdb="FE4 F3S B1104 " pdb=" S2 F3S B1104 " ideal model delta sigma weight residual 103.63 74.90 28.73 3.00e+00 1.11e-01 9.17e+01 ... (remaining 26517 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.86: 10509 25.86 - 51.72: 545 51.72 - 77.58: 53 77.58 - 103.44: 16 103.44 - 129.31: 4 Dihedral angle restraints: 11127 sinusoidal: 4407 harmonic: 6720 Sorted by residual: dihedral pdb=" C PRO B 588 " pdb=" N PRO B 588 " pdb=" CA PRO B 588 " pdb=" CB PRO B 588 " ideal model delta harmonic sigma weight residual -120.70 -103.04 -17.66 0 2.50e+00 1.60e-01 4.99e+01 dihedral pdb=" N PRO B 588 " pdb=" C PRO B 588 " pdb=" CA PRO B 588 " pdb=" CB PRO B 588 " ideal model delta harmonic sigma weight residual 115.10 98.34 16.76 0 2.50e+00 1.60e-01 4.50e+01 dihedral pdb=" CA GLY C 216 " pdb=" C GLY C 216 " pdb=" N TRP C 217 " pdb=" CA TRP C 217 " ideal model delta harmonic sigma weight residual -180.00 -151.08 -28.92 0 5.00e+00 4.00e-02 3.35e+01 ... (remaining 11124 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 2.744: 2855 2.744 - 5.488: 0 5.488 - 8.232: 0 8.232 - 10.976: 0 10.976 - 13.720: 1 Chirality restraints: 2856 Sorted by residual: chirality pdb=" S2 F3S B1104 " pdb="FE1 F3S B1104 " pdb="FE3 F3S B1104 " pdb="FE4 F3S B1104 " both_signs ideal model delta sigma weight residual False 10.77 -2.95 13.72 2.00e-01 2.50e+01 4.71e+03 chirality pdb=" CA LEU B 298 " pdb=" N LEU B 298 " pdb=" C LEU B 298 " pdb=" CB LEU B 298 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 8.97e+00 chirality pdb=" CA ARG E 80 " pdb=" N ARG E 80 " pdb=" C ARG E 80 " pdb=" CB ARG E 80 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.90e+00 ... (remaining 2853 not shown) Planarity restraints: 3339 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC E 201 " 0.015 2.00e-02 2.50e+03 5.63e-02 7.14e+01 pdb=" C2C HEC E 201 " -0.154 2.00e-02 2.50e+03 pdb=" C3C HEC E 201 " 0.019 2.00e-02 2.50e+03 pdb=" C4C HEC E 201 " 0.005 2.00e-02 2.50e+03 pdb=" CAC HEC E 201 " 0.035 2.00e-02 2.50e+03 pdb=" CHC HEC E 201 " 0.031 2.00e-02 2.50e+03 pdb=" CHD HEC E 201 " -0.006 2.00e-02 2.50e+03 pdb=" CMC HEC E 201 " 0.044 2.00e-02 2.50e+03 pdb=" NC HEC E 201 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC A 305 " -0.015 2.00e-02 2.50e+03 4.30e-02 4.16e+01 pdb=" C2C HEC A 305 " 0.118 2.00e-02 2.50e+03 pdb=" C3C HEC A 305 " -0.011 2.00e-02 2.50e+03 pdb=" C4C HEC A 305 " -0.005 2.00e-02 2.50e+03 pdb=" CAC HEC A 305 " -0.028 2.00e-02 2.50e+03 pdb=" CHC HEC A 305 " -0.022 2.00e-02 2.50e+03 pdb=" CHD HEC A 305 " 0.005 2.00e-02 2.50e+03 pdb=" CMC HEC A 305 " -0.033 2.00e-02 2.50e+03 pdb=" NC HEC A 305 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC A 303 " 0.015 2.00e-02 2.50e+03 3.77e-02 3.21e+01 pdb=" C2C HEC A 303 " -0.102 2.00e-02 2.50e+03 pdb=" C3C HEC A 303 " 0.009 2.00e-02 2.50e+03 pdb=" C4C HEC A 303 " -0.006 2.00e-02 2.50e+03 pdb=" CAC HEC A 303 " 0.030 2.00e-02 2.50e+03 pdb=" CHC HEC A 303 " 0.026 2.00e-02 2.50e+03 pdb=" CHD HEC A 303 " 0.002 2.00e-02 2.50e+03 pdb=" CMC HEC A 303 " 0.023 2.00e-02 2.50e+03 pdb=" NC HEC A 303 " 0.003 2.00e-02 2.50e+03 ... (remaining 3336 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 219 2.56 - 3.15: 15557 3.15 - 3.73: 32017 3.73 - 4.32: 47269 4.32 - 4.90: 76009 Nonbonded interactions: 171071 Sorted by model distance: nonbonded pdb=" NE2 HIS A 225 " pdb="FE HEC A 301 " model vdw 1.981 3.080 nonbonded pdb=" NE2 HIS A 66 " pdb="FE HEC A 305 " model vdw 2.003 3.080 nonbonded pdb=" NE2 HIS A 140 " pdb="FE HEC A 302 " model vdw 2.024 3.080 nonbonded pdb=" NE2 HIS A 63 " pdb="FE HEC A 304 " model vdw 2.131 3.080 nonbonded pdb=" OG1 THR B 145 " pdb=" OE1 GLN B 150 " model vdw 2.168 2.440 ... (remaining 171066 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 3.420 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 52.970 Find NCS groups from input model: 0.580 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 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 : 0.025 1.984 19374 Z= 1.605 Angle : 1.205 74.167 26522 Z= 0.552 Chirality : 0.262 13.720 2856 Planarity : 0.006 0.074 3339 Dihedral : 15.691 129.306 6821 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.97 % Favored : 90.03 % Rotamer: Outliers : 0.21 % Allowed : 7.43 % Favored : 92.36 % Cbeta Deviations : 0.19 % 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: -5.41 (0.14), residues: 2317 helix: -4.11 (0.09), residues: 1037 sheet: -4.01 (0.31), residues: 164 loop : -2.91 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 170 HIS 0.006 0.001 HIS B 471 PHE 0.022 0.002 PHE C 266 TYR 0.020 0.002 TYR A 134 ARG 0.004 0.000 ARG B 903 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 300 time to evaluate : 2.178 Fit side-chains REVERT: A 205 ARG cc_start: 0.8143 (ttp80) cc_final: 0.7900 (ttp80) REVERT: A 210 TYR cc_start: 0.8940 (m-10) cc_final: 0.8691 (m-10) REVERT: B 83 LYS cc_start: 0.8200 (mtpp) cc_final: 0.7923 (mttp) REVERT: B 223 LYS cc_start: 0.8887 (mtpt) cc_final: 0.8639 (mttp) REVERT: B 252 ARG cc_start: 0.7754 (mtm-85) cc_final: 0.7540 (ttp-110) REVERT: B 541 VAL cc_start: 0.9141 (p) cc_final: 0.8890 (t) REVERT: B 988 LYS cc_start: 0.8792 (mmtt) cc_final: 0.8539 (mtpt) REVERT: D 132 MET cc_start: 0.7545 (tmm) cc_final: 0.7177 (tmm) REVERT: E 84 ASP cc_start: 0.8036 (p0) cc_final: 0.7161 (p0) REVERT: F 388 TYR cc_start: 0.8467 (p90) cc_final: 0.8216 (p90) outliers start: 4 outliers final: 2 residues processed: 303 average time/residue: 0.3756 time to fit residues: 167.5695 Evaluate side-chains 246 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 244 time to evaluate : 2.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 862 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 193 optimal weight: 6.9990 chunk 173 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 chunk 92 optimal weight: 0.5980 chunk 179 optimal weight: 9.9990 chunk 69 optimal weight: 0.0980 chunk 109 optimal weight: 0.6980 chunk 133 optimal weight: 0.5980 chunk 207 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 100 GLN A 127 HIS A 156 GLN A 190 ASN A 198 ASN A 199 GLN B 234 ASN B 279 GLN B 373 GLN ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 602 GLN B 625 ASN B 654 HIS B 816 ASN ** B 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 874 ASN B 955 GLN B 975 GLN C 23 GLN C 141 HIS ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN C 365 GLN E 107 GLN E 181 HIS ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 HIS F 68 HIS F 176 GLN F 249 HIS F 386 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.226 19374 Z= 0.233 Angle : 0.971 56.280 26522 Z= 0.396 Chirality : 0.054 1.682 2856 Planarity : 0.005 0.060 3339 Dihedral : 9.096 93.774 2655 Min Nonbonded Distance : 1.452 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 2.08 % Allowed : 11.54 % Favored : 86.38 % 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: -4.01 (0.15), residues: 2317 helix: -2.51 (0.13), residues: 1046 sheet: -3.69 (0.31), residues: 166 loop : -2.56 (0.18), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 186 HIS 0.004 0.001 HIS A 66 PHE 0.020 0.002 PHE F 373 TYR 0.014 0.001 TYR A 134 ARG 0.007 0.000 ARG E 110 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 271 time to evaluate : 2.221 Fit side-chains revert: symmetry clash REVERT: B 541 VAL cc_start: 0.9161 (p) cc_final: 0.8876 (t) REVERT: B 820 MET cc_start: 0.8645 (ttp) cc_final: 0.8394 (ttp) REVERT: B 988 LYS cc_start: 0.8726 (mmtt) cc_final: 0.8504 (mtpt) REVERT: C 418 VAL cc_start: 0.9237 (p) cc_final: 0.9024 (t) REVERT: E 84 ASP cc_start: 0.8062 (p0) cc_final: 0.7594 (p0) REVERT: F 388 TYR cc_start: 0.8400 (p90) cc_final: 0.8149 (p90) outliers start: 40 outliers final: 25 residues processed: 293 average time/residue: 0.3023 time to fit residues: 137.3411 Evaluate side-chains 262 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 237 time to evaluate : 2.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 854 ASN Chi-restraints excluded: chain B residue 862 CYS Chi-restraints excluded: chain B residue 898 VAL Chi-restraints excluded: chain B residue 945 MET Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 347 PHE Chi-restraints excluded: chain F residue 361 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 115 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 173 optimal weight: 8.9990 chunk 141 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 208 optimal weight: 1.9990 chunk 225 optimal weight: 1.9990 chunk 185 optimal weight: 9.9990 chunk 206 optimal weight: 9.9990 chunk 71 optimal weight: 0.0470 chunk 167 optimal weight: 0.3980 overall best weight: 1.4884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 ASN A 198 ASN ** B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 816 ASN ** B 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.116 19374 Z= 0.265 Angle : 0.857 81.977 26522 Z= 0.359 Chirality : 0.053 1.515 2856 Planarity : 0.005 0.062 3339 Dihedral : 8.593 81.540 2655 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 2.91 % Allowed : 14.35 % Favored : 82.74 % 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: -3.23 (0.16), residues: 2317 helix: -1.63 (0.14), residues: 1067 sheet: -3.49 (0.31), residues: 166 loop : -2.40 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 186 HIS 0.005 0.001 HIS E 181 PHE 0.016 0.001 PHE C 433 TYR 0.014 0.001 TYR A 134 ARG 0.004 0.000 ARG F 320 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 253 time to evaluate : 2.112 Fit side-chains revert: symmetry clash REVERT: B 156 MET cc_start: 0.8795 (ttt) cc_final: 0.8415 (ttt) REVERT: B 223 LYS cc_start: 0.8840 (mtpt) cc_final: 0.8640 (mttp) REVERT: B 317 ARG cc_start: 0.8083 (mtp-110) cc_final: 0.7187 (ttp-110) REVERT: B 541 VAL cc_start: 0.9210 (p) cc_final: 0.8881 (t) REVERT: B 820 MET cc_start: 0.8766 (ttp) cc_final: 0.8462 (ttp) REVERT: B 988 LYS cc_start: 0.8758 (mmtt) cc_final: 0.8526 (mtpt) REVERT: B 992 SER cc_start: 0.9245 (p) cc_final: 0.8887 (p) REVERT: E 84 ASP cc_start: 0.8153 (p0) cc_final: 0.7692 (p0) REVERT: F 388 TYR cc_start: 0.8437 (p90) cc_final: 0.8170 (p90) outliers start: 56 outliers final: 38 residues processed: 284 average time/residue: 0.3142 time to fit residues: 137.2675 Evaluate side-chains 278 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 240 time to evaluate : 2.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 843 HIS Chi-restraints excluded: chain B residue 854 ASN Chi-restraints excluded: chain B residue 898 VAL Chi-restraints excluded: chain B residue 922 VAL Chi-restraints excluded: chain B residue 927 GLU Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain D residue 147 ASN Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 347 PHE Chi-restraints excluded: chain F residue 361 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 205 optimal weight: 0.7980 chunk 156 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 99 optimal weight: 0.7980 chunk 139 optimal weight: 0.7980 chunk 209 optimal weight: 0.6980 chunk 221 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 198 optimal weight: 0.0370 chunk 59 optimal weight: 6.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 ASN A 198 ASN ** B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 HIS B 473 ASN ** B 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 19374 Z= 0.189 Angle : 0.823 83.328 26522 Z= 0.343 Chirality : 0.051 1.478 2856 Planarity : 0.004 0.059 3339 Dihedral : 8.167 83.119 2654 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 2.96 % Allowed : 15.85 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.17), residues: 2317 helix: -0.99 (0.15), residues: 1051 sheet: -3.25 (0.32), residues: 161 loop : -2.16 (0.19), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 186 HIS 0.005 0.001 HIS E 181 PHE 0.015 0.001 PHE F 373 TYR 0.013 0.001 TYR A 134 ARG 0.009 0.000 ARG E 110 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 263 time to evaluate : 1.882 Fit side-chains revert: symmetry clash REVERT: B 196 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7738 (tt) REVERT: B 988 LYS cc_start: 0.8711 (mmtt) cc_final: 0.8423 (mtpt) REVERT: B 990 ARG cc_start: 0.9137 (tpp80) cc_final: 0.8485 (tpp-160) REVERT: B 992 SER cc_start: 0.9212 (p) cc_final: 0.8849 (p) REVERT: C 160 MET cc_start: 0.7889 (mmm) cc_final: 0.7536 (tpt) REVERT: C 285 LEU cc_start: 0.8752 (mt) cc_final: 0.8536 (mt) REVERT: D 100 ASN cc_start: 0.8866 (t0) cc_final: 0.8593 (t0) REVERT: D 132 MET cc_start: 0.7273 (OUTLIER) cc_final: 0.6781 (ptm) REVERT: E 84 ASP cc_start: 0.8091 (p0) cc_final: 0.7665 (p0) REVERT: F 65 MET cc_start: 0.8863 (mtt) cc_final: 0.8593 (mtt) REVERT: F 300 MET cc_start: 0.8824 (mmp) cc_final: 0.8164 (mmm) outliers start: 57 outliers final: 40 residues processed: 297 average time/residue: 0.3085 time to fit residues: 141.7953 Evaluate side-chains 285 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 243 time to evaluate : 1.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 843 HIS Chi-restraints excluded: chain B residue 854 ASN Chi-restraints excluded: chain B residue 898 VAL Chi-restraints excluded: chain B residue 922 VAL Chi-restraints excluded: chain B residue 927 GLU Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 147 ASN Chi-restraints excluded: chain E residue 47 GLN Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 347 PHE Chi-restraints excluded: chain F residue 348 HIS Chi-restraints excluded: chain F residue 361 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 184 optimal weight: 8.9990 chunk 125 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 164 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 188 optimal weight: 0.8980 chunk 153 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 198 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 ASN B 101 HIS ** B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 GLN B 597 ASN ** B 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 GLN ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 304 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.096 19374 Z= 0.483 Angle : 0.952 84.555 26522 Z= 0.403 Chirality : 0.057 1.478 2856 Planarity : 0.005 0.062 3339 Dihedral : 8.521 75.970 2654 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer: Outliers : 4.26 % Allowed : 15.90 % Favored : 79.83 % 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: -2.70 (0.17), residues: 2317 helix: -1.06 (0.15), residues: 1070 sheet: -3.09 (0.33), residues: 177 loop : -2.28 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 186 HIS 0.005 0.001 HIS B 662 PHE 0.019 0.002 PHE C 433 TYR 0.015 0.002 TYR C 269 ARG 0.009 0.001 ARG F 320 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 254 time to evaluate : 2.110 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 83 LYS cc_start: 0.8266 (mtpp) cc_final: 0.7897 (mttp) REVERT: B 223 LYS cc_start: 0.8882 (mtpt) cc_final: 0.8661 (mttp) REVERT: B 317 ARG cc_start: 0.8047 (mtp-110) cc_final: 0.7246 (ttp-110) REVERT: B 799 MET cc_start: 0.8509 (mmp) cc_final: 0.7830 (mmt) REVERT: B 843 HIS cc_start: 0.9042 (OUTLIER) cc_final: 0.8766 (t-90) REVERT: B 988 LYS cc_start: 0.8861 (mmtt) cc_final: 0.8631 (mtpt) REVERT: C 87 ASP cc_start: 0.8461 (OUTLIER) cc_final: 0.8218 (p0) REVERT: C 126 MET cc_start: 0.8542 (tmm) cc_final: 0.8173 (ttp) REVERT: C 285 LEU cc_start: 0.8819 (mt) cc_final: 0.8581 (mt) REVERT: C 415 THR cc_start: 0.8272 (t) cc_final: 0.7974 (p) REVERT: E 84 ASP cc_start: 0.8326 (p0) cc_final: 0.7917 (p0) REVERT: F 65 MET cc_start: 0.9059 (mtt) cc_final: 0.8808 (mtt) REVERT: F 300 MET cc_start: 0.8835 (mmp) cc_final: 0.8197 (mmm) REVERT: F 388 TYR cc_start: 0.8507 (p90) cc_final: 0.8186 (p90) outliers start: 82 outliers final: 55 residues processed: 307 average time/residue: 0.3137 time to fit residues: 148.4071 Evaluate side-chains 298 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 241 time to evaluate : 2.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 623 THR Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain B residue 788 VAL Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 843 HIS Chi-restraints excluded: chain B residue 854 ASN Chi-restraints excluded: chain B residue 862 CYS Chi-restraints excluded: chain B residue 898 VAL Chi-restraints excluded: chain B residue 922 VAL Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 347 PHE Chi-restraints excluded: chain F residue 350 ASP Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 361 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 74 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 221 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 18 optimal weight: 0.2980 chunk 73 optimal weight: 0.8980 chunk 116 optimal weight: 7.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 ASN ** B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C 365 GLN ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 19374 Z= 0.230 Angle : 0.845 83.771 26522 Z= 0.355 Chirality : 0.052 1.469 2856 Planarity : 0.004 0.064 3339 Dihedral : 8.190 81.320 2654 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 3.64 % Allowed : 17.46 % Favored : 78.90 % 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: -2.34 (0.17), residues: 2317 helix: -0.72 (0.16), residues: 1058 sheet: -2.89 (0.35), residues: 174 loop : -2.13 (0.19), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 186 HIS 0.004 0.001 HIS D 143 PHE 0.015 0.001 PHE C 433 TYR 0.014 0.001 TYR A 134 ARG 0.009 0.000 ARG E 110 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 248 time to evaluate : 2.186 Fit side-chains revert: symmetry clash REVERT: B 156 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8126 (ttt) REVERT: B 196 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7864 (tt) REVERT: B 223 LYS cc_start: 0.8865 (mtpt) cc_final: 0.8618 (mttp) REVERT: B 317 ARG cc_start: 0.7899 (mtp-110) cc_final: 0.7188 (ttp-110) REVERT: B 918 CYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8187 (t) REVERT: B 990 ARG cc_start: 0.9165 (tpp80) cc_final: 0.7992 (tpp80) REVERT: B 992 SER cc_start: 0.9248 (p) cc_final: 0.8950 (p) REVERT: C 160 MET cc_start: 0.8021 (mmm) cc_final: 0.7698 (tpt) REVERT: C 285 LEU cc_start: 0.8749 (mt) cc_final: 0.8525 (mt) REVERT: C 360 ASN cc_start: 0.8962 (OUTLIER) cc_final: 0.8752 (m-40) REVERT: C 390 MET cc_start: 0.8892 (mmm) cc_final: 0.8618 (mmp) REVERT: D 172 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.7145 (tt) REVERT: E 84 ASP cc_start: 0.8216 (p0) cc_final: 0.7836 (p0) REVERT: F 65 MET cc_start: 0.8975 (mtt) cc_final: 0.8689 (mtt) REVERT: F 300 MET cc_start: 0.8827 (mmp) cc_final: 0.8234 (mmm) REVERT: F 388 TYR cc_start: 0.8451 (p90) cc_final: 0.8199 (p90) outliers start: 70 outliers final: 45 residues processed: 293 average time/residue: 0.3152 time to fit residues: 142.2336 Evaluate side-chains 292 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 242 time to evaluate : 2.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 668 THR Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 843 HIS Chi-restraints excluded: chain B residue 854 ASN Chi-restraints excluded: chain B residue 862 CYS Chi-restraints excluded: chain B residue 898 VAL Chi-restraints excluded: chain B residue 918 CYS Chi-restraints excluded: chain B residue 922 VAL Chi-restraints excluded: chain B residue 927 GLU Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain D residue 147 ASN Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain E residue 47 GLN Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 347 PHE Chi-restraints excluded: chain F residue 361 THR Chi-restraints excluded: chain F residue 390 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 213 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 161 optimal weight: 5.9990 chunk 125 optimal weight: 0.9980 chunk 186 optimal weight: 2.9990 chunk 123 optimal weight: 0.4980 chunk 220 optimal weight: 0.7980 chunk 138 optimal weight: 0.9980 chunk 134 optimal weight: 0.9980 chunk 101 optimal weight: 0.0050 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN ** B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 816 ASN ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 GLN ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN ** F 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 19374 Z= 0.200 Angle : 0.828 83.610 26522 Z= 0.345 Chirality : 0.051 1.472 2856 Planarity : 0.004 0.058 3339 Dihedral : 7.950 79.645 2654 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 3.48 % Allowed : 17.98 % Favored : 78.53 % 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: -2.07 (0.17), residues: 2317 helix: -0.47 (0.16), residues: 1057 sheet: -2.97 (0.34), residues: 162 loop : -2.01 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 186 HIS 0.004 0.001 HIS E 181 PHE 0.015 0.001 PHE C 433 TYR 0.011 0.001 TYR A 134 ARG 0.009 0.000 ARG F 320 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 263 time to evaluate : 2.019 Fit side-chains revert: symmetry clash REVERT: A 71 MET cc_start: 0.7851 (mtt) cc_final: 0.7565 (mtt) REVERT: B 196 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7806 (tt) REVERT: B 223 LYS cc_start: 0.8790 (mtpt) cc_final: 0.8555 (mttp) REVERT: B 317 ARG cc_start: 0.7831 (mtp-110) cc_final: 0.7189 (ttp-110) REVERT: B 799 MET cc_start: 0.8343 (mmp) cc_final: 0.7593 (mmt) REVERT: B 918 CYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8132 (t) REVERT: B 990 ARG cc_start: 0.9177 (tpp80) cc_final: 0.8522 (tpp-160) REVERT: B 992 SER cc_start: 0.9241 (p) cc_final: 0.8918 (p) REVERT: C 200 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7472 (ttm-80) REVERT: C 390 MET cc_start: 0.8867 (mmm) cc_final: 0.8571 (mmp) REVERT: D 172 LEU cc_start: 0.7370 (OUTLIER) cc_final: 0.6972 (tt) REVERT: E 84 ASP cc_start: 0.8177 (p0) cc_final: 0.7795 (p0) REVERT: E 188 ASN cc_start: 0.8156 (OUTLIER) cc_final: 0.7804 (p0) REVERT: F 65 MET cc_start: 0.8951 (mtt) cc_final: 0.8630 (mtp) REVERT: F 300 MET cc_start: 0.8799 (mmp) cc_final: 0.8160 (mmm) outliers start: 67 outliers final: 47 residues processed: 306 average time/residue: 0.3119 time to fit residues: 146.8536 Evaluate side-chains 302 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 250 time to evaluate : 1.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 479 GLU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 843 HIS Chi-restraints excluded: chain B residue 854 ASN Chi-restraints excluded: chain B residue 898 VAL Chi-restraints excluded: chain B residue 918 CYS Chi-restraints excluded: chain B residue 922 VAL Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain D residue 147 ASN Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain F residue 206 PHE Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 347 PHE Chi-restraints excluded: chain F residue 350 ASP Chi-restraints excluded: chain F residue 361 THR Chi-restraints excluded: chain F residue 390 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 136 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 173 optimal weight: 10.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 386 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 19374 Z= 0.211 Angle : 0.832 83.586 26522 Z= 0.346 Chirality : 0.052 1.478 2856 Planarity : 0.004 0.058 3339 Dihedral : 7.859 80.011 2654 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 3.48 % Allowed : 18.66 % Favored : 77.86 % 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: -1.90 (0.18), residues: 2317 helix: -0.33 (0.16), residues: 1062 sheet: -2.79 (0.35), residues: 160 loop : -1.95 (0.20), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 186 HIS 0.004 0.001 HIS E 181 PHE 0.015 0.001 PHE C 433 TYR 0.011 0.001 TYR A 134 ARG 0.010 0.000 ARG E 110 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 256 time to evaluate : 1.934 Fit side-chains REVERT: A 71 MET cc_start: 0.7781 (mtt) cc_final: 0.7523 (mtt) REVERT: A 168 MET cc_start: 0.7904 (ttt) cc_final: 0.7612 (ttt) REVERT: B 196 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7775 (tt) REVERT: B 223 LYS cc_start: 0.8790 (mtpt) cc_final: 0.8536 (mttp) REVERT: B 799 MET cc_start: 0.8353 (mmp) cc_final: 0.7604 (mmt) REVERT: B 918 CYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8128 (t) REVERT: B 990 ARG cc_start: 0.9182 (tpp80) cc_final: 0.8528 (tpp-160) REVERT: B 992 SER cc_start: 0.9229 (p) cc_final: 0.8914 (p) REVERT: C 59 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8065 (tp) REVERT: C 160 MET cc_start: 0.7903 (mmm) cc_final: 0.7486 (tpt) REVERT: C 200 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7498 (ttm-80) REVERT: D 172 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.6946 (tt) REVERT: E 188 ASN cc_start: 0.8162 (OUTLIER) cc_final: 0.7821 (p0) REVERT: F 65 MET cc_start: 0.8933 (mtt) cc_final: 0.8648 (mtp) outliers start: 67 outliers final: 51 residues processed: 303 average time/residue: 0.3045 time to fit residues: 142.9713 Evaluate side-chains 311 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 254 time to evaluate : 2.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 479 GLU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 502 TYR Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 843 HIS Chi-restraints excluded: chain B residue 854 ASN Chi-restraints excluded: chain B residue 862 CYS Chi-restraints excluded: chain B residue 898 VAL Chi-restraints excluded: chain B residue 918 CYS Chi-restraints excluded: chain B residue 922 VAL Chi-restraints excluded: chain B residue 927 GLU Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain D residue 147 ASN Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain F residue 206 PHE Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 347 PHE Chi-restraints excluded: chain F residue 350 ASP Chi-restraints excluded: chain F residue 361 THR Chi-restraints excluded: chain F residue 390 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 200 optimal weight: 1.9990 chunk 211 optimal weight: 0.6980 chunk 192 optimal weight: 4.9990 chunk 205 optimal weight: 0.9980 chunk 123 optimal weight: 0.0980 chunk 89 optimal weight: 0.9980 chunk 161 optimal weight: 0.0870 chunk 63 optimal weight: 0.0670 chunk 185 optimal weight: 0.5980 chunk 194 optimal weight: 0.8980 chunk 204 optimal weight: 0.8980 overall best weight: 0.3096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 GLN ** F 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 386 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 19374 Z= 0.173 Angle : 0.818 83.257 26522 Z= 0.339 Chirality : 0.051 1.488 2856 Planarity : 0.004 0.057 3339 Dihedral : 7.687 82.151 2654 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 2.96 % Allowed : 19.23 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.18), residues: 2317 helix: -0.12 (0.16), residues: 1054 sheet: -2.65 (0.36), residues: 160 loop : -1.85 (0.20), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 115 HIS 0.004 0.001 HIS E 181 PHE 0.014 0.001 PHE C 433 TYR 0.012 0.001 TYR C 424 ARG 0.008 0.000 ARG F 320 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 272 time to evaluate : 2.212 Fit side-chains REVERT: A 95 MET cc_start: 0.8392 (mmm) cc_final: 0.8102 (mmm) REVERT: A 168 MET cc_start: 0.7836 (ttt) cc_final: 0.7596 (ttt) REVERT: A 190 ASN cc_start: 0.8242 (t0) cc_final: 0.7873 (p0) REVERT: B 196 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7749 (tt) REVERT: B 223 LYS cc_start: 0.8751 (mtpt) cc_final: 0.8522 (mttp) REVERT: B 918 CYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8111 (t) REVERT: B 990 ARG cc_start: 0.9134 (tpp80) cc_final: 0.8529 (tpp-160) REVERT: B 992 SER cc_start: 0.9122 (p) cc_final: 0.8773 (p) REVERT: C 200 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7480 (ttm-80) REVERT: D 172 LEU cc_start: 0.7271 (OUTLIER) cc_final: 0.6822 (tt) REVERT: E 188 ASN cc_start: 0.8138 (OUTLIER) cc_final: 0.7831 (p0) REVERT: F 16 LEU cc_start: 0.7699 (tt) cc_final: 0.7476 (tp) outliers start: 57 outliers final: 44 residues processed: 310 average time/residue: 0.3281 time to fit residues: 155.9112 Evaluate side-chains 300 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 251 time to evaluate : 2.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 479 GLU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 502 TYR Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 843 HIS Chi-restraints excluded: chain B residue 854 ASN Chi-restraints excluded: chain B residue 862 CYS Chi-restraints excluded: chain B residue 898 VAL Chi-restraints excluded: chain B residue 918 CYS Chi-restraints excluded: chain B residue 920 PHE Chi-restraints excluded: chain B residue 922 VAL Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain D residue 147 ASN Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain F residue 206 PHE Chi-restraints excluded: chain F residue 245 VAL Chi-restraints excluded: chain F residue 350 ASP Chi-restraints excluded: chain F residue 361 THR Chi-restraints excluded: chain F residue 390 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 135 optimal weight: 1.9990 chunk 217 optimal weight: 0.0270 chunk 132 optimal weight: 0.0030 chunk 103 optimal weight: 0.2980 chunk 151 optimal weight: 0.9980 chunk 228 optimal weight: 0.5980 chunk 209 optimal weight: 0.6980 chunk 181 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 overall best weight: 0.3248 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 999 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 ASN ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 386 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 19374 Z= 0.178 Angle : 0.819 83.136 26522 Z= 0.340 Chirality : 0.051 1.500 2856 Planarity : 0.004 0.056 3339 Dihedral : 7.611 83.755 2654 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 2.70 % Allowed : 19.80 % Favored : 77.49 % 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: -1.54 (0.18), residues: 2317 helix: 0.00 (0.16), residues: 1060 sheet: -2.58 (0.36), residues: 169 loop : -1.79 (0.20), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 193 HIS 0.012 0.001 HIS D 143 PHE 0.018 0.001 PHE A 167 TYR 0.013 0.001 TYR D 45 ARG 0.010 0.000 ARG E 70 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4634 Ramachandran restraints generated. 2317 Oldfield, 0 Emsley, 2317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 261 time to evaluate : 2.128 Fit side-chains REVERT: A 168 MET cc_start: 0.7918 (ttt) cc_final: 0.7586 (ttt) REVERT: A 190 ASN cc_start: 0.8127 (t0) cc_final: 0.7836 (p0) REVERT: A 198 ASN cc_start: 0.8312 (p0) cc_final: 0.8045 (p0) REVERT: B 87 GLU cc_start: 0.6403 (mt-10) cc_final: 0.3176 (tt0) REVERT: B 196 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7631 (tt) REVERT: B 223 LYS cc_start: 0.8697 (mtpt) cc_final: 0.8456 (mttp) REVERT: B 419 MET cc_start: 0.8180 (mtp) cc_final: 0.7978 (mtm) REVERT: B 466 GLN cc_start: 0.7393 (mm-40) cc_final: 0.7108 (mt0) REVERT: B 649 TRP cc_start: 0.8966 (t-100) cc_final: 0.8725 (t-100) REVERT: B 918 CYS cc_start: 0.8397 (OUTLIER) cc_final: 0.8080 (t) REVERT: B 990 ARG cc_start: 0.9125 (tpp80) cc_final: 0.8530 (tpp-160) REVERT: C 200 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7493 (ttm-80) REVERT: D 132 MET cc_start: 0.7072 (ppp) cc_final: 0.6836 (tmm) REVERT: D 172 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6755 (tt) REVERT: E 188 ASN cc_start: 0.8118 (OUTLIER) cc_final: 0.7819 (p0) REVERT: F 16 LEU cc_start: 0.7748 (tt) cc_final: 0.7520 (tp) outliers start: 52 outliers final: 43 residues processed: 296 average time/residue: 0.3152 time to fit residues: 143.7758 Evaluate side-chains 301 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 253 time to evaluate : 1.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 479 GLU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 502 TYR Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 750 ILE Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 823 LEU Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 843 HIS Chi-restraints excluded: chain B residue 854 ASN Chi-restraints excluded: chain B residue 862 CYS Chi-restraints excluded: chain B residue 918 CYS Chi-restraints excluded: chain B residue 920 PHE Chi-restraints excluded: chain B residue 922 VAL Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain D residue 147 ASN Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 206 PHE Chi-restraints excluded: chain F residue 348 HIS Chi-restraints excluded: chain F residue 350 ASP Chi-restraints excluded: chain F residue 361 THR Chi-restraints excluded: chain F residue 390 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 144 optimal weight: 0.9980 chunk 193 optimal weight: 8.9990 chunk 55 optimal weight: 6.9990 chunk 167 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 181 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 186 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 GLN ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.119279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.110271 restraints weight = 23758.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.109273 restraints weight = 34087.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.108086 restraints weight = 25033.464| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 19374 Z= 0.228 Angle : 0.835 83.223 26522 Z= 0.347 Chirality : 0.052 1.506 2856 Planarity : 0.004 0.057 3339 Dihedral : 7.698 83.732 2654 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 2.70 % Allowed : 20.22 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.18), residues: 2317 helix: 0.04 (0.16), residues: 1059 sheet: -2.38 (0.38), residues: 170 loop : -1.80 (0.20), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 193 HIS 0.010 0.001 HIS D 143 PHE 0.016 0.001 PHE C 433 TYR 0.012 0.001 TYR C 349 ARG 0.008 0.000 ARG E 110 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3796.19 seconds wall clock time: 70 minutes 1.16 seconds (4201.16 seconds total)