Starting phenix.real_space_refine on Tue Nov 19 02:16:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ipt_35643/11_2024/8ipt_35643.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ipt_35643/11_2024/8ipt_35643.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ipt_35643/11_2024/8ipt_35643.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ipt_35643/11_2024/8ipt_35643.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ipt_35643/11_2024/8ipt_35643.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ipt_35643/11_2024/8ipt_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-5513/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: 10.12, 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: 4.85 Conformation dependent library (CDL) restraints added in 2.2 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: 1.97 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: 6.13 Time building geometry restraints manager: 5.51 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.830 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: 0.680 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 40.230 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.790 ------------------------------------------------------------------------------- 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= 0.205 Angle : 0.672 9.982 25216 Z= 0.383 Chirality : 0.039 0.190 2928 Planarity : 0.004 0.045 3206 Dihedral : 18.348 89.402 6840 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.95 % Favored : 91.88 % Rotamer: Outliers : 0.32 % Allowed : 31.97 % Favored : 67.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.19), residues: 2314 helix: 1.91 (0.15), residues: 1294 sheet: -1.68 (0.50), residues: 108 loop : -2.93 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 550 HIS 0.004 0.001 HIS A 519 PHE 0.012 0.001 PHE C 145 TYR 0.012 0.001 TYR A 88 ARG 0.005 0.000 ARG A 220 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 259 time to evaluate : 2.013 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: 0.3640 time to fit residues: 138.5388 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 : 2.223 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 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= 0.221 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 *********************** 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 : 2.164 Fit side-chains revert: symmetry clash REVERT: C 567 TYR cc_start: 0.7370 (t80) cc_final: 0.7050 (t80) REVERT: A 240 MET cc_start: 0.8476 (mmm) cc_final: 0.8110 (mtp) REVERT: A 361 GLU cc_start: 0.7267 (tt0) cc_final: 0.6549 (pp20) REVERT: A 396 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8381 (mt) outliers start: 63 outliers final: 33 residues processed: 217 average time/residue: 0.3227 time to fit residues: 106.0555 Evaluate side-chains 169 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 135 time to evaluate : 2.151 ------------------------------------------------------------------------------- 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 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 396 LEU 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 116 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 173 optimal weight: 0.7980 chunk 142 optimal weight: 0.4980 chunk 57 optimal weight: 0.9990 chunk 209 optimal weight: 0.2980 chunk 226 optimal weight: 10.0000 chunk 186 optimal weight: 4.9990 chunk 207 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 167 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 208 GLN C 302 GLN A 461 ASN A 482 GLN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18542 Z= 0.166 Angle : 0.568 8.283 25216 Z= 0.289 Chirality : 0.038 0.168 2928 Planarity : 0.004 0.045 3206 Dihedral : 7.286 83.009 2668 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.12 % Favored : 91.79 % Rotamer: Outliers : 4.08 % Allowed : 29.11 % Favored : 66.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.19), residues: 2314 helix: 2.29 (0.15), residues: 1328 sheet: -1.58 (0.51), residues: 108 loop : -3.03 (0.19), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 427 HIS 0.003 0.001 HIS A 334 PHE 0.013 0.001 PHE D 57 TYR 0.015 0.001 TYR C 55 ARG 0.002 0.000 ARG A 337 *********************** 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 227 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 150 time to evaluate : 2.356 Fit side-chains REVERT: C 80 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7809 (tm-30) REVERT: C 567 TYR cc_start: 0.7387 (t80) cc_final: 0.7136 (t80) REVERT: A 16 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.6664 (mp10) REVERT: A 240 MET cc_start: 0.8479 (mmm) cc_final: 0.8040 (mtp) REVERT: A 361 GLU cc_start: 0.7262 (tt0) cc_final: 0.6548 (pp20) REVERT: A 396 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8324 (mt) REVERT: A 456 GLN cc_start: 0.8406 (mm-40) cc_final: 0.8099 (mp10) REVERT: A 539 MET cc_start: 0.7017 (OUTLIER) cc_final: 0.6794 (ttp) outliers start: 77 outliers final: 30 residues processed: 217 average time/residue: 0.3113 time to fit residues: 104.1731 Evaluate side-chains 164 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 2.109 ------------------------------------------------------------------------------- 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 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 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 A residue 16 GLN Chi-restraints excluded: chain A residue 396 LEU 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 97 ILE 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 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 E residue 152 LEU 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 416 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 206 optimal weight: 8.9990 chunk 157 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 209 optimal weight: 1.9990 chunk 222 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 199 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 190 GLN C 208 GLN C 547 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18542 Z= 0.268 Angle : 0.626 10.530 25216 Z= 0.319 Chirality : 0.041 0.145 2928 Planarity : 0.004 0.045 3206 Dihedral : 7.218 83.179 2668 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.08 % Favored : 90.84 % Rotamer: Outliers : 4.45 % Allowed : 29.37 % Favored : 66.17 % 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: 1338 sheet: -1.69 (0.49), residues: 114 loop : -3.07 (0.19), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 550 HIS 0.006 0.001 HIS E 312 PHE 0.015 0.001 PHE E 467 TYR 0.017 0.001 TYR C 7 ARG 0.004 0.000 ARG A 584 *********************** 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 223 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 139 time to evaluate : 2.096 Fit side-chains REVERT: C 80 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7850 (tm-30) REVERT: C 172 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7666 (mt) REVERT: C 524 LYS cc_start: 0.6261 (OUTLIER) cc_final: 0.6012 (mmtp) REVERT: C 567 TYR cc_start: 0.7383 (t80) cc_final: 0.7124 (t80) REVERT: A 16 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.6480 (mp10) REVERT: A 240 MET cc_start: 0.8623 (mmm) cc_final: 0.8086 (mtp) REVERT: A 344 LEU cc_start: 0.6916 (tp) cc_final: 0.6637 (tt) REVERT: A 456 GLN cc_start: 0.8457 (mm-40) cc_final: 0.8141 (mp10) REVERT: A 550 TRP cc_start: 0.5344 (m100) cc_final: 0.4995 (m100) REVERT: D 4 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8416 (mp) REVERT: D 534 ARG cc_start: 0.7277 (tpp-160) cc_final: 0.6828 (tpp-160) REVERT: E 54 MET cc_start: 0.7556 (OUTLIER) cc_final: 0.7323 (mtm) outliers start: 84 outliers final: 52 residues processed: 209 average time/residue: 0.3132 time to fit residues: 101.4682 Evaluate side-chains 182 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 125 time to evaluate : 2.208 ------------------------------------------------------------------------------- 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 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 268 PHE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 360 SER 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 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 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 408 ILE Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 544 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 185 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 189 optimal weight: 0.3980 chunk 153 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 113 optimal weight: 4.9990 chunk 199 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 18542 Z= 0.371 Angle : 0.672 12.687 25216 Z= 0.347 Chirality : 0.043 0.152 2928 Planarity : 0.005 0.050 3206 Dihedral : 7.493 81.958 2668 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.59 % Favored : 90.32 % Rotamer: Outliers : 5.36 % Allowed : 29.48 % Favored : 65.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.18), residues: 2314 helix: 1.70 (0.15), residues: 1324 sheet: -1.66 (0.49), residues: 114 loop : -3.10 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 550 HIS 0.006 0.001 HIS E 312 PHE 0.017 0.002 PHE C 89 TYR 0.018 0.002 TYR C 7 ARG 0.005 0.001 ARG E 485 *********************** 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 229 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 128 time to evaluate : 2.173 Fit side-chains REVERT: C 80 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7871 (tm-30) REVERT: C 524 LYS cc_start: 0.6189 (OUTLIER) cc_final: 0.5936 (mmtp) REVERT: C 567 TYR cc_start: 0.7305 (t80) cc_final: 0.7044 (t80) REVERT: A 16 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.6581 (mp10) REVERT: A 159 PHE cc_start: 0.8550 (OUTLIER) cc_final: 0.8165 (t80) REVERT: A 240 MET cc_start: 0.8695 (mmm) cc_final: 0.8072 (mtp) REVERT: A 344 LEU cc_start: 0.7009 (tp) cc_final: 0.6701 (tt) REVERT: A 441 ASP cc_start: 0.7334 (t70) cc_final: 0.6911 (m-30) REVERT: A 456 GLN cc_start: 0.8493 (mm-40) cc_final: 0.8055 (mt0) REVERT: D 534 ARG cc_start: 0.7174 (tpp-160) cc_final: 0.6824 (tpp-160) REVERT: E 159 PHE cc_start: 0.8530 (OUTLIER) cc_final: 0.7977 (t80) REVERT: E 336 GLN cc_start: 0.7841 (tp-100) cc_final: 0.7641 (tp40) REVERT: E 542 HIS cc_start: 0.8461 (OUTLIER) cc_final: 0.8225 (t70) outliers start: 101 outliers final: 61 residues processed: 216 average time/residue: 0.2929 time to fit residues: 99.2436 Evaluate side-chains 183 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 117 time to evaluate : 1.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 416 ILE 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 547 ASN Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 396 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 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 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 425 LEU Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain D residue 543 ILE 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 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 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 74 optimal weight: 0.6980 chunk 200 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 222 optimal weight: 0.7980 chunk 184 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 18 optimal weight: 0.0870 chunk 73 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN D 273 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2880 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= 0.181 Angle : 0.582 11.831 25216 Z= 0.295 Chirality : 0.039 0.205 2928 Planarity : 0.004 0.050 3206 Dihedral : 7.244 86.052 2668 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.17 % Favored : 91.75 % Rotamer: Outliers : 3.76 % Allowed : 31.02 % Favored : 65.22 % 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: 0.17 (0.19), residues: 2314 helix: 2.10 (0.15), residues: 1324 sheet: -1.50 (0.49), residues: 114 loop : -3.03 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 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 0.004 0.000 ARG E 384 *********************** 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 200 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 129 time to evaluate : 2.158 Fit side-chains REVERT: C 80 GLU cc_start: 0.8057 (tm-30) cc_final: 0.7727 (tm-30) REVERT: C 172 LEU cc_start: 0.8166 (mm) cc_final: 0.7691 (mt) REVERT: C 430 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9059 (tt) REVERT: C 524 LYS cc_start: 0.6358 (OUTLIER) cc_final: 0.6144 (mmtp) REVERT: C 567 TYR cc_start: 0.7331 (t80) cc_final: 0.7090 (t80) REVERT: A 16 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.6681 (mp10) REVERT: A 240 MET cc_start: 0.8506 (mmm) cc_final: 0.8008 (mtp) REVERT: A 344 LEU cc_start: 0.7014 (tp) cc_final: 0.6714 (tt) REVERT: A 556 MET cc_start: 0.7192 (tmm) cc_final: 0.6411 (ttt) REVERT: A 587 GLU cc_start: 0.5319 (OUTLIER) cc_final: 0.4604 (mp0) REVERT: D 60 MET cc_start: 0.8168 (tpp) cc_final: 0.7841 (tmm) REVERT: D 301 PHE cc_start: 0.8743 (OUTLIER) cc_final: 0.8291 (t80) REVERT: E 336 GLN cc_start: 0.7687 (tp-100) cc_final: 0.7469 (tp40) outliers start: 71 outliers final: 42 residues processed: 194 average time/residue: 0.3033 time to fit residues: 90.2669 Evaluate side-chains 170 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 123 time to evaluate : 1.975 ------------------------------------------------------------------------------- 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 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 158 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 231 ILE 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 416 ILE Chi-restraints excluded: chain C residue 430 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 19 ILE Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 461 ASN 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 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 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 416 ILE Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 525 THR 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 324 LEU Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 532 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 214 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 126 optimal weight: 0.2980 chunk 162 optimal weight: 8.9990 chunk 125 optimal weight: 0.5980 chunk 187 optimal weight: 0.4980 chunk 124 optimal weight: 0.9980 chunk 221 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 chunk 135 optimal weight: 0.2980 chunk 102 optimal weight: 20.0000 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 18542 Z= 0.163 Angle : 0.571 14.617 25216 Z= 0.288 Chirality : 0.038 0.157 2928 Planarity : 0.004 0.044 3206 Dihedral : 6.984 85.655 2668 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.43 % Favored : 91.49 % Rotamer: Outliers : 3.29 % Allowed : 31.28 % Favored : 65.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.19), residues: 2314 helix: 2.31 (0.15), residues: 1310 sheet: -1.44 (0.49), residues: 114 loop : -3.03 (0.19), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 427 HIS 0.002 0.000 HIS C 94 PHE 0.012 0.001 PHE D 57 TYR 0.016 0.001 TYR A 88 ARG 0.008 0.000 ARG E 220 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 129 time to evaluate : 2.020 Fit side-chains revert: symmetry clash REVERT: C 80 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7691 (tm-30) REVERT: C 172 LEU cc_start: 0.8165 (mm) cc_final: 0.7699 (mt) REVERT: C 430 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.9022 (tt) REVERT: C 524 LYS cc_start: 0.6300 (OUTLIER) cc_final: 0.6063 (mmtp) REVERT: C 567 TYR cc_start: 0.7321 (t80) cc_final: 0.7106 (t80) REVERT: A 16 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.6702 (mp10) REVERT: A 240 MET cc_start: 0.8459 (mmm) cc_final: 0.8051 (mtp) REVERT: A 556 MET cc_start: 0.7318 (tmm) cc_final: 0.6341 (ttt) REVERT: A 587 GLU cc_start: 0.5261 (OUTLIER) cc_final: 0.4594 (mp0) REVERT: D 60 MET cc_start: 0.8010 (tpp) cc_final: 0.7798 (tmm) REVERT: D 301 PHE cc_start: 0.8687 (OUTLIER) cc_final: 0.8226 (t80) REVERT: D 541 GLN cc_start: 0.7704 (mp10) cc_final: 0.7489 (mp10) REVERT: E 584 ARG cc_start: 0.6432 (tpm170) cc_final: 0.6034 (tpt170) outliers start: 62 outliers final: 40 residues processed: 183 average time/residue: 0.3052 time to fit residues: 86.4453 Evaluate side-chains 166 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 121 time to evaluate : 2.358 ------------------------------------------------------------------------------- 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 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 270 VAL 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 416 ILE Chi-restraints excluded: chain C residue 430 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 324 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 443 VAL Chi-restraints excluded: chain A residue 461 ASN Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 587 GLU 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 525 THR Chi-restraints excluded: chain D residue 543 ILE Chi-restraints excluded: chain E residue 54 MET 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 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 137 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 151 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 174 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 HIS ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 18542 Z= 0.320 Angle : 0.655 14.424 25216 Z= 0.331 Chirality : 0.042 0.275 2928 Planarity : 0.004 0.043 3206 Dihedral : 7.174 88.231 2668 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.64 % Favored : 90.28 % Rotamer: Outliers : 3.98 % Allowed : 31.02 % Favored : 65.01 % 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: 1.82 (0.15), residues: 1338 sheet: -1.51 (0.49), residues: 114 loop : -3.06 (0.19), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 427 HIS 0.006 0.001 HIS E 312 PHE 0.014 0.002 PHE C 89 TYR 0.018 0.002 TYR A 88 ARG 0.005 0.000 ARG E 220 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 119 time to evaluate : 2.174 Fit side-chains REVERT: C 80 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7772 (tm-30) REVERT: C 172 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7732 (mt) REVERT: C 430 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9127 (tt) REVERT: C 524 LYS cc_start: 0.6354 (OUTLIER) cc_final: 0.6112 (mmtp) REVERT: C 567 TYR cc_start: 0.7306 (t80) cc_final: 0.7073 (t80) REVERT: A 16 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.6707 (mp10) REVERT: A 240 MET cc_start: 0.8630 (mmm) cc_final: 0.8078 (mtp) REVERT: A 441 ASP cc_start: 0.7365 (t70) cc_final: 0.7126 (m-30) REVERT: A 521 GLU cc_start: 0.6786 (OUTLIER) cc_final: 0.5256 (pp20) REVERT: A 587 GLU cc_start: 0.5382 (OUTLIER) cc_final: 0.4676 (mp0) REVERT: D 60 MET cc_start: 0.7986 (tpp) cc_final: 0.7735 (tmm) REVERT: D 301 PHE cc_start: 0.8773 (OUTLIER) cc_final: 0.8387 (t80) REVERT: E 159 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.7929 (t80) REVERT: E 344 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.6992 (mt) REVERT: E 584 ARG cc_start: 0.6626 (tpm170) cc_final: 0.6378 (tpt170) outliers start: 75 outliers final: 50 residues processed: 185 average time/residue: 0.3011 time to fit residues: 87.8439 Evaluate side-chains 173 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 114 time to evaluate : 2.027 ------------------------------------------------------------------------------- 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 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 172 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 231 ILE 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 416 ILE Chi-restraints excluded: chain C residue 430 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 222 GLU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain A residue 396 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 561 ILE Chi-restraints excluded: chain A residue 587 GLU 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 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 425 LEU Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain D residue 543 ILE 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 344 LEU Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 532 SER Chi-restraints excluded: chain E residue 542 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 201 optimal weight: 0.5980 chunk 212 optimal weight: 1.9990 chunk 193 optimal weight: 3.9990 chunk 206 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 89 optimal weight: 0.0670 chunk 162 optimal weight: 6.9990 chunk 63 optimal weight: 0.1980 chunk 186 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 chunk 205 optimal weight: 7.9990 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 547 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18542 Z= 0.186 Angle : 0.595 15.299 25216 Z= 0.298 Chirality : 0.039 0.243 2928 Planarity : 0.004 0.042 3206 Dihedral : 7.046 88.800 2668 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.51 % Favored : 91.40 % Rotamer: Outliers : 3.23 % Allowed : 31.71 % Favored : 65.06 % 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: 0.27 (0.19), residues: 2314 helix: 2.21 (0.15), residues: 1310 sheet: -1.40 (0.49), residues: 114 loop : -2.96 (0.19), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 427 HIS 0.003 0.001 HIS E 312 PHE 0.010 0.001 PHE D 57 TYR 0.014 0.001 TYR A 88 ARG 0.006 0.000 ARG E 220 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 120 time to evaluate : 2.286 Fit side-chains REVERT: C 80 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7731 (tm-30) REVERT: C 172 LEU cc_start: 0.8202 (mm) cc_final: 0.7723 (mt) REVERT: C 430 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9063 (tt) REVERT: C 524 LYS cc_start: 0.6353 (OUTLIER) cc_final: 0.6146 (mmtp) REVERT: C 567 TYR cc_start: 0.7247 (t80) cc_final: 0.7014 (t80) REVERT: A 16 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.6667 (mp10) REVERT: A 240 MET cc_start: 0.8464 (mmm) cc_final: 0.7985 (mtp) REVERT: A 521 GLU cc_start: 0.6734 (OUTLIER) cc_final: 0.5219 (pp20) REVERT: A 556 MET cc_start: 0.7099 (tmm) cc_final: 0.6366 (ttt) REVERT: A 587 GLU cc_start: 0.5353 (OUTLIER) cc_final: 0.4665 (mp0) REVERT: D 301 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.8305 (t80) REVERT: D 353 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7912 (mp10) REVERT: E 344 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.7028 (mt) REVERT: E 584 ARG cc_start: 0.6534 (tpm170) cc_final: 0.6034 (tpt170) outliers start: 61 outliers final: 45 residues processed: 174 average time/residue: 0.3250 time to fit residues: 87.5102 Evaluate side-chains 169 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 116 time to evaluate : 2.025 ------------------------------------------------------------------------------- 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 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 304 LEU Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 430 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 324 LEU Chi-restraints excluded: chain A residue 396 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 561 ILE Chi-restraints excluded: chain A residue 587 GLU 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 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 525 THR Chi-restraints excluded: chain D residue 543 ILE 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 324 LEU Chi-restraints excluded: chain E residue 339 GLU Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 532 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 135 optimal weight: 1.9990 chunk 218 optimal weight: 7.9990 chunk 133 optimal weight: 1.9990 chunk 103 optimal weight: 0.0670 chunk 151 optimal weight: 9.9990 chunk 229 optimal weight: 4.9990 chunk 210 optimal weight: 1.9990 chunk 182 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 111 optimal weight: 20.0000 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18542 Z= 0.217 Angle : 0.616 15.588 25216 Z= 0.307 Chirality : 0.040 0.242 2928 Planarity : 0.004 0.042 3206 Dihedral : 7.001 88.880 2668 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.90 % Favored : 91.01 % Rotamer: Outliers : 3.08 % Allowed : 32.03 % 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: 0.21 (0.19), residues: 2314 helix: 2.14 (0.15), residues: 1318 sheet: -1.35 (0.49), residues: 114 loop : -3.00 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 427 HIS 0.003 0.001 HIS E 312 PHE 0.010 0.001 PHE D 145 TYR 0.015 0.001 TYR A 88 ARG 0.006 0.000 ARG E 220 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4628 Ramachandran restraints generated. 2314 Oldfield, 0 Emsley, 2314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 120 time to evaluate : 2.169 Fit side-chains REVERT: C 80 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7734 (tt0) REVERT: C 172 LEU cc_start: 0.8209 (mm) cc_final: 0.7728 (mt) REVERT: C 430 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9066 (tt) REVERT: C 524 LYS cc_start: 0.6347 (OUTLIER) cc_final: 0.6100 (mmtp) REVERT: C 567 TYR cc_start: 0.7248 (t80) cc_final: 0.7018 (t80) REVERT: A 16 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.6542 (mp10) REVERT: A 159 PHE cc_start: 0.8513 (OUTLIER) cc_final: 0.8238 (t80) REVERT: A 240 MET cc_start: 0.8498 (mmm) cc_final: 0.8039 (mtp) REVERT: A 521 GLU cc_start: 0.6732 (OUTLIER) cc_final: 0.5216 (pp20) REVERT: A 556 MET cc_start: 0.7120 (tmm) cc_final: 0.6402 (ttt) REVERT: A 587 GLU cc_start: 0.5476 (OUTLIER) cc_final: 0.4751 (mp0) REVERT: D 301 PHE cc_start: 0.8752 (OUTLIER) cc_final: 0.8304 (t80) REVERT: D 353 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7926 (mp10) REVERT: D 417 SER cc_start: 0.8292 (OUTLIER) cc_final: 0.8077 (p) REVERT: E 344 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.6954 (mt) REVERT: E 584 ARG cc_start: 0.6555 (tpm170) cc_final: 0.6108 (tpt170) outliers start: 58 outliers final: 45 residues processed: 172 average time/residue: 0.3068 time to fit residues: 82.9464 Evaluate side-chains 171 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 116 time to evaluate : 2.309 ------------------------------------------------------------------------------- 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 215 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 430 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 159 PHE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 461 ASN Chi-restraints excluded: chain A residue 521 GLU Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 587 GLU 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 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 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 417 SER 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 114 ILE Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 532 SER Chi-restraints excluded: chain E residue 542 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 144 optimal weight: 0.9980 chunk 194 optimal weight: 1.9990 chunk 55 optimal weight: 0.0870 chunk 168 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 187 optimal weight: 0.0270 chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 overall best weight: 1.0220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.126370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.095184 restraints weight = 34622.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.097957 restraints weight = 18171.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.099835 restraints weight = 11743.747| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3187 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= 0.187 Angle : 0.602 15.713 25216 Z= 0.299 Chirality : 0.039 0.235 2928 Planarity : 0.004 0.042 3206 Dihedral : 6.962 88.165 2668 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.69 % Favored : 91.23 % Rotamer: Outliers : 3.18 % Allowed : 32.08 % Favored : 64.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.19), residues: 2314 helix: 2.24 (0.15), residues: 1312 sheet: -1.30 (0.49), residues: 114 loop : -2.95 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 550 HIS 0.003 0.001 HIS E 312 PHE 0.009 0.001 PHE D 145 TYR 0.015 0.001 TYR A 88 ARG 0.006 0.000 ARG E 220 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3247.62 seconds wall clock time: 60 minutes 49.08 seconds (3649.08 seconds total)