Starting phenix.real_space_refine on Mon May 19 07:30:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ipt_35643/05_2025/8ipt_35643.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ipt_35643/05_2025/8ipt_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/cci-nas-00/data/ceres_data/8ipt_35643/05_2025/8ipt_35643.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ipt_35643/05_2025/8ipt_35643.map" model { file = "/net/cci-nas-00/data/ceres_data/8ipt_35643/05_2025/8ipt_35643.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ipt_35643/05_2025/8ipt_35643.cif" } 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. Time to flip 25 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 10.24, per 1000 atoms: 0.56 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 - 3.00 Amino acid : True - 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: 4.45 Conformation dependent library (CDL) restraints added in 2.3 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... Secondary structure from input PDB file: 94 helices and 10 sheets defined 64.6% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'C' and resid 1 through 3 No H-bonds generated for 'chain 'C' and resid 1 through 3' Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 14 through 49 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) removed outlier: 4.320A pdb=" N ALA C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 59 No H-bonds generated for 'chain 'C' and resid 57 through 59' Processing helix chain 'C' and resid 60 through 104 removed outlier: 3.660A pdb=" N GLY C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA C 69 " --> pdb=" O GLY C 65 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE C 71 " --> pdb=" O ARG C 67 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR C 72 " --> pdb=" O GLY C 68 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N THR C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG C 77 " --> pdb=" O ARG C 73 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL C 83 " --> pdb=" O PHE C 79 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP C 86 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG C 90 " --> pdb=" O ASP C 86 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N HIS C 94 " --> pdb=" O ARG C 90 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE C 100 " --> pdb=" O ARG C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 125 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 130 through 136 Processing helix chain 'C' and resid 138 through 156 Processing helix chain 'C' and resid 159 through 207 removed outlier: 3.716A pdb=" N ALA C 163 " --> pdb=" O ASP C 159 " (cutoff:3.500A) 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) removed outlier: 3.529A pdb=" N LEU C 207 " --> pdb=" O LEU C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 216 Processing helix chain 'C' and resid 219 through 266 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) removed outlier: 3.610A pdb=" N ALA C 266 " --> pdb=" O MET C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 295 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) Processing helix chain 'C' and resid 296 through 303 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) Processing helix chain 'C' and resid 303 through 319 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 378 through 386 removed outlier: 3.688A pdb=" N LEU C 382 " --> pdb=" O GLY C 378 " (cutoff:3.500A) 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 408 through 413 removed outlier: 3.523A pdb=" N ARG C 413 " --> pdb=" O GLU C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 435 Processing helix chain 'C' and resid 444 through 453 removed outlier: 3.691A pdb=" N VAL C 453 " --> pdb=" O ILE C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 487 Processing helix chain 'C' and resid 506 through 521 Processing helix chain 'C' and resid 557 through 562 Processing helix chain 'C' and resid 566 through 572 removed outlier: 3.942A pdb=" N LYS C 570 " --> pdb=" O TYR C 566 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLN C 571 " --> pdb=" O TYR C 567 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY C 572 " --> pdb=" O GLN C 568 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 566 through 572' Processing helix chain 'A' and resid 2 through 16 removed outlier: 3.962A pdb=" N GLN A 16 " --> pdb=" O TRP A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 55 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) removed outlier: 3.697A pdb=" N GLU A 55 " --> pdb=" O HIS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 61 removed outlier: 3.515A pdb=" N ALA A 61 " --> pdb=" O PRO A 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 58 through 61' Processing helix chain 'A' and resid 62 through 110 removed outlier: 4.360A pdb=" N PHE A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 115 removed outlier: 3.504A pdb=" N ILE A 114 " --> pdb=" O GLY A 110 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLN A 115 " --> pdb=" O PRO A 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 110 through 115' Processing helix chain 'A' and resid 118 through 132 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) Processing helix chain 'A' and resid 133 through 139 Processing helix chain 'A' and resid 139 through 159 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 Processing helix chain 'A' and resid 162 through 173 removed outlier: 3.943A pdb=" N ALA A 166 " --> pdb=" O ASN A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 181 removed outlier: 4.380A pdb=" N LEU A 178 " --> pdb=" O PRO A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 211 removed outlier: 3.836A pdb=" N ARG A 192 " --> pdb=" O ALA A 188 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY A 211 " --> pdb=" O ASP A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 219 removed outlier: 3.680A pdb=" N LEU A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 273 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) removed outlier: 4.103A pdb=" N LEU A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 328 removed outlier: 3.570A pdb=" N GLY A 290 " --> pdb=" O THR A 286 " (cutoff:3.500A) 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) Processing helix chain 'A' and resid 388 through 398 Processing helix chain 'A' and resid 412 through 416 removed outlier: 3.681A pdb=" N ASP A 415 " --> pdb=" O GLU A 412 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU A 416 " --> pdb=" O LEU A 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 412 through 416' Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 423 through 425 No H-bonds generated for 'chain 'A' and resid 423 through 425' Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.651A pdb=" N VAL A 443 " --> pdb=" O LEU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 461 removed outlier: 3.797A pdb=" N GLN A 456 " --> pdb=" O GLU A 452 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN A 461 " --> pdb=" O ALA A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 471 removed outlier: 3.557A pdb=" N LEU A 471 " --> pdb=" O LEU A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 500 removed outlier: 3.834A pdb=" N GLN A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) 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 517 through 533 Processing helix chain 'A' and resid 566 through 571 Processing helix chain 'A' and resid 575 through 588 removed outlier: 3.516A pdb=" N ILE A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 1 through 3 No H-bonds generated for 'chain 'D' and resid 1 through 3' Processing helix chain 'D' and resid 4 through 9 Processing helix chain 'D' and resid 14 through 49 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) removed outlier: 4.321A pdb=" N ALA D 49 " --> pdb=" O ALA D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 59 No H-bonds generated for 'chain 'D' and resid 57 through 59' Processing helix chain 'D' and resid 60 through 104 removed outlier: 3.660A pdb=" N GLY D 68 " --> pdb=" O ALA D 64 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA D 69 " --> pdb=" O GLY D 65 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE D 71 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR D 72 " --> pdb=" O GLY D 68 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG D 73 " --> pdb=" O ALA D 69 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N THR D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG D 77 " --> pdb=" O ARG D 73 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL D 83 " --> pdb=" O PHE D 79 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER D 84 " --> pdb=" O GLU D 80 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP D 86 " --> pdb=" O LEU D 82 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG D 90 " --> pdb=" O ASP D 86 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N HIS D 94 " --> pdb=" O ARG D 90 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE D 100 " --> pdb=" O ARG D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 125 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 130 through 136 Processing helix chain 'D' and resid 138 through 156 Processing helix chain 'D' and resid 159 through 207 removed outlier: 3.716A pdb=" N ALA D 163 " --> pdb=" O ASP D 159 " (cutoff:3.500A) 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) removed outlier: 3.529A pdb=" N LEU D 207 " --> pdb=" O LEU D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 216 Processing helix chain 'D' and resid 219 through 266 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) removed outlier: 3.610A pdb=" N ALA D 266 " --> pdb=" O MET D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 295 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) Processing helix chain 'D' and resid 296 through 303 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) Processing helix chain 'D' and resid 303 through 319 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 378 through 386 removed outlier: 3.688A pdb=" N LEU D 382 " --> pdb=" O GLY D 378 " (cutoff:3.500A) 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 408 through 413 removed outlier: 3.523A pdb=" N ARG D 413 " --> pdb=" O GLU D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 435 Processing helix chain 'D' and resid 444 through 453 removed outlier: 3.692A pdb=" N VAL D 453 " --> pdb=" O ILE D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 487 Processing helix chain 'D' and resid 506 through 521 Processing helix chain 'D' and resid 557 through 562 Processing helix chain 'D' and resid 566 through 572 removed outlier: 3.941A pdb=" N LYS D 570 " --> pdb=" O TYR D 566 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLN D 571 " --> pdb=" O TYR D 567 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY D 572 " --> pdb=" O GLN D 568 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 566 through 572' Processing helix chain 'E' and resid 2 through 16 removed outlier: 3.962A pdb=" N GLN E 16 " --> pdb=" O TRP E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 55 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) removed outlier: 3.697A pdb=" N GLU E 55 " --> pdb=" O HIS E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 61 removed outlier: 3.515A pdb=" N ALA E 61 " --> pdb=" O PRO E 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 58 through 61' Processing helix chain 'E' and resid 62 through 110 removed outlier: 4.361A pdb=" N PHE E 66 " --> pdb=" O LEU E 62 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR E 67 " --> pdb=" O LEU E 63 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU E 68 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE E 94 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG E 95 " --> pdb=" O GLY E 91 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY E 110 " --> pdb=" O LEU E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 115 removed outlier: 3.503A pdb=" N ILE E 114 " --> pdb=" O GLY E 110 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLN E 115 " --> pdb=" O PRO E 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 110 through 115' Processing helix chain 'E' and resid 118 through 132 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) Processing helix chain 'E' and resid 133 through 139 Processing helix chain 'E' and resid 139 through 159 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 Processing helix chain 'E' and resid 162 through 173 removed outlier: 3.943A pdb=" N ALA E 166 " --> pdb=" O ASN E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 181 removed outlier: 4.380A pdb=" N LEU E 178 " --> pdb=" O PRO E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 211 removed outlier: 3.835A pdb=" N ARG E 192 " --> pdb=" O ALA E 188 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY E 211 " --> pdb=" O ASP E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 219 removed outlier: 3.680A pdb=" N LEU E 215 " --> pdb=" O GLY E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 273 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) removed outlier: 4.103A pdb=" N LEU E 273 " --> pdb=" O GLY E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 328 removed outlier: 3.570A pdb=" N GLY E 290 " --> pdb=" O THR E 286 " (cutoff:3.500A) 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) Processing helix chain 'E' and resid 388 through 398 Processing helix chain 'E' and resid 412 through 416 removed outlier: 3.681A pdb=" N ASP E 415 " --> pdb=" O GLU E 412 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU E 416 " --> pdb=" O LEU E 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 412 through 416' Processing helix chain 'E' and resid 417 through 422 Processing helix chain 'E' and resid 423 through 425 No H-bonds generated for 'chain 'E' and resid 423 through 425' Processing helix chain 'E' and resid 438 through 443 removed outlier: 3.650A pdb=" N VAL E 443 " --> pdb=" O LEU E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 461 removed outlier: 3.796A pdb=" N GLN E 456 " --> pdb=" O GLU E 452 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN E 461 " --> pdb=" O ALA E 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 467 through 471 removed outlier: 3.557A pdb=" N LEU E 471 " --> pdb=" O LEU E 468 " (cutoff:3.500A) Processing helix chain 'E' and resid 488 through 500 removed outlier: 3.834A pdb=" N GLN E 492 " --> pdb=" O VAL E 488 " (cutoff:3.500A) 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 517 through 533 Processing helix chain 'E' and resid 566 through 571 Processing helix chain 'E' and resid 575 through 588 removed outlier: 3.516A pdb=" N ILE E 588 " --> pdb=" O ARG E 584 " (cutoff:3.500A) Processing sheet with id=AA1, 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=AA2, first strand: chain 'C' and resid 417 through 419 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: 6.738A pdb=" N ILE C 369 " --> pdb=" O MET C 528 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N HIS C 368 " --> pdb=" O GLN C 540 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N ILE C 542 " --> pdb=" O HIS C 368 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ALA C 370 " --> pdb=" O ILE C 542 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N VAL C 544 " --> pdb=" O ALA C 370 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU C 372 " --> pdb=" O VAL C 544 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLN C 541 " --> pdb=" O GLU C 552 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N GLU C 552 " --> pdb=" O GLN C 541 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ILE C 543 " --> pdb=" O ILE C 550 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 369 through 372 removed outlier: 5.646A pdb=" N LEU A 369 " --> pdb=" O ASP A 354 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 380 through 382 removed outlier: 6.612A pdb=" N VAL A 380 " --> pdb=" O TRP A 554 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N MET A 556 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N VAL A 382 " --> pdb=" O MET A 556 " (cutoff:3.500A) 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=AA5, first strand: chain 'A' and resid 507 through 509 removed outlier: 6.591A pdb=" N LEU A 507 " --> pdb=" O LEU A 538 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, 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=AA7, first strand: chain 'D' and resid 417 through 419 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: 6.739A pdb=" N ILE D 369 " --> pdb=" O MET D 528 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N HIS D 368 " --> pdb=" O GLN D 540 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N ILE D 542 " --> pdb=" O HIS D 368 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ALA D 370 " --> pdb=" O ILE D 542 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N VAL D 544 " --> pdb=" O ALA D 370 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU D 372 " --> pdb=" O VAL D 544 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLN D 541 " --> pdb=" O GLU D 552 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N GLU D 552 " --> pdb=" O GLN D 541 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ILE D 543 " --> pdb=" O ILE D 550 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 369 through 372 removed outlier: 5.646A pdb=" N LEU E 369 " --> pdb=" O ASP E 354 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 380 through 382 removed outlier: 6.611A pdb=" N VAL E 380 " --> pdb=" O TRP E 554 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N MET E 556 " --> pdb=" O VAL E 380 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N VAL E 382 " --> pdb=" O MET E 556 " (cutoff:3.500A) 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=AB1, first strand: chain 'E' and resid 507 through 509 removed outlier: 6.592A pdb=" N LEU E 507 " --> pdb=" O LEU E 538 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 960 hydrogen bonds defined for protein. 2844 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: 5.60 Time building geometry restraints manager: 5.23 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: 0.00 - 2.00: 24704 2.00 - 3.99: 391 3.99 - 5.99: 100 5.99 - 7.99: 15 7.99 - 9.98: 6 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: 1371 2.74 - 3.28: 18002 3.28 - 3.82: 28524 3.82 - 4.36: 31212 4.36 - 4.90: 56484 Nonbonded interactions: 135593 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 3.120 nonbonded pdb=" NH2 ARG E 99 " pdb=" OD1 ASP E 131 " model vdw 2.269 3.120 nonbonded pdb=" CG2 THR C 555 " pdb=" OE1 GLU C 558 " model vdw 2.295 3.460 ... (remaining 135588 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.10 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'A' selection = chain 'E' } 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: 1.640 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: 0.730 Check model and map are aligned: 0.120 Set scattering table: 0.180 Process input model: 39.960 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.210 ------------------------------------------------------------------------------- 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= 0.181 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 Details of bonding type rmsd hydrogen bonds : bond 0.14672 ( 960) hydrogen bonds : angle 5.45333 ( 2844) covalent geometry : bond 0.00312 (18542) covalent geometry : angle 0.67189 (25216) *********************** 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 to be fit. rotamer outliers: 6 poor density : 259 time to evaluate : 1.955 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: 0.3493 time to fit residues: 133.3847 Evaluate side-chains 153 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 150 time to evaluate : 1.985 ------------------------------------------------------------------------------- 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: 0.9990 chunk 174 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 93 optimal weight: 8.9990 chunk 180 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 chunk 208 optimal weight: 0.7980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 GLN A 394 ASN A 403 GLN ** A 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 ASN ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 421 GLN ** D 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.129153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.097523 restraints weight = 34691.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.100327 restraints weight = 18056.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.102249 restraints weight = 11595.471| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18542 Z= 0.157 Angle : 0.620 9.544 25216 Z= 0.318 Chirality : 0.040 0.203 2928 Planarity : 0.005 0.078 3206 Dihedral : 7.877 76.115 2672 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.08 % Favored : 90.84 % Rotamer: Outliers : 3.34 % Allowed : 29.80 % Favored : 66.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.19), residues: 2314 helix: 2.01 (0.15), residues: 1336 sheet: -1.48 (0.52), residues: 108 loop : -3.16 (0.19), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 550 HIS 0.008 0.001 HIS A 542 PHE 0.012 0.001 PHE C 216 TYR 0.014 0.001 TYR C 78 ARG 0.006 0.000 ARG C 374 Details of bonding type rmsd hydrogen bonds : bond 0.07283 ( 960) hydrogen bonds : angle 4.21482 ( 2844) covalent geometry : bond 0.00338 (18542) covalent geometry : angle 0.61984 (25216) *********************** 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 227 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 164 time to evaluate : 1.916 Fit side-chains revert: symmetry clash REVERT: C 80 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7668 (tm-30) REVERT: C 301 PHE cc_start: 0.8733 (OUTLIER) cc_final: 0.8509 (m-80) REVERT: C 567 TYR cc_start: 0.7649 (t80) cc_final: 0.7340 (t80) REVERT: A 361 GLU cc_start: 0.7804 (tt0) cc_final: 0.6730 (pp20) REVERT: A 556 MET cc_start: 0.7380 (ttt) cc_final: 0.5959 (tmm) outliers start: 63 outliers final: 33 residues processed: 217 average time/residue: 0.3002 time to fit residues: 98.6948 Evaluate side-chains 168 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 134 time to evaluate : 1.951 ------------------------------------------------------------------------------- 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 138 ILE Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 301 PHE Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 371 ILE 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 532 SER Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 97 ILE 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 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 62 LEU Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 510 ASP 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 61 optimal weight: 8.9990 chunk 188 optimal weight: 6.9990 chunk 219 optimal weight: 0.9990 chunk 177 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 96 optimal weight: 8.9990 chunk 42 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 220 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 190 GLN ** C 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 461 ASN ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 553 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 = 0.3878 r_free = 0.3878 target = 0.127068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.095219 restraints weight = 34697.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.098017 restraints weight = 18274.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.099734 restraints weight = 11858.423| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18542 Z= 0.159 Angle : 0.595 8.184 25216 Z= 0.306 Chirality : 0.040 0.167 2928 Planarity : 0.004 0.048 3206 Dihedral : 7.466 85.082 2668 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.90 % Favored : 91.01 % Rotamer: Outliers : 4.72 % Allowed : 29.37 % Favored : 65.91 % 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: 0.09 (0.19), residues: 2314 helix: 2.01 (0.15), residues: 1340 sheet: -1.64 (0.51), residues: 108 loop : -3.11 (0.19), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 427 HIS 0.004 0.001 HIS E 312 PHE 0.013 0.001 PHE D 57 TYR 0.016 0.001 TYR C 7 ARG 0.003 0.000 ARG E 59 Details of bonding type rmsd hydrogen bonds : bond 0.07472 ( 960) hydrogen bonds : angle 4.11194 ( 2844) covalent geometry : bond 0.00348 (18542) covalent geometry : angle 0.59495 (25216) *********************** 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 236 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 147 time to evaluate : 1.956 Fit side-chains REVERT: C 80 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7570 (tm-30) REVERT: C 407 LEU cc_start: 0.8704 (mt) cc_final: 0.8419 (mt) REVERT: C 434 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.7310 (tt) REVERT: C 567 TYR cc_start: 0.7712 (t80) cc_final: 0.7439 (t80) REVERT: A 16 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.6236 (mp10) REVERT: A 344 LEU cc_start: 0.7244 (tp) cc_final: 0.6916 (tt) REVERT: A 361 GLU cc_start: 0.7819 (tt0) cc_final: 0.6760 (pp20) REVERT: A 456 GLN cc_start: 0.8896 (mm-40) cc_final: 0.8161 (mp10) REVERT: A 539 MET cc_start: 0.7427 (OUTLIER) cc_final: 0.7158 (ttp) REVERT: A 556 MET cc_start: 0.7626 (ttt) cc_final: 0.6192 (tmm) REVERT: D 512 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8248 (mt0) REVERT: E 584 ARG cc_start: 0.6317 (tpm170) cc_final: 0.6107 (tpm170) outliers start: 89 outliers final: 45 residues processed: 224 average time/residue: 0.2845 time to fit residues: 99.1673 Evaluate side-chains 182 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 133 time to evaluate : 2.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 102 LYS 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 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 371 ILE Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 434 LEU 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 242 VAL Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 539 MET 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 106 LEU Chi-restraints excluded: chain D residue 111 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 499 ASP Chi-restraints excluded: chain D residue 512 GLN 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 62 LEU Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 252 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 132 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 202 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 200 optimal weight: 8.9990 chunk 86 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 139 optimal weight: 0.6980 chunk 136 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 302 GLN A 394 ASN ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 336 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.126323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.094504 restraints weight = 34825.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.097317 restraints weight = 18399.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.099221 restraints weight = 11852.833| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18542 Z= 0.155 Angle : 0.591 10.193 25216 Z= 0.301 Chirality : 0.040 0.139 2928 Planarity : 0.004 0.049 3206 Dihedral : 7.260 79.189 2668 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.86 % Favored : 91.05 % Rotamer: Outliers : 4.83 % Allowed : 29.53 % Favored : 65.64 % 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: 0.18 (0.19), residues: 2314 helix: 2.11 (0.15), residues: 1328 sheet: -1.64 (0.48), residues: 114 loop : -3.04 (0.19), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 427 HIS 0.003 0.001 HIS E 312 PHE 0.011 0.001 PHE D 57 TYR 0.015 0.001 TYR C 7 ARG 0.004 0.000 ARG A 584 Details of bonding type rmsd hydrogen bonds : bond 0.07386 ( 960) hydrogen bonds : angle 4.04891 ( 2844) covalent geometry : bond 0.00338 (18542) covalent geometry : angle 0.59146 (25216) *********************** 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 233 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 142 time to evaluate : 1.985 Fit side-chains REVERT: C 1 MET cc_start: 0.7869 (mtp) cc_final: 0.7664 (mtp) REVERT: C 80 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7540 (tm-30) REVERT: C 407 LEU cc_start: 0.8775 (mt) cc_final: 0.8479 (mt) REVERT: C 434 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7312 (tt) REVERT: C 524 LYS cc_start: 0.6229 (OUTLIER) cc_final: 0.5975 (mmtp) REVERT: C 567 TYR cc_start: 0.7642 (t80) cc_final: 0.7390 (t80) REVERT: A 16 GLN cc_start: 0.7740 (OUTLIER) cc_final: 0.6219 (mp10) REVERT: A 159 PHE cc_start: 0.8234 (OUTLIER) cc_final: 0.7877 (t80) REVERT: A 344 LEU cc_start: 0.7323 (tp) cc_final: 0.6978 (tt) REVERT: A 456 GLN cc_start: 0.8899 (mm-40) cc_final: 0.8168 (mp10) REVERT: A 533 LEU cc_start: 0.8361 (mm) cc_final: 0.8063 (mm) REVERT: A 539 MET cc_start: 0.7510 (OUTLIER) cc_final: 0.7290 (mtp) REVERT: A 550 TRP cc_start: 0.6046 (m100) cc_final: 0.5509 (m100) REVERT: A 556 MET cc_start: 0.7687 (ttt) cc_final: 0.6335 (tmm) REVERT: A 558 ASP cc_start: 0.7001 (t70) cc_final: 0.6522 (t70) REVERT: D 512 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.8115 (mt0) outliers start: 91 outliers final: 59 residues processed: 220 average time/residue: 0.2789 time to fit residues: 95.2400 Evaluate side-chains 195 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 130 time to evaluate : 2.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 ARG 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 95 LEU Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 102 LYS 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 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 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 371 ILE Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 524 LYS Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 545 MET Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 539 MET 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 120 LEU Chi-restraints excluded: chain D residue 204 THR 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 360 SER Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 512 GLN Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain D residue 543 ILE Chi-restraints excluded: chain E residue 59 ARG Chi-restraints excluded: chain E residue 62 LEU 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 242 VAL Chi-restraints excluded: chain E residue 252 ILE 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 401 SER Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 510 ASP Chi-restraints excluded: chain E residue 532 SER 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 10 optimal weight: 5.9990 chunk 105 optimal weight: 0.0670 chunk 92 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 206 optimal weight: 8.9990 chunk 102 optimal weight: 20.0000 chunk 58 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 147 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 91 optimal weight: 20.0000 overall best weight: 1.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 547 ASN A 394 ASN ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 547 ASN ** 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 = 0.3852 r_free = 0.3852 target = 0.124968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.093096 restraints weight = 35046.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.095855 restraints weight = 18550.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.097699 restraints weight = 12028.249| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 18542 Z= 0.166 Angle : 0.592 13.289 25216 Z= 0.304 Chirality : 0.040 0.137 2928 Planarity : 0.004 0.051 3206 Dihedral : 7.254 84.697 2668 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.95 % Favored : 90.97 % Rotamer: Outliers : 5.25 % Allowed : 29.48 % 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: 0.14 (0.19), residues: 2314 helix: 2.02 (0.15), residues: 1338 sheet: -1.56 (0.49), residues: 114 loop : -3.01 (0.19), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 550 HIS 0.004 0.001 HIS E 312 PHE 0.013 0.001 PHE D 57 TYR 0.014 0.001 TYR C 7 ARG 0.003 0.000 ARG E 485 Details of bonding type rmsd hydrogen bonds : bond 0.07689 ( 960) hydrogen bonds : angle 4.08268 ( 2844) covalent geometry : bond 0.00370 (18542) covalent geometry : angle 0.59159 (25216) *********************** 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 236 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 137 time to evaluate : 2.085 Fit side-chains REVERT: C 80 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7524 (tm-30) REVERT: C 407 LEU cc_start: 0.8762 (mt) cc_final: 0.8464 (mt) REVERT: C 430 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8132 (tt) REVERT: C 434 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7336 (tt) REVERT: C 524 LYS cc_start: 0.6183 (OUTLIER) cc_final: 0.5860 (mmtp) REVERT: C 567 TYR cc_start: 0.7626 (t80) cc_final: 0.7383 (t80) REVERT: A 16 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.6150 (mp10) REVERT: A 159 PHE cc_start: 0.8326 (OUTLIER) cc_final: 0.7963 (t80) REVERT: A 185 MET cc_start: 0.5798 (pmm) cc_final: 0.5440 (pmm) REVERT: A 207 ASP cc_start: 0.8550 (t0) cc_final: 0.8297 (t0) REVERT: A 344 LEU cc_start: 0.7352 (tp) cc_final: 0.7070 (tt) REVERT: A 423 LYS cc_start: 0.8079 (mtmm) cc_final: 0.7827 (mtmm) REVERT: A 456 GLN cc_start: 0.8908 (mm-40) cc_final: 0.8169 (mp10) REVERT: A 533 LEU cc_start: 0.8318 (mm) cc_final: 0.7985 (mm) REVERT: A 539 MET cc_start: 0.7515 (OUTLIER) cc_final: 0.6847 (ttm) REVERT: A 556 MET cc_start: 0.7699 (ttt) cc_final: 0.6350 (tmm) REVERT: A 558 ASP cc_start: 0.7237 (t70) cc_final: 0.6905 (t70) REVERT: D 512 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.8083 (mt0) REVERT: E 159 PHE cc_start: 0.8714 (OUTLIER) cc_final: 0.8181 (t80) outliers start: 99 outliers final: 67 residues processed: 223 average time/residue: 0.2863 time to fit residues: 99.2804 Evaluate side-chains 199 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 124 time to evaluate : 1.972 ------------------------------------------------------------------------------- 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 97 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 138 ILE 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 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 377 CYS Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 409 GLU Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 524 LYS Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 545 MET Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 461 ASN Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 158 LEU 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 265 MET Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 360 SER 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 510 GLU Chi-restraints excluded: chain D residue 512 GLN Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain D residue 543 ILE Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 59 ARG Chi-restraints excluded: chain E residue 62 LEU 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 180 MET Chi-restraints excluded: chain E residue 242 VAL 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 345 THR Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 532 SER 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 91 optimal weight: 30.0000 chunk 225 optimal weight: 3.9990 chunk 216 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 7 optimal weight: 8.9990 chunk 228 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 141 optimal weight: 3.9990 chunk 173 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 547 ASN A 394 ASN D 273 ASN ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.121346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.089326 restraints weight = 35059.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.091855 restraints weight = 18825.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.093755 restraints weight = 12396.144| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 18542 Z= 0.227 Angle : 0.652 10.801 25216 Z= 0.337 Chirality : 0.042 0.141 2928 Planarity : 0.004 0.052 3206 Dihedral : 7.464 85.291 2668 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.59 % Favored : 90.32 % Rotamer: Outliers : 5.62 % Allowed : 30.01 % Favored : 64.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.19), residues: 2314 helix: 1.72 (0.15), residues: 1336 sheet: -1.59 (0.49), residues: 114 loop : -3.13 (0.19), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 550 HIS 0.007 0.001 HIS D 94 PHE 0.015 0.002 PHE C 89 TYR 0.017 0.002 TYR E 88 ARG 0.006 0.000 ARG A 560 Details of bonding type rmsd hydrogen bonds : bond 0.08904 ( 960) hydrogen bonds : angle 4.33636 ( 2844) covalent geometry : bond 0.00532 (18542) covalent geometry : angle 0.65204 (25216) *********************** 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 231 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 125 time to evaluate : 1.990 Fit side-chains revert: symmetry clash REVERT: C 80 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7506 (tm-30) REVERT: C 407 LEU cc_start: 0.8784 (mt) cc_final: 0.8497 (mt) REVERT: C 430 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8224 (tt) REVERT: C 434 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7324 (tt) REVERT: C 524 LYS cc_start: 0.6218 (OUTLIER) cc_final: 0.5916 (mmtp) REVERT: C 567 TYR cc_start: 0.7582 (t80) cc_final: 0.7334 (t80) REVERT: A 16 GLN cc_start: 0.7769 (OUTLIER) cc_final: 0.6229 (mp10) REVERT: A 159 PHE cc_start: 0.8383 (OUTLIER) cc_final: 0.7996 (t80) REVERT: A 207 ASP cc_start: 0.8696 (t0) cc_final: 0.8475 (t0) REVERT: A 344 LEU cc_start: 0.7411 (tp) cc_final: 0.7090 (tt) REVERT: A 441 ASP cc_start: 0.7298 (t70) cc_final: 0.6693 (m-30) REVERT: A 533 LEU cc_start: 0.8351 (mm) cc_final: 0.7996 (mm) REVERT: A 539 MET cc_start: 0.7519 (OUTLIER) cc_final: 0.7000 (ttm) REVERT: A 556 MET cc_start: 0.7681 (ttt) cc_final: 0.6427 (tmm) REVERT: A 558 ASP cc_start: 0.7334 (t70) cc_final: 0.6721 (t70) REVERT: D 97 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8651 (mp) REVERT: D 301 PHE cc_start: 0.8505 (OUTLIER) cc_final: 0.8141 (t80) REVERT: D 540 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7773 (mm-40) REVERT: E 115 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.8628 (pp30) REVERT: E 159 PHE cc_start: 0.8707 (OUTLIER) cc_final: 0.8193 (t80) REVERT: E 584 ARG cc_start: 0.5769 (tpt170) cc_final: 0.5506 (tpt170) outliers start: 106 outliers final: 68 residues processed: 220 average time/residue: 0.2769 time to fit residues: 95.8103 Evaluate side-chains 197 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 118 time to evaluate : 2.124 ------------------------------------------------------------------------------- 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 66 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 138 ILE 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 304 LEU Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 409 GLU Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 524 LYS Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 545 MET Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain C residue 555 THR Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 461 ASN Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 572 VAL 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 158 LEU Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 265 MET 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 339 LEU Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain D residue 512 GLN Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 543 ILE Chi-restraints excluded: chain E residue 59 ARG Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 79 VAL 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 155 VAL Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain E residue 408 ILE Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 532 SER Chi-restraints excluded: chain E residue 544 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 169 optimal weight: 1.9990 chunk 173 optimal weight: 0.9990 chunk 145 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 213 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 223 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 HIS A 394 ASN ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 547 ASN ** 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 = 0.3869 r_free = 0.3869 target = 0.126317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.095051 restraints weight = 34618.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.097860 restraints weight = 18174.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.099734 restraints weight = 11697.129| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18542 Z= 0.136 Angle : 0.575 14.668 25216 Z= 0.293 Chirality : 0.039 0.171 2928 Planarity : 0.004 0.050 3206 Dihedral : 7.253 86.494 2668 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.99 % Favored : 91.92 % Rotamer: Outliers : 3.82 % Allowed : 31.28 % Favored : 64.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.19), residues: 2314 helix: 2.19 (0.15), residues: 1314 sheet: -1.38 (0.49), residues: 114 loop : -3.04 (0.19), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 550 HIS 0.006 0.001 HIS A 542 PHE 0.012 0.001 PHE D 57 TYR 0.015 0.001 TYR A 88 ARG 0.002 0.000 ARG D 534 Details of bonding type rmsd hydrogen bonds : bond 0.07001 ( 960) hydrogen bonds : angle 3.94618 ( 2844) covalent geometry : bond 0.00267 (18542) covalent geometry : angle 0.57541 (25216) *********************** 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 208 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 136 time to evaluate : 1.866 Fit side-chains REVERT: C 80 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7488 (tm-30) REVERT: C 407 LEU cc_start: 0.8797 (mt) cc_final: 0.8504 (mt) REVERT: C 430 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8181 (tt) REVERT: C 434 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7335 (tt) REVERT: C 524 LYS cc_start: 0.6281 (OUTLIER) cc_final: 0.6002 (mmtp) REVERT: C 567 TYR cc_start: 0.7552 (t80) cc_final: 0.7311 (t80) REVERT: A 16 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.6247 (mp10) REVERT: A 207 ASP cc_start: 0.8653 (t0) cc_final: 0.8445 (t0) REVERT: A 344 LEU cc_start: 0.7430 (tp) cc_final: 0.7107 (tt) REVERT: A 521 GLU cc_start: 0.6664 (OUTLIER) cc_final: 0.5366 (pp20) REVERT: A 533 LEU cc_start: 0.8358 (mm) cc_final: 0.8047 (mm) REVERT: A 539 MET cc_start: 0.7510 (OUTLIER) cc_final: 0.6848 (ttm) REVERT: A 556 MET cc_start: 0.7694 (ttt) cc_final: 0.6429 (tmm) REVERT: A 558 ASP cc_start: 0.7288 (t70) cc_final: 0.6750 (t70) REVERT: A 587 GLU cc_start: 0.5401 (OUTLIER) cc_final: 0.4527 (mp0) REVERT: D 60 MET cc_start: 0.8286 (tpp) cc_final: 0.7964 (tmm) REVERT: D 97 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8518 (mp) REVERT: D 301 PHE cc_start: 0.8450 (OUTLIER) cc_final: 0.8011 (t80) REVERT: D 512 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.8056 (mt0) REVERT: E 584 ARG cc_start: 0.5569 (tpt170) cc_final: 0.5349 (tpt170) outliers start: 72 outliers final: 49 residues processed: 199 average time/residue: 0.2797 time to fit residues: 86.1174 Evaluate side-chains 181 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 122 time to evaluate : 1.845 ------------------------------------------------------------------------------- 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 97 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 377 CYS Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 409 GLU Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 524 LYS Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 545 MET Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 461 ASN Chi-restraints excluded: chain A residue 521 GLU Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 587 GLU 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 158 LEU Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 377 CYS Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain D residue 512 GLN Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 59 ARG Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 416 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 34 optimal weight: 2.9990 chunk 188 optimal weight: 0.5980 chunk 193 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 48 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 179 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.123075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.091349 restraints weight = 34805.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.094072 restraints weight = 18572.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.095901 restraints weight = 12042.099| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 18542 Z= 0.185 Angle : 0.630 14.559 25216 Z= 0.321 Chirality : 0.041 0.200 2928 Planarity : 0.004 0.047 3206 Dihedral : 7.247 89.528 2668 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.29 % Favored : 90.62 % Rotamer: Outliers : 4.03 % Allowed : 31.28 % Favored : 64.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.19), residues: 2314 helix: 1.98 (0.15), residues: 1314 sheet: -1.39 (0.49), residues: 114 loop : -2.97 (0.19), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 550 HIS 0.005 0.001 HIS E 312 PHE 0.012 0.001 PHE D 57 TYR 0.015 0.001 TYR A 88 ARG 0.006 0.000 ARG E 220 Details of bonding type rmsd hydrogen bonds : bond 0.07996 ( 960) hydrogen bonds : angle 4.12196 ( 2844) covalent geometry : bond 0.00419 (18542) covalent geometry : angle 0.62993 (25216) *********************** 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 198 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 122 time to evaluate : 1.912 Fit side-chains REVERT: C 80 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7485 (tm-30) REVERT: C 172 LEU cc_start: 0.7847 (mm) cc_final: 0.7405 (mt) REVERT: C 407 LEU cc_start: 0.8795 (mt) cc_final: 0.8477 (mt) REVERT: C 434 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7364 (tt) REVERT: C 524 LYS cc_start: 0.6271 (OUTLIER) cc_final: 0.5952 (mmtp) REVERT: C 567 TYR cc_start: 0.7526 (t80) cc_final: 0.7282 (t80) REVERT: A 16 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.6247 (mp10) REVERT: A 207 ASP cc_start: 0.8717 (t0) cc_final: 0.8514 (t0) REVERT: A 441 ASP cc_start: 0.7197 (t70) cc_final: 0.6686 (m-30) REVERT: A 533 LEU cc_start: 0.8342 (mm) cc_final: 0.8027 (mm) REVERT: A 556 MET cc_start: 0.7710 (ttt) cc_final: 0.6522 (tmm) REVERT: A 558 ASP cc_start: 0.7305 (t70) cc_final: 0.6743 (t70) REVERT: A 587 GLU cc_start: 0.5438 (OUTLIER) cc_final: 0.4582 (mp0) REVERT: D 60 MET cc_start: 0.8292 (tpp) cc_final: 0.7963 (tmm) REVERT: D 97 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8611 (mp) REVERT: D 301 PHE cc_start: 0.8476 (OUTLIER) cc_final: 0.8049 (t80) REVERT: D 353 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7887 (mp10) REVERT: D 512 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.8037 (mt0) REVERT: E 159 PHE cc_start: 0.8697 (OUTLIER) cc_final: 0.8184 (t80) outliers start: 76 outliers final: 56 residues processed: 189 average time/residue: 0.2871 time to fit residues: 85.0466 Evaluate side-chains 184 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 119 time to evaluate : 1.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 138 ILE 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 304 LEU Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 377 CYS 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 434 LEU Chi-restraints excluded: chain C residue 524 LYS Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 545 MET Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 461 ASN Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 587 GLU 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 158 LEU Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 353 GLN Chi-restraints excluded: chain D residue 360 SER 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 510 GLU Chi-restraints excluded: chain D residue 512 GLN Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain D residue 543 ILE Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 59 ARG Chi-restraints excluded: chain E residue 62 LEU 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 242 VAL Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 532 SER Chi-restraints excluded: chain E residue 542 HIS Chi-restraints excluded: chain E residue 544 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 180 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 52 optimal weight: 8.9990 chunk 176 optimal weight: 0.7980 chunk 129 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.126646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.095484 restraints weight = 34744.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.098268 restraints weight = 18208.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.100124 restraints weight = 11733.521| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18542 Z= 0.134 Angle : 0.583 15.325 25216 Z= 0.295 Chirality : 0.039 0.219 2928 Planarity : 0.004 0.046 3206 Dihedral : 7.074 88.170 2668 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.51 % Favored : 91.40 % Rotamer: Outliers : 3.34 % Allowed : 31.87 % Favored : 64.79 % 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: 0.30 (0.19), residues: 2314 helix: 2.23 (0.15), residues: 1308 sheet: -1.32 (0.49), residues: 114 loop : -2.94 (0.19), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 427 HIS 0.003 0.001 HIS A 542 PHE 0.012 0.001 PHE D 57 TYR 0.014 0.001 TYR A 88 ARG 0.006 0.000 ARG E 220 Details of bonding type rmsd hydrogen bonds : bond 0.06796 ( 960) hydrogen bonds : angle 3.88323 ( 2844) covalent geometry : bond 0.00266 (18542) covalent geometry : angle 0.58295 (25216) *********************** 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 188 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 125 time to evaluate : 1.952 Fit side-chains REVERT: C 80 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7459 (tm-30) REVERT: C 172 LEU cc_start: 0.7817 (mm) cc_final: 0.7380 (mt) REVERT: C 407 LEU cc_start: 0.8806 (mt) cc_final: 0.8480 (mt) REVERT: C 430 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8231 (tt) REVERT: C 434 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7364 (tt) REVERT: C 524 LYS cc_start: 0.6229 (OUTLIER) cc_final: 0.5956 (mmtp) REVERT: C 567 TYR cc_start: 0.7509 (t80) cc_final: 0.7266 (t80) REVERT: A 16 GLN cc_start: 0.7586 (OUTLIER) cc_final: 0.6238 (mp10) REVERT: A 207 ASP cc_start: 0.8620 (t0) cc_final: 0.8408 (t0) REVERT: A 441 ASP cc_start: 0.7095 (t70) cc_final: 0.6629 (m-30) REVERT: A 533 LEU cc_start: 0.8313 (mm) cc_final: 0.7986 (mm) REVERT: A 539 MET cc_start: 0.7861 (ttp) cc_final: 0.7438 (ttm) REVERT: A 558 ASP cc_start: 0.7277 (t70) cc_final: 0.6728 (t70) REVERT: A 572 VAL cc_start: 0.6631 (OUTLIER) cc_final: 0.6425 (t) REVERT: A 587 GLU cc_start: 0.5422 (OUTLIER) cc_final: 0.4551 (mp0) REVERT: D 97 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8482 (mp) REVERT: D 301 PHE cc_start: 0.8457 (OUTLIER) cc_final: 0.8026 (t80) REVERT: D 417 SER cc_start: 0.7940 (OUTLIER) cc_final: 0.7721 (p) REVERT: D 512 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.8046 (mt0) outliers start: 63 outliers final: 50 residues processed: 182 average time/residue: 0.2839 time to fit residues: 79.9715 Evaluate side-chains 180 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 120 time to evaluate : 1.870 ------------------------------------------------------------------------------- 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 97 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 138 ILE 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 361 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 377 CYS 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 430 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 524 LYS Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 545 MET Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 461 ASN 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 A residue 587 GLU 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 158 LEU Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 417 SER Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain D residue 512 GLN Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 59 ARG Chi-restraints excluded: chain E residue 62 LEU 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 180 MET 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 401 SER Chi-restraints excluded: chain E residue 416 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 32 optimal weight: 0.7980 chunk 35 optimal weight: 20.0000 chunk 19 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 180 optimal weight: 4.9990 chunk 102 optimal weight: 20.0000 chunk 167 optimal weight: 4.9990 chunk 229 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 54 optimal weight: 9.9990 chunk 47 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.126234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.094994 restraints weight = 34665.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.097774 restraints weight = 18233.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.099650 restraints weight = 11726.643| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18542 Z= 0.141 Angle : 0.597 15.454 25216 Z= 0.300 Chirality : 0.039 0.218 2928 Planarity : 0.004 0.041 3206 Dihedral : 6.979 87.784 2668 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.69 % Favored : 91.23 % Rotamer: Outliers : 3.55 % Allowed : 31.92 % Favored : 64.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.19), residues: 2314 helix: 2.16 (0.15), residues: 1322 sheet: -1.25 (0.49), residues: 114 loop : -2.91 (0.20), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 550 HIS 0.003 0.001 HIS E 312 PHE 0.009 0.001 PHE D 145 TYR 0.014 0.001 TYR A 88 ARG 0.006 0.000 ARG E 220 Details of bonding type rmsd hydrogen bonds : bond 0.06848 ( 960) hydrogen bonds : angle 3.87733 ( 2844) covalent geometry : bond 0.00296 (18542) covalent geometry : angle 0.59720 (25216) ********************** 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 192 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 125 time to evaluate : 2.021 Fit side-chains REVERT: C 80 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7564 (tt0) REVERT: C 172 LEU cc_start: 0.7852 (mm) cc_final: 0.7412 (mt) REVERT: C 407 LEU cc_start: 0.8773 (mt) cc_final: 0.8460 (mt) REVERT: C 430 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8267 (tt) REVERT: C 434 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7360 (tt) REVERT: C 524 LYS cc_start: 0.6180 (OUTLIER) cc_final: 0.5863 (mmtp) REVERT: C 567 TYR cc_start: 0.7451 (t80) cc_final: 0.7211 (t80) REVERT: A 16 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.6223 (mp10) REVERT: A 207 ASP cc_start: 0.8622 (t0) cc_final: 0.8409 (t0) REVERT: A 441 ASP cc_start: 0.7108 (t70) cc_final: 0.6641 (m-30) REVERT: A 533 LEU cc_start: 0.8320 (mm) cc_final: 0.7992 (mm) REVERT: A 539 MET cc_start: 0.7858 (ttp) cc_final: 0.7060 (ttm) REVERT: A 558 ASP cc_start: 0.7231 (t70) cc_final: 0.6691 (t70) REVERT: A 572 VAL cc_start: 0.6637 (OUTLIER) cc_final: 0.6428 (t) REVERT: A 587 GLU cc_start: 0.5510 (OUTLIER) cc_final: 0.4642 (mp0) REVERT: D 97 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8503 (mp) REVERT: D 301 PHE cc_start: 0.8452 (OUTLIER) cc_final: 0.8024 (t80) REVERT: D 353 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7858 (mp10) REVERT: D 512 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.8066 (mt0) REVERT: E 159 PHE cc_start: 0.8638 (OUTLIER) cc_final: 0.8101 (t80) REVERT: E 587 GLU cc_start: 0.5546 (OUTLIER) cc_final: 0.4844 (mt-10) outliers start: 67 outliers final: 53 residues processed: 186 average time/residue: 0.2931 time to fit residues: 84.7044 Evaluate side-chains 187 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 122 time to evaluate : 2.119 ------------------------------------------------------------------------------- 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 97 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 138 ILE 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 304 LEU Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 377 CYS 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 430 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 524 LYS Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 545 MET Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 461 ASN 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 A residue 587 GLU Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 353 GLN Chi-restraints excluded: chain D residue 360 SER 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 510 GLU Chi-restraints excluded: chain D residue 512 GLN Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain D residue 543 ILE Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 59 ARG Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 114 ILE 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 242 VAL Chi-restraints excluded: chain E residue 324 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 532 SER Chi-restraints excluded: chain E residue 587 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 77 optimal weight: 3.9990 chunk 105 optimal weight: 7.9990 chunk 195 optimal weight: 0.6980 chunk 162 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 209 optimal weight: 6.9990 chunk 175 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 chunk 150 optimal weight: 0.0030 chunk 128 optimal weight: 2.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 302 GLN ** C 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.129082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.098359 restraints weight = 34669.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.101244 restraints weight = 18011.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.102938 restraints weight = 11460.327| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18542 Z= 0.126 Angle : 0.584 15.953 25216 Z= 0.292 Chirality : 0.038 0.217 2928 Planarity : 0.004 0.047 3206 Dihedral : 6.807 87.745 2668 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.08 % Favored : 91.83 % Rotamer: Outliers : 3.29 % Allowed : 32.24 % Favored : 64.48 % 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: 0.48 (0.19), residues: 2314 helix: 2.33 (0.15), residues: 1320 sheet: -1.16 (0.49), residues: 114 loop : -2.88 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 427 HIS 0.003 0.000 HIS A 542 PHE 0.010 0.001 PHE D 145 TYR 0.015 0.001 TYR A 88 ARG 0.015 0.000 ARG C 565 Details of bonding type rmsd hydrogen bonds : bond 0.06015 ( 960) hydrogen bonds : angle 3.72509 ( 2844) covalent geometry : bond 0.00254 (18542) covalent geometry : angle 0.58391 (25216) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5241.03 seconds wall clock time: 92 minutes 25.54 seconds (5545.54 seconds total)