Starting phenix.real_space_refine on Sat Feb 17 08:52:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ipt_35643/02_2024/8ipt_35643_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ipt_35643/02_2024/8ipt_35643.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/8ipt_35643/02_2024/8ipt_35643.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ipt_35643/02_2024/8ipt_35643.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ipt_35643/02_2024/8ipt_35643_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ipt_35643/02_2024/8ipt_35643_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= 0.003 sd= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 60 5.16 5 C 11618 2.51 5 N 3198 2.21 5 O 3290 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 456": "OE1" <-> "OE2" Residue "C ASP 499": "OD1" <-> "OD2" Residue "C PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 8": "OE1" <-> "OE2" Residue "A TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 419": "OE1" <-> "OE2" Residue "A ASP 449": "OD1" <-> "OD2" Residue "A ASP 517": "OD1" <-> "OD2" Residue "A GLU 521": "OE1" <-> "OE2" Residue "D TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 456": "OE1" <-> "OE2" Residue "D ASP 499": "OD1" <-> "OD2" Residue "D PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 8": "OE1" <-> "OE2" Residue "E PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 419": "OE1" <-> "OE2" Residue "E ASP 449": "OD1" <-> "OD2" Residue "E ASP 517": "OD1" <-> "OD2" Residue "E GLU 521": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18178 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 4433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4433 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 18, 'TRANS': 554} Chain: "A" Number of atoms: 4594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4594 Classifications: {'peptide': 588} Link IDs: {'PTRANS': 27, 'TRANS': 560} Chain: "D" Number of atoms: 4433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4433 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 18, 'TRANS': 554} Chain: "E" Number of atoms: 4594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4594 Classifications: {'peptide': 588} Link IDs: {'PTRANS': 27, 'TRANS': 560} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.21, per 1000 atoms: 0.51 Number of scatterers: 18178 At special positions: 0 Unit cell: (90.24, 106.56, 229.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 P 12 15.00 O 3290 8.00 N 3198 7.00 C 11618 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=0, symmetry=0 Time building additional restraints: 6.97 Conformation dependent library (CDL) restraints added in 3.5 seconds 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4296 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 78 helices and 10 sheets defined 59.3% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.66 Creating SS restraints... Processing helix chain 'C' and resid 2 through 8 Proline residue: C 6 - end of helix Processing helix chain 'C' and resid 15 through 48 removed outlier: 3.570A pdb=" N GLY C 21 " --> pdb=" O MET C 17 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE C 22 " --> pdb=" O LEU C 18 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA C 47 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL C 48 " --> pdb=" O SER C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 104 Proline residue: C 62 - end of helix removed outlier: 3.903A pdb=" N GLY C 65 " --> pdb=" O PRO C 62 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL C 66 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ARG C 67 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLY C 68 " --> pdb=" O GLY C 65 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA C 70 " --> pdb=" O ARG C 67 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE C 71 " --> pdb=" O GLY C 68 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N THR C 72 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ARG C 73 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA C 75 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLY C 76 " --> pdb=" O ARG C 73 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TYR C 78 " --> pdb=" O ALA C 75 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE C 79 " --> pdb=" O GLY C 76 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG C 81 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU C 82 " --> pdb=" O PHE C 79 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL C 83 " --> pdb=" O GLU C 80 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER C 84 " --> pdb=" O ARG C 81 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N HIS C 85 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N PHE C 89 " --> pdb=" O ASP C 86 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N GLN C 93 " --> pdb=" O ARG C 90 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N THR C 99 " --> pdb=" O ARG C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 124 removed outlier: 4.215A pdb=" N LEU C 120 " --> pdb=" O GLN C 116 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ASN C 121 " --> pdb=" O GLY C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 135 Processing helix chain 'C' and resid 139 through 157 removed outlier: 4.235A pdb=" N PHE C 157 " --> pdb=" O ILE C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 206 Proline residue: C 178 - end of helix removed outlier: 4.614A pdb=" N ARG C 183 " --> pdb=" O PRO C 179 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ALA C 184 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY C 185 " --> pdb=" O PHE C 181 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER C 187 " --> pdb=" O ARG C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 215 Processing helix chain 'C' and resid 220 through 265 removed outlier: 4.010A pdb=" N GLN C 232 " --> pdb=" O ASN C 228 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N TRP C 233 " --> pdb=" O THR C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 318 removed outlier: 3.510A pdb=" N ALA C 287 " --> pdb=" O PHE C 283 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N PHE C 291 " --> pdb=" O ALA C 287 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N GLU C 292 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ALA C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU C 294 " --> pdb=" O ALA C 290 " (cutoff:3.500A) Proline residue: C 296 - end of helix removed outlier: 5.174A pdb=" N GLY C 299 " --> pdb=" O ALA C 295 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA C 300 " --> pdb=" O PRO C 296 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE C 301 " --> pdb=" O VAL C 297 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N HIS C 303 " --> pdb=" O GLY C 299 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LEU C 304 " --> pdb=" O ALA C 300 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N GLY C 305 " --> pdb=" O PHE C 301 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N GLN C 306 " --> pdb=" O GLN C 302 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL C 307 " --> pdb=" O HIS C 303 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE C 308 " --> pdb=" O LEU C 304 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ALA C 309 " --> pdb=" O GLY C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 386 removed outlier: 3.673A pdb=" N LEU C 383 " --> pdb=" O LYS C 379 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU C 386 " --> pdb=" O LEU C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 412 No H-bonds generated for 'chain 'C' and resid 409 through 412' Processing helix chain 'C' and resid 430 through 434 Processing helix chain 'C' and resid 445 through 452 Processing helix chain 'C' and resid 479 through 488 removed outlier: 3.718A pdb=" N ALA C 488 " --> pdb=" O ALA C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 520 Processing helix chain 'C' and resid 558 through 561 No H-bonds generated for 'chain 'C' and resid 558 through 561' Processing helix chain 'C' and resid 567 through 571 removed outlier: 4.073A pdb=" N GLN C 571 " --> pdb=" O TYR C 567 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 567 through 571' Processing helix chain 'A' and resid 3 through 17 removed outlier: 3.962A pdb=" N GLN A 16 " --> pdb=" O TRP A 12 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 54 removed outlier: 3.820A pdb=" N ILE A 26 " --> pdb=" O ARG A 22 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 39 " --> pdb=" O GLY A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 109 removed outlier: 4.914A pdb=" N LEU A 64 " --> pdb=" O ALA A 61 " (cutoff:3.500A) Proline residue: A 65 - end of helix removed outlier: 3.770A pdb=" N HIS A 93 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE A 94 " --> pdb=" O GLY A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 116 removed outlier: 4.031A pdb=" N GLN A 115 " --> pdb=" O PRO A 111 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLY A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 111 through 116' Processing helix chain 'A' and resid 119 through 138 removed outlier: 3.785A pdb=" N GLN A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE A 130 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N MET A 133 " --> pdb=" O GLN A 129 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N HIS A 134 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ASP A 135 " --> pdb=" O ASP A 131 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N TYR A 136 " --> pdb=" O ASP A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 161 removed outlier: 4.458A pdb=" N ALA A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL A 148 " --> pdb=" O MET A 144 " (cutoff:3.500A) Proline residue: A 151 - end of helix Proline residue: A 160 - end of helix Processing helix chain 'A' and resid 163 through 180 Proline residue: A 174 - end of helix Proline residue: A 177 - end of helix Processing helix chain 'A' and resid 184 through 210 removed outlier: 3.836A pdb=" N ARG A 192 " --> pdb=" O ALA A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 218 Processing helix chain 'A' and resid 223 through 272 removed outlier: 3.595A pdb=" N ARG A 238 " --> pdb=" O ASP A 234 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 245 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR A 272 " --> pdb=" O PHE A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 329 Proline residue: A 298 - end of helix Proline residue: A 303 - end of helix removed outlier: 4.079A pdb=" N HIS A 312 " --> pdb=" O GLY A 308 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA A 313 " --> pdb=" O THR A 309 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP A 322 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N SER A 323 " --> pdb=" O GLY A 319 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU A 324 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS A 325 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR A 326 " --> pdb=" O ASP A 322 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE A 327 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET A 328 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU A 329 " --> pdb=" O LYS A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 397 Processing helix chain 'A' and resid 413 through 415 No H-bonds generated for 'chain 'A' and resid 413 through 415' Processing helix chain 'A' and resid 418 through 424 removed outlier: 4.334A pdb=" N LYS A 423 " --> pdb=" O GLU A 419 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N HIS A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 442 No H-bonds generated for 'chain 'A' and resid 439 through 442' Processing helix chain 'A' and resid 453 through 460 Processing helix chain 'A' and resid 468 through 470 No H-bonds generated for 'chain 'A' and resid 468 through 470' Processing helix chain 'A' and resid 489 through 500 removed outlier: 4.168A pdb=" N ARG A 493 " --> pdb=" O GLY A 489 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL A 494 " --> pdb=" O GLN A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 534 removed outlier: 4.469A pdb=" N ARG A 534 " --> pdb=" O ALA A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 570 No H-bonds generated for 'chain 'A' and resid 567 through 570' Processing helix chain 'A' and resid 576 through 587 Processing helix chain 'D' and resid 2 through 8 Proline residue: D 6 - end of helix Processing helix chain 'D' and resid 15 through 48 removed outlier: 3.570A pdb=" N GLY D 21 " --> pdb=" O MET D 17 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE D 22 " --> pdb=" O LEU D 18 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU D 36 " --> pdb=" O SER D 32 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA D 47 " --> pdb=" O LEU D 43 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL D 48 " --> pdb=" O SER D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 104 Proline residue: D 62 - end of helix removed outlier: 3.903A pdb=" N GLY D 65 " --> pdb=" O PRO D 62 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL D 66 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ARG D 67 " --> pdb=" O ALA D 64 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLY D 68 " --> pdb=" O GLY D 65 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA D 70 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE D 71 " --> pdb=" O GLY D 68 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N THR D 72 " --> pdb=" O ALA D 69 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ARG D 73 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA D 75 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLY D 76 " --> pdb=" O ARG D 73 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TYR D 78 " --> pdb=" O ALA D 75 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE D 79 " --> pdb=" O GLY D 76 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG D 81 " --> pdb=" O TYR D 78 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU D 82 " --> pdb=" O PHE D 79 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL D 83 " --> pdb=" O GLU D 80 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER D 84 " --> pdb=" O ARG D 81 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N HIS D 85 " --> pdb=" O LEU D 82 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N PHE D 89 " --> pdb=" O ASP D 86 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N GLN D 93 " --> pdb=" O ARG D 90 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N THR D 99 " --> pdb=" O ARG D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 124 removed outlier: 4.215A pdb=" N LEU D 120 " --> pdb=" O GLN D 116 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ASN D 121 " --> pdb=" O GLY D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 135 Processing helix chain 'D' and resid 139 through 157 removed outlier: 4.235A pdb=" N PHE D 157 " --> pdb=" O ILE D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 206 Proline residue: D 178 - end of helix removed outlier: 4.614A pdb=" N ARG D 183 " --> pdb=" O PRO D 179 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ALA D 184 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY D 185 " --> pdb=" O PHE D 181 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER D 187 " --> pdb=" O ARG D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 215 Processing helix chain 'D' and resid 220 through 265 removed outlier: 4.010A pdb=" N GLN D 232 " --> pdb=" O ASN D 228 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N TRP D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 318 removed outlier: 3.510A pdb=" N ALA D 287 " --> pdb=" O PHE D 283 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N PHE D 291 " --> pdb=" O ALA D 287 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N GLU D 292 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ALA D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU D 294 " --> pdb=" O ALA D 290 " (cutoff:3.500A) Proline residue: D 296 - end of helix removed outlier: 5.173A pdb=" N GLY D 299 " --> pdb=" O ALA D 295 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA D 300 " --> pdb=" O PRO D 296 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE D 301 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N HIS D 303 " --> pdb=" O GLY D 299 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LEU D 304 " --> pdb=" O ALA D 300 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N GLY D 305 " --> pdb=" O PHE D 301 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N GLN D 306 " --> pdb=" O GLN D 302 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL D 307 " --> pdb=" O HIS D 303 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE D 308 " --> pdb=" O LEU D 304 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ALA D 309 " --> pdb=" O GLY D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 386 removed outlier: 3.673A pdb=" N LEU D 383 " --> pdb=" O LYS D 379 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU D 386 " --> pdb=" O LEU D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 412 No H-bonds generated for 'chain 'D' and resid 409 through 412' Processing helix chain 'D' and resid 430 through 434 Processing helix chain 'D' and resid 445 through 452 Processing helix chain 'D' and resid 479 through 488 removed outlier: 3.717A pdb=" N ALA D 488 " --> pdb=" O ALA D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 507 through 520 Processing helix chain 'D' and resid 558 through 561 No H-bonds generated for 'chain 'D' and resid 558 through 561' Processing helix chain 'D' and resid 567 through 571 removed outlier: 4.073A pdb=" N GLN D 571 " --> pdb=" O TYR D 567 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 567 through 571' Processing helix chain 'E' and resid 3 through 17 removed outlier: 3.962A pdb=" N GLN E 16 " --> pdb=" O TRP E 12 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER E 17 " --> pdb=" O LEU E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 54 removed outlier: 3.821A pdb=" N ILE E 26 " --> pdb=" O ARG E 22 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE E 39 " --> pdb=" O GLY E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 109 removed outlier: 4.914A pdb=" N LEU E 64 " --> pdb=" O ALA E 61 " (cutoff:3.500A) Proline residue: E 65 - end of helix removed outlier: 3.770A pdb=" N HIS E 93 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE E 94 " --> pdb=" O GLY E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 116 removed outlier: 4.031A pdb=" N GLN E 115 " --> pdb=" O PRO E 111 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLY E 116 " --> pdb=" O ALA E 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 111 through 116' Processing helix chain 'E' and resid 119 through 138 removed outlier: 3.785A pdb=" N GLN E 129 " --> pdb=" O LEU E 125 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE E 130 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N MET E 133 " --> pdb=" O GLN E 129 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N HIS E 134 " --> pdb=" O ILE E 130 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ASP E 135 " --> pdb=" O ASP E 131 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N TYR E 136 " --> pdb=" O ASP E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 161 removed outlier: 4.459A pdb=" N ALA E 145 " --> pdb=" O LEU E 141 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL E 148 " --> pdb=" O MET E 144 " (cutoff:3.500A) Proline residue: E 151 - end of helix Proline residue: E 160 - end of helix Processing helix chain 'E' and resid 163 through 180 Proline residue: E 174 - end of helix Proline residue: E 177 - end of helix Processing helix chain 'E' and resid 184 through 210 removed outlier: 3.835A pdb=" N ARG E 192 " --> pdb=" O ALA E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 218 Processing helix chain 'E' and resid 223 through 272 removed outlier: 3.595A pdb=" N ARG E 238 " --> pdb=" O ASP E 234 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU E 245 " --> pdb=" O GLU E 241 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR E 272 " --> pdb=" O PHE E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 329 Proline residue: E 298 - end of helix Proline residue: E 303 - end of helix removed outlier: 4.079A pdb=" N HIS E 312 " --> pdb=" O GLY E 308 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA E 313 " --> pdb=" O THR E 309 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP E 322 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N SER E 323 " --> pdb=" O GLY E 319 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU E 324 " --> pdb=" O ALA E 320 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS E 325 " --> pdb=" O ALA E 321 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR E 326 " --> pdb=" O ASP E 322 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE E 327 " --> pdb=" O SER E 323 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET E 328 " --> pdb=" O LEU E 324 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU E 329 " --> pdb=" O LYS E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 397 Processing helix chain 'E' and resid 413 through 415 No H-bonds generated for 'chain 'E' and resid 413 through 415' Processing helix chain 'E' and resid 418 through 424 removed outlier: 4.333A pdb=" N LYS E 423 " --> pdb=" O GLU E 419 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N HIS E 424 " --> pdb=" O SER E 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 442 No H-bonds generated for 'chain 'E' and resid 439 through 442' Processing helix chain 'E' and resid 453 through 460 Processing helix chain 'E' and resid 468 through 470 No H-bonds generated for 'chain 'E' and resid 468 through 470' Processing helix chain 'E' and resid 489 through 500 removed outlier: 4.168A pdb=" N ARG E 493 " --> pdb=" O GLY E 489 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL E 494 " --> pdb=" O GLN E 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 518 through 534 removed outlier: 4.469A pdb=" N ARG E 534 " --> pdb=" O ALA E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 567 through 570 No H-bonds generated for 'chain 'E' and resid 567 through 570' Processing helix chain 'E' and resid 576 through 587 Processing sheet with id= A, first strand: chain 'C' and resid 361 through 363 removed outlier: 3.645A pdb=" N THR C 340 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG C 342 " --> pdb=" O GLU C 396 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLU C 396 " --> pdb=" O ARG C 342 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N VAL C 344 " --> pdb=" O GLN C 394 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLN C 394 " --> pdb=" O VAL C 344 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 540 through 543 removed outlier: 5.971A pdb=" N VAL C 526 " --> pdb=" O ILE C 369 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ILE C 371 " --> pdb=" O VAL C 526 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N MET C 528 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU C 527 " --> pdb=" O VAL C 496 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU C 498 " --> pdb=" O LEU C 527 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N SER C 417 " --> pdb=" O LEU C 497 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 380 through 382 removed outlier: 3.816A pdb=" N GLU A 563 " --> pdb=" O VAL A 555 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N GLN A 557 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ILE A 561 " --> pdb=" O GLN A 557 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 507 through 509 Processing sheet with id= E, first strand: chain 'A' and resid 351 through 355 removed outlier: 5.646A pdb=" N LEU A 369 " --> pdb=" O ASP A 354 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 361 through 363 removed outlier: 3.645A pdb=" N THR D 340 " --> pdb=" O LEU D 398 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG D 342 " --> pdb=" O GLU D 396 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLU D 396 " --> pdb=" O ARG D 342 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N VAL D 344 " --> pdb=" O GLN D 394 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLN D 394 " --> pdb=" O VAL D 344 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 540 through 543 removed outlier: 5.970A pdb=" N VAL D 526 " --> pdb=" O ILE D 369 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ILE D 371 " --> pdb=" O VAL D 526 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N MET D 528 " --> pdb=" O ILE D 371 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU D 527 " --> pdb=" O VAL D 496 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU D 498 " --> pdb=" O LEU D 527 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N SER D 417 " --> pdb=" O LEU D 497 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 380 through 382 removed outlier: 3.815A pdb=" N GLU E 563 " --> pdb=" O VAL E 555 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N GLN E 557 " --> pdb=" O ILE E 561 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ILE E 561 " --> pdb=" O GLN E 557 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 507 through 509 Processing sheet with id= J, first strand: chain 'E' and resid 351 through 355 removed outlier: 5.646A pdb=" N LEU E 369 " --> pdb=" O ASP E 354 " (cutoff:3.500A) 878 hydrogen bonds defined for protein. 2226 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: 5.18 Time building geometry restraints manager: 7.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5322 1.34 - 1.45: 2719 1.45 - 1.57: 10367 1.57 - 1.69: 20 1.69 - 1.81: 114 Bond restraints: 18542 Sorted by residual: bond pdb=" N PHE E 159 " pdb=" CA PHE E 159 " ideal model delta sigma weight residual 1.462 1.489 -0.027 8.50e-03 1.38e+04 1.02e+01 bond pdb=" N ILE A 158 " pdb=" CA ILE A 158 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.21e-02 6.83e+03 8.58e+00 bond pdb=" N ILE A 357 " pdb=" CA ILE A 357 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.24e-02 6.50e+03 8.37e+00 bond pdb=" N ILE E 357 " pdb=" CA ILE E 357 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.24e-02 6.50e+03 8.06e+00 bond pdb=" N ILE E 158 " pdb=" CA ILE E 158 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.33e-02 5.65e+03 7.47e+00 ... (remaining 18537 not shown) Histogram of bond angle deviations from ideal: 100.10 - 106.96: 542 106.96 - 113.82: 10450 113.82 - 120.68: 7968 120.68 - 127.55: 6045 127.55 - 134.41: 211 Bond angle restraints: 25216 Sorted by residual: angle pdb=" PB ATP E 601 " pdb=" O3B ATP E 601 " pdb=" PG ATP E 601 " ideal model delta sigma weight residual 139.87 129.89 9.98 1.00e+00 1.00e+00 9.96e+01 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 129.90 9.97 1.00e+00 1.00e+00 9.95e+01 angle pdb=" PB ATP D 601 " pdb=" O3B ATP D 601 " pdb=" PG ATP D 601 " ideal model delta sigma weight residual 139.87 130.25 9.62 1.00e+00 1.00e+00 9.26e+01 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 130.26 9.61 1.00e+00 1.00e+00 9.23e+01 angle pdb=" PA ATP A 601 " pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 136.83 129.59 7.24 1.00e+00 1.00e+00 5.24e+01 ... (remaining 25211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 9247 17.88 - 35.76: 1455 35.76 - 53.64: 339 53.64 - 71.52: 59 71.52 - 89.40: 36 Dihedral angle restraints: 11136 sinusoidal: 4474 harmonic: 6662 Sorted by residual: dihedral pdb=" CA ASN C 58 " pdb=" C ASN C 58 " pdb=" N TYR C 59 " pdb=" CA TYR C 59 " ideal model delta harmonic sigma weight residual -180.00 -158.61 -21.39 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA ASN D 58 " pdb=" C ASN D 58 " pdb=" N TYR D 59 " pdb=" CA TYR D 59 " ideal model delta harmonic sigma weight residual -180.00 -158.67 -21.33 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA PHE C 57 " pdb=" C PHE C 57 " pdb=" N ASN C 58 " pdb=" CA ASN C 58 " ideal model delta harmonic sigma weight residual -180.00 -162.10 -17.90 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 11133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2139 0.038 - 0.076: 613 0.076 - 0.114: 147 0.114 - 0.152: 23 0.152 - 0.190: 6 Chirality restraints: 2928 Sorted by residual: chirality pdb=" CA ILE A 357 " pdb=" N ILE A 357 " pdb=" C ILE A 357 " pdb=" CB ILE A 357 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.01e-01 chirality pdb=" CA ILE E 357 " pdb=" N ILE E 357 " pdb=" C ILE E 357 " pdb=" CB ILE E 357 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.97e-01 chirality pdb=" CA ILE A 158 " pdb=" N ILE A 158 " pdb=" C ILE A 158 " pdb=" CB ILE A 158 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.62e-01 ... (remaining 2925 not shown) Planarity restraints: 3206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN D 273 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.85e+00 pdb=" C ASN D 273 " -0.038 2.00e-02 2.50e+03 pdb=" O ASN D 273 " 0.014 2.00e-02 2.50e+03 pdb=" N ALA D 274 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 273 " -0.011 2.00e-02 2.50e+03 2.18e-02 4.75e+00 pdb=" C ASN C 273 " 0.038 2.00e-02 2.50e+03 pdb=" O ASN C 273 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA C 274 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL E 150 " 0.029 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO E 151 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO E 151 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 151 " 0.025 5.00e-02 4.00e+02 ... (remaining 3203 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1377 2.74 - 3.28: 18103 3.28 - 3.82: 28444 3.82 - 4.36: 31455 4.36 - 4.90: 56542 Nonbonded interactions: 135921 Sorted by model distance: nonbonded pdb=" NE2 GLN C 553 " pdb=" CG2 THR C 555 " model vdw 2.200 3.540 nonbonded pdb=" NE2 GLN D 553 " pdb=" CG2 THR D 555 " model vdw 2.200 3.540 nonbonded pdb=" NH2 ARG A 99 " pdb=" OD1 ASP A 131 " model vdw 2.269 2.520 nonbonded pdb=" NH2 ARG E 99 " pdb=" OD1 ASP E 131 " model vdw 2.269 2.520 nonbonded pdb=" CG2 THR C 555 " pdb=" OE1 GLU C 558 " model vdw 2.295 3.460 ... (remaining 135916 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 1.480 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: 7.660 Check model and map are aligned: 0.320 Set scattering table: 0.190 Process input model: 47.390 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 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 : 0.003 0.042 18542 Z= 0.203 Angle : 0.672 9.982 25216 Z= 0.383 Chirality : 0.039 0.190 2928 Planarity : 0.004 0.045 3206 Dihedral : 18.348 89.402 6840 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.95 % Favored : 91.88 % Rotamer: Outliers : 0.32 % Allowed : 31.97 % Favored : 67.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.19), residues: 2314 helix: 1.91 (0.15), residues: 1294 sheet: -1.68 (0.50), residues: 108 loop : -2.93 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 550 HIS 0.004 0.001 HIS A 519 PHE 0.012 0.001 PHE C 145 TYR 0.012 0.001 TYR A 88 ARG 0.005 0.000 ARG A 220 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 259 time to evaluate : 2.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.8344 (mmm) cc_final: 0.8114 (mtp) REVERT: E 159 PHE cc_start: 0.8528 (OUTLIER) cc_final: 0.8086 (t80) outliers start: 6 outliers final: 2 residues processed: 265 average time/residue: 0.3439 time to fit residues: 131.4446 Evaluate side-chains 153 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 150 time to evaluate : 2.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 416 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 194 optimal weight: 0.9980 chunk 174 optimal weight: 0.7980 chunk 96 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 117 optimal weight: 0.8980 chunk 93 optimal weight: 7.9990 chunk 180 optimal weight: 0.5980 chunk 69 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 chunk 208 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 208 GLN ** C 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 GLN A 394 ASN ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 GLN ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 421 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18542 Z= 0.181 Angle : 0.580 8.692 25216 Z= 0.299 Chirality : 0.039 0.200 2928 Planarity : 0.005 0.057 3206 Dihedral : 7.725 70.522 2672 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.95 % Favored : 90.97 % Rotamer: Outliers : 2.55 % Allowed : 31.02 % Favored : 66.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.19), residues: 2314 helix: 1.68 (0.15), residues: 1302 sheet: -1.50 (0.51), residues: 108 loop : -2.86 (0.19), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 550 HIS 0.008 0.001 HIS A 542 PHE 0.011 0.001 PHE C 57 TYR 0.016 0.001 TYR C 78 ARG 0.006 0.000 ARG C 374 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 169 time to evaluate : 2.169 Fit side-chains REVERT: C 251 MET cc_start: 0.8412 (tpp) cc_final: 0.7662 (tpp) REVERT: C 301 PHE cc_start: 0.8841 (OUTLIER) cc_final: 0.8616 (m-80) REVERT: C 567 TYR cc_start: 0.7508 (t80) cc_final: 0.7205 (t80) REVERT: A 240 MET cc_start: 0.8355 (mmm) cc_final: 0.8061 (mtp) REVERT: A 361 GLU cc_start: 0.7247 (tt0) cc_final: 0.6603 (pp20) REVERT: A 396 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8388 (mt) REVERT: A 456 GLN cc_start: 0.8401 (mm-40) cc_final: 0.7980 (mp10) outliers start: 48 outliers final: 23 residues processed: 211 average time/residue: 0.3085 time to fit residues: 100.5294 Evaluate side-chains 161 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 136 time to evaluate : 2.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 301 PHE Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 377 CYS Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain D residue 543 ILE Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 544 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 116 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 173 optimal weight: 0.7980 chunk 142 optimal weight: 0.0060 chunk 57 optimal weight: 2.9990 chunk 209 optimal weight: 0.0270 chunk 226 optimal weight: 4.9990 chunk 186 optimal weight: 0.8980 chunk 207 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 167 optimal weight: 4.9990 overall best weight: 0.5054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 208 GLN C 302 GLN ** C 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 2 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18542 Z= 0.154 Angle : 0.540 10.325 25216 Z= 0.276 Chirality : 0.037 0.154 2928 Planarity : 0.004 0.043 3206 Dihedral : 7.252 82.802 2666 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.47 % Favored : 91.44 % Rotamer: Outliers : 3.82 % Allowed : 29.90 % Favored : 66.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.19), residues: 2314 helix: 1.61 (0.15), residues: 1302 sheet: -1.58 (0.49), residues: 114 loop : -2.75 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 550 HIS 0.004 0.001 HIS A 542 PHE 0.026 0.001 PHE A 205 TYR 0.011 0.001 TYR C 78 ARG 0.003 0.000 ARG C 532 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 149 time to evaluate : 1.932 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 80 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7577 (tp30) REVERT: C 251 MET cc_start: 0.8384 (tpp) cc_final: 0.7666 (tpp) REVERT: C 567 TYR cc_start: 0.7428 (t80) cc_final: 0.7199 (t80) REVERT: A 240 MET cc_start: 0.8362 (mmm) cc_final: 0.7996 (mtp) REVERT: A 361 GLU cc_start: 0.7307 (tt0) cc_final: 0.6603 (pp20) REVERT: A 396 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8365 (mt) REVERT: D 534 ARG cc_start: 0.7177 (ttm-80) cc_final: 0.6812 (tpp-160) REVERT: E 2 ASN cc_start: 0.7897 (OUTLIER) cc_final: 0.7123 (p0) REVERT: E 159 PHE cc_start: 0.8366 (OUTLIER) cc_final: 0.7750 (t80) outliers start: 72 outliers final: 32 residues processed: 216 average time/residue: 0.3108 time to fit residues: 103.4381 Evaluate side-chains 170 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 134 time to evaluate : 2.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 377 CYS Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 499 ASP Chi-restraints excluded: chain E residue 2 ASN Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 438 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 206 optimal weight: 8.9990 chunk 157 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 99 optimal weight: 8.9990 chunk 140 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 chunk 222 optimal weight: 0.7980 chunk 109 optimal weight: 5.9990 chunk 199 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 190 GLN ** C 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 GLN ** C 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 2 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 18542 Z= 0.278 Angle : 0.611 10.166 25216 Z= 0.312 Chirality : 0.041 0.147 2928 Planarity : 0.005 0.045 3206 Dihedral : 7.312 81.230 2666 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.46 % Favored : 90.45 % Rotamer: Outliers : 4.29 % Allowed : 30.43 % Favored : 65.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.18), residues: 2314 helix: 1.36 (0.15), residues: 1296 sheet: -1.53 (0.50), residues: 114 loop : -2.97 (0.19), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 41 HIS 0.006 0.001 HIS E 312 PHE 0.015 0.001 PHE C 89 TYR 0.017 0.001 TYR C 7 ARG 0.006 0.000 ARG E 220 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 141 time to evaluate : 1.849 Fit side-chains revert: symmetry clash REVERT: C 172 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7647 (mt) REVERT: C 524 LYS cc_start: 0.6299 (OUTLIER) cc_final: 0.6069 (mmtp) REVERT: C 567 TYR cc_start: 0.7497 (t80) cc_final: 0.7285 (t80) REVERT: A 16 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.6551 (mp10) REVERT: A 159 PHE cc_start: 0.8474 (OUTLIER) cc_final: 0.8187 (t80) REVERT: A 240 MET cc_start: 0.8592 (mmm) cc_final: 0.8067 (mtp) REVERT: A 344 LEU cc_start: 0.6986 (tp) cc_final: 0.6683 (tt) REVERT: A 361 GLU cc_start: 0.7431 (tt0) cc_final: 0.6646 (pp20) REVERT: A 456 GLN cc_start: 0.8429 (mm-40) cc_final: 0.8097 (mp10) REVERT: E 2 ASN cc_start: 0.8053 (OUTLIER) cc_final: 0.7200 (p0) REVERT: E 159 PHE cc_start: 0.8535 (OUTLIER) cc_final: 0.7965 (t80) REVERT: E 344 LEU cc_start: 0.7216 (OUTLIER) cc_final: 0.6950 (mt) outliers start: 81 outliers final: 44 residues processed: 212 average time/residue: 0.3189 time to fit residues: 104.7775 Evaluate side-chains 178 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 127 time to evaluate : 2.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 524 LYS Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain D residue 543 ILE Chi-restraints excluded: chain E residue 2 ASN Chi-restraints excluded: chain E residue 54 MET Chi-restraints excluded: chain E residue 59 ARG Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 544 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 185 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 165 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 chunk 189 optimal weight: 10.0000 chunk 153 optimal weight: 0.0870 chunk 0 optimal weight: 7.9990 chunk 113 optimal weight: 5.9990 chunk 199 optimal weight: 4.9990 chunk 56 optimal weight: 20.0000 overall best weight: 3.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 GLN A 394 ASN ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 2 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 18542 Z= 0.442 Angle : 0.710 9.867 25216 Z= 0.368 Chirality : 0.045 0.170 2928 Planarity : 0.005 0.051 3206 Dihedral : 7.695 86.691 2666 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.29 % Favored : 89.63 % Rotamer: Outliers : 5.46 % Allowed : 30.12 % Favored : 64.42 % 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: -1.22 (0.18), residues: 2314 helix: 0.67 (0.15), residues: 1300 sheet: -1.76 (0.47), residues: 122 loop : -3.03 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 427 HIS 0.007 0.001 HIS A 542 PHE 0.027 0.002 PHE A 205 TYR 0.021 0.002 TYR C 7 ARG 0.005 0.001 ARG C 221 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 121 time to evaluate : 1.977 Fit side-chains REVERT: C 58 ASN cc_start: 0.8101 (OUTLIER) cc_final: 0.7840 (m-40) REVERT: C 524 LYS cc_start: 0.6305 (OUTLIER) cc_final: 0.6008 (mmtp) REVERT: C 567 TYR cc_start: 0.7410 (t80) cc_final: 0.7200 (t80) REVERT: A 16 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.6525 (mp10) REVERT: A 159 PHE cc_start: 0.8625 (OUTLIER) cc_final: 0.8234 (t80) REVERT: A 240 MET cc_start: 0.8643 (mmm) cc_final: 0.8092 (mtp) REVERT: A 344 LEU cc_start: 0.6887 (tp) cc_final: 0.6566 (tt) REVERT: A 361 GLU cc_start: 0.7664 (tt0) cc_final: 0.7352 (pt0) REVERT: A 389 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7493 (mttp) REVERT: A 456 GLN cc_start: 0.8493 (mm-40) cc_final: 0.8041 (mt0) REVERT: D 127 VAL cc_start: 0.9048 (OUTLIER) cc_final: 0.8848 (t) REVERT: E 2 ASN cc_start: 0.8278 (OUTLIER) cc_final: 0.7555 (p0) REVERT: E 159 PHE cc_start: 0.8582 (OUTLIER) cc_final: 0.8114 (t80) REVERT: E 542 HIS cc_start: 0.8334 (OUTLIER) cc_final: 0.8043 (t70) outliers start: 103 outliers final: 56 residues processed: 214 average time/residue: 0.2829 time to fit residues: 94.5991 Evaluate side-chains 181 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 116 time to evaluate : 2.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 506 ASP Chi-restraints excluded: chain C residue 524 LYS Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 389 LYS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 93 GLN Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain D residue 543 ILE Chi-restraints excluded: chain E residue 2 ASN Chi-restraints excluded: chain E residue 59 ARG Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 542 HIS Chi-restraints excluded: chain E residue 544 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 74 optimal weight: 0.6980 chunk 200 optimal weight: 0.7980 chunk 43 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 222 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 2 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18542 Z= 0.203 Angle : 0.578 13.736 25216 Z= 0.295 Chirality : 0.039 0.143 2928 Planarity : 0.004 0.051 3206 Dihedral : 7.349 88.605 2666 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.33 % Favored : 90.58 % Rotamer: Outliers : 3.71 % Allowed : 31.87 % Favored : 64.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.18), residues: 2314 helix: 1.05 (0.15), residues: 1306 sheet: -1.38 (0.50), residues: 112 loop : -2.97 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 427 HIS 0.003 0.001 HIS E 312 PHE 0.011 0.001 PHE D 160 TYR 0.014 0.001 TYR C 7 ARG 0.005 0.000 ARG E 220 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 129 time to evaluate : 2.057 Fit side-chains REVERT: A 16 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.6697 (mp10) REVERT: A 159 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.8203 (t80) REVERT: A 185 MET cc_start: 0.7088 (pmm) cc_final: 0.6840 (pmm) REVERT: A 240 MET cc_start: 0.8561 (mmm) cc_final: 0.8022 (mtp) REVERT: A 344 LEU cc_start: 0.6985 (tp) cc_final: 0.6674 (tt) REVERT: A 361 GLU cc_start: 0.7671 (tt0) cc_final: 0.7360 (pt0) REVERT: A 389 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7482 (mttp) REVERT: A 456 GLN cc_start: 0.8441 (mm-40) cc_final: 0.8099 (mp10) REVERT: A 550 TRP cc_start: 0.6488 (t-100) cc_final: 0.5589 (m100) REVERT: D 301 PHE cc_start: 0.8767 (OUTLIER) cc_final: 0.8333 (t80) REVERT: E 2 ASN cc_start: 0.8011 (OUTLIER) cc_final: 0.7426 (p0) REVERT: E 159 PHE cc_start: 0.8576 (OUTLIER) cc_final: 0.8015 (t80) REVERT: E 542 HIS cc_start: 0.8234 (OUTLIER) cc_final: 0.8007 (t70) outliers start: 70 outliers final: 42 residues processed: 193 average time/residue: 0.2849 time to fit residues: 85.3805 Evaluate side-chains 168 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 119 time to evaluate : 1.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 506 ASP Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 389 LYS Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain D residue 93 GLN Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 377 CYS Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain D residue 543 ILE Chi-restraints excluded: chain E residue 2 ASN Chi-restraints excluded: chain E residue 59 ARG Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 542 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 214 optimal weight: 0.0970 chunk 25 optimal weight: 7.9990 chunk 126 optimal weight: 5.9990 chunk 162 optimal weight: 3.9990 chunk 125 optimal weight: 0.0870 chunk 187 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 221 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 102 optimal weight: 20.0000 overall best weight: 0.6362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 GLN A 461 ASN D 273 ASN ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 2 ASN E 115 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18542 Z= 0.162 Angle : 0.562 13.028 25216 Z= 0.284 Chirality : 0.037 0.142 2928 Planarity : 0.004 0.049 3206 Dihedral : 7.098 88.831 2666 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.73 % Favored : 91.18 % Rotamer: Outliers : 3.55 % Allowed : 32.18 % Favored : 64.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.19), residues: 2314 helix: 1.31 (0.15), residues: 1304 sheet: -1.33 (0.50), residues: 114 loop : -2.90 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 427 HIS 0.002 0.000 HIS E 89 PHE 0.011 0.001 PHE A 205 TYR 0.019 0.001 TYR C 567 ARG 0.004 0.000 ARG E 220 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 132 time to evaluate : 2.242 Fit side-chains REVERT: C 172 LEU cc_start: 0.7997 (mm) cc_final: 0.7744 (mp) REVERT: A 16 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.6752 (mp10) REVERT: A 159 PHE cc_start: 0.8428 (OUTLIER) cc_final: 0.8209 (t80) REVERT: A 185 MET cc_start: 0.6934 (pmm) cc_final: 0.6665 (pmm) REVERT: A 240 MET cc_start: 0.8459 (mmm) cc_final: 0.8032 (mtp) REVERT: A 389 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7563 (mttp) REVERT: A 456 GLN cc_start: 0.8423 (mm-40) cc_final: 0.8093 (mp10) REVERT: A 533 LEU cc_start: 0.7493 (mm) cc_final: 0.7288 (mm) REVERT: A 550 TRP cc_start: 0.6409 (t-100) cc_final: 0.5714 (m100) REVERT: D 301 PHE cc_start: 0.8695 (OUTLIER) cc_final: 0.8245 (t80) REVERT: D 541 GLN cc_start: 0.7644 (mp10) cc_final: 0.7404 (mp10) REVERT: E 2 ASN cc_start: 0.7698 (OUTLIER) cc_final: 0.7096 (p0) REVERT: E 159 PHE cc_start: 0.8547 (OUTLIER) cc_final: 0.7945 (t80) REVERT: E 384 ARG cc_start: 0.7861 (mtp85) cc_final: 0.7561 (ttm-80) REVERT: E 506 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8713 (tt) outliers start: 67 outliers final: 46 residues processed: 196 average time/residue: 0.2907 time to fit residues: 88.2291 Evaluate side-chains 176 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 123 time to evaluate : 1.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 506 ASP Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 59 ARG Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 389 LYS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 273 ASN Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 377 CYS Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain D residue 543 ILE Chi-restraints excluded: chain E residue 2 ASN Chi-restraints excluded: chain E residue 54 MET Chi-restraints excluded: chain E residue 59 ARG Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 115 GLN Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain E residue 532 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 137 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 132 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 43 optimal weight: 0.0970 chunk 42 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 151 optimal weight: 10.0000 chunk 109 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 174 optimal weight: 0.9980 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 273 ASN ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18542 Z= 0.165 Angle : 0.562 15.291 25216 Z= 0.282 Chirality : 0.038 0.190 2928 Planarity : 0.004 0.045 3206 Dihedral : 7.017 88.837 2666 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.60 % Favored : 91.31 % Rotamer: Outliers : 3.18 % Allowed : 32.66 % Favored : 64.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.19), residues: 2314 helix: 1.39 (0.15), residues: 1304 sheet: -1.22 (0.50), residues: 114 loop : -2.89 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 427 HIS 0.002 0.000 HIS E 312 PHE 0.017 0.001 PHE A 205 TYR 0.010 0.001 TYR C 7 ARG 0.004 0.000 ARG E 220 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 128 time to evaluate : 1.934 Fit side-chains revert: symmetry clash REVERT: C 172 LEU cc_start: 0.8005 (mm) cc_final: 0.7742 (mp) REVERT: A 16 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.6781 (mp10) REVERT: A 159 PHE cc_start: 0.8418 (OUTLIER) cc_final: 0.8194 (t80) REVERT: A 185 MET cc_start: 0.6926 (pmm) cc_final: 0.6691 (pmm) REVERT: A 240 MET cc_start: 0.8422 (mmm) cc_final: 0.8018 (mtp) REVERT: A 389 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7550 (mttp) REVERT: A 456 GLN cc_start: 0.8409 (mm-40) cc_final: 0.8078 (mp10) REVERT: A 550 TRP cc_start: 0.6186 (t-100) cc_final: 0.5746 (m100) REVERT: A 556 MET cc_start: 0.7171 (tmm) cc_final: 0.6505 (ttt) REVERT: D 301 PHE cc_start: 0.8688 (OUTLIER) cc_final: 0.8232 (t80) REVERT: D 479 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7608 (mt-10) REVERT: D 541 GLN cc_start: 0.7651 (mp10) cc_final: 0.7397 (mp10) REVERT: E 159 PHE cc_start: 0.8543 (OUTLIER) cc_final: 0.7940 (t80) REVERT: E 384 ARG cc_start: 0.7857 (mtp85) cc_final: 0.7517 (ttm-80) REVERT: E 506 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8693 (tt) outliers start: 60 outliers final: 48 residues processed: 183 average time/residue: 0.2950 time to fit residues: 83.3563 Evaluate side-chains 178 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 123 time to evaluate : 1.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 506 ASP Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 389 LYS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 273 ASN Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 377 CYS Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 479 GLU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain D residue 543 ILE Chi-restraints excluded: chain E residue 54 MET Chi-restraints excluded: chain E residue 59 ARG Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 115 GLN Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 506 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 201 optimal weight: 3.9990 chunk 212 optimal weight: 5.9990 chunk 193 optimal weight: 2.9990 chunk 206 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 162 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 186 optimal weight: 0.9990 chunk 195 optimal weight: 0.6980 chunk 205 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 273 ASN ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18542 Z= 0.172 Angle : 0.565 14.890 25216 Z= 0.283 Chirality : 0.038 0.169 2928 Planarity : 0.004 0.040 3206 Dihedral : 6.958 89.152 2666 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.51 % Favored : 91.40 % Rotamer: Outliers : 3.55 % Allowed : 32.18 % Favored : 64.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.19), residues: 2314 helix: 1.38 (0.15), residues: 1312 sheet: -1.17 (0.50), residues: 114 loop : -2.90 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 427 HIS 0.003 0.001 HIS A 542 PHE 0.017 0.001 PHE A 205 TYR 0.019 0.001 TYR C 567 ARG 0.004 0.000 ARG E 220 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 125 time to evaluate : 2.179 Fit side-chains revert: symmetry clash REVERT: C 172 LEU cc_start: 0.8021 (mm) cc_final: 0.7753 (mp) REVERT: A 16 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.6663 (mp10) REVERT: A 159 PHE cc_start: 0.8425 (OUTLIER) cc_final: 0.8199 (t80) REVERT: A 185 MET cc_start: 0.6985 (pmm) cc_final: 0.6754 (pmm) REVERT: A 240 MET cc_start: 0.8442 (mmm) cc_final: 0.8056 (mtp) REVERT: A 389 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7596 (mttp) REVERT: A 456 GLN cc_start: 0.8390 (mm-40) cc_final: 0.8060 (mp10) REVERT: A 550 TRP cc_start: 0.6215 (t-100) cc_final: 0.5838 (m100) REVERT: D 67 ARG cc_start: 0.7152 (OUTLIER) cc_final: 0.6195 (ptt90) REVERT: D 301 PHE cc_start: 0.8688 (OUTLIER) cc_final: 0.8232 (t80) REVERT: D 479 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7592 (mt-10) REVERT: D 541 GLN cc_start: 0.7648 (mp10) cc_final: 0.7385 (mp10) REVERT: E 159 PHE cc_start: 0.8543 (OUTLIER) cc_final: 0.7937 (t80) REVERT: E 506 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8698 (tt) outliers start: 67 outliers final: 52 residues processed: 188 average time/residue: 0.2940 time to fit residues: 85.4995 Evaluate side-chains 182 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 122 time to evaluate : 2.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 506 ASP Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 389 LYS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 273 ASN Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 377 CYS Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 479 GLU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain D residue 543 ILE Chi-restraints excluded: chain E residue 54 MET Chi-restraints excluded: chain E residue 59 ARG Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain E residue 532 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 135 optimal weight: 3.9990 chunk 218 optimal weight: 0.0970 chunk 133 optimal weight: 0.5980 chunk 103 optimal weight: 5.9990 chunk 151 optimal weight: 10.0000 chunk 229 optimal weight: 10.0000 chunk 210 optimal weight: 2.9990 chunk 182 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 111 optimal weight: 0.1980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 474 GLN E 115 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18542 Z= 0.176 Angle : 0.565 14.679 25216 Z= 0.283 Chirality : 0.038 0.161 2928 Planarity : 0.004 0.040 3206 Dihedral : 6.912 89.849 2666 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.69 % Favored : 91.23 % Rotamer: Outliers : 3.50 % Allowed : 32.29 % Favored : 64.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.19), residues: 2314 helix: 1.43 (0.15), residues: 1308 sheet: -1.15 (0.49), residues: 114 loop : -2.88 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 427 HIS 0.003 0.000 HIS E 312 PHE 0.016 0.001 PHE A 205 TYR 0.011 0.001 TYR C 7 ARG 0.004 0.000 ARG E 220 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 125 time to evaluate : 1.909 Fit side-chains REVERT: A 16 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.6722 (mp10) REVERT: A 159 PHE cc_start: 0.8431 (OUTLIER) cc_final: 0.8205 (t80) REVERT: A 185 MET cc_start: 0.6989 (pmm) cc_final: 0.6752 (pmm) REVERT: A 240 MET cc_start: 0.8442 (mmm) cc_final: 0.8057 (mtp) REVERT: A 389 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7593 (mttp) REVERT: A 456 GLN cc_start: 0.8374 (mm-40) cc_final: 0.8057 (mp10) REVERT: A 550 TRP cc_start: 0.6439 (t-100) cc_final: 0.5960 (m100) REVERT: A 556 MET cc_start: 0.7117 (tmm) cc_final: 0.6385 (ttt) REVERT: D 67 ARG cc_start: 0.7154 (OUTLIER) cc_final: 0.6196 (ptt90) REVERT: D 301 PHE cc_start: 0.8687 (OUTLIER) cc_final: 0.8228 (t80) REVERT: D 479 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7611 (mt-10) REVERT: D 541 GLN cc_start: 0.7679 (mp10) cc_final: 0.7418 (mp10) REVERT: E 159 PHE cc_start: 0.8546 (OUTLIER) cc_final: 0.7934 (t80) REVERT: E 506 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8697 (tt) outliers start: 66 outliers final: 52 residues processed: 186 average time/residue: 0.2879 time to fit residues: 82.8113 Evaluate side-chains 184 residues out of total 1886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 124 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 506 ASP Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 389 LYS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 377 CYS Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 479 GLU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain D residue 543 ILE Chi-restraints excluded: chain E residue 54 MET Chi-restraints excluded: chain E residue 59 ARG Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 115 GLN Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain E residue 532 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 144 optimal weight: 0.7980 chunk 194 optimal weight: 0.9980 chunk 55 optimal weight: 20.0000 chunk 168 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 182 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 187 optimal weight: 0.0370 chunk 23 optimal weight: 0.7980 chunk 33 optimal weight: 30.0000 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 GLN ** C 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 273 ASN ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.126296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.095474 restraints weight = 34919.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.098286 restraints weight = 18205.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.100167 restraints weight = 11730.591| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 18542 Z= 0.164 Angle : 0.565 15.096 25216 Z= 0.283 Chirality : 0.038 0.157 2928 Planarity : 0.004 0.040 3206 Dihedral : 6.852 89.853 2666 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.43 % Favored : 91.49 % Rotamer: Outliers : 3.18 % Allowed : 32.61 % Favored : 64.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.19), residues: 2314 helix: 1.49 (0.15), residues: 1302 sheet: -1.07 (0.49), residues: 114 loop : -2.84 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 427 HIS 0.002 0.000 HIS E 312 PHE 0.016 0.001 PHE A 205 TYR 0.020 0.001 TYR C 567 ARG 0.005 0.000 ARG E 584 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3285.55 seconds wall clock time: 60 minutes 46.91 seconds (3646.91 seconds total)