Starting phenix.real_space_refine on Fri Mar 15 15:01:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wr4_21876/03_2024/6wr4_21876_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wr4_21876/03_2024/6wr4_21876.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wr4_21876/03_2024/6wr4_21876.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wr4_21876/03_2024/6wr4_21876.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wr4_21876/03_2024/6wr4_21876_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wr4_21876/03_2024/6wr4_21876_updated.pdb" } resolution = 2.9 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= 0.009 sd= 0.160 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: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 7896 2.51 5 N 1941 2.21 5 O 2037 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 125": "NH1" <-> "NH2" Residue "A ARG 186": "NH1" <-> "NH2" Residue "A ARG 201": "NH1" <-> "NH2" Residue "A ARG 279": "NH1" <-> "NH2" Residue "A ARG 285": "NH1" <-> "NH2" Residue "A ARG 322": "NH1" <-> "NH2" Residue "A ARG 341": "NH1" <-> "NH2" Residue "B ARG 125": "NH1" <-> "NH2" Residue "B ARG 186": "NH1" <-> "NH2" Residue "B ARG 201": "NH1" <-> "NH2" Residue "B ARG 279": "NH1" <-> "NH2" Residue "B ARG 285": "NH1" <-> "NH2" Residue "B ARG 322": "NH1" <-> "NH2" Residue "B ARG 341": "NH1" <-> "NH2" Residue "C ARG 125": "NH1" <-> "NH2" Residue "C ARG 186": "NH1" <-> "NH2" Residue "C ARG 201": "NH1" <-> "NH2" Residue "C ARG 279": "NH1" <-> "NH2" Residue "C ARG 285": "NH1" <-> "NH2" Residue "C ARG 322": "NH1" <-> "NH2" Residue "C ARG 341": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11934 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3862 Classifications: {'peptide': 470} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 452} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 3862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3862 Classifications: {'peptide': 470} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 452} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 3862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3862 Classifications: {'peptide': 470} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 452} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 116 Unusual residues: {'LMN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 116 Unusual residues: {'LMN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 116 Unusual residues: {'LMN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 10 Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" C1 LMN A 901 " occ=0.50 ... (67 atoms not shown) pdb=" OCB LMN A 901 " occ=0.50 residue: pdb=" C1 LMN A 902 " occ=0.50 ... (45 atoms not shown) pdb=" OBY LMN A 902 " occ=0.50 residue: pdb=" C1 LMN B 901 " occ=0.50 ... (67 atoms not shown) pdb=" OCB LMN B 901 " occ=0.50 residue: pdb=" C1 LMN B 902 " occ=0.50 ... (45 atoms not shown) pdb=" OBY LMN B 902 " occ=0.50 residue: pdb=" C1 LMN C 901 " occ=0.50 ... (67 atoms not shown) pdb=" OCB LMN C 901 " occ=0.50 residue: pdb=" C1 LMN C 902 " occ=0.50 ... (45 atoms not shown) pdb=" OBY LMN C 902 " occ=0.50 Time building chain proxies: 6.70, per 1000 atoms: 0.56 Number of scatterers: 11934 At special positions: 0 Unit cell: (132.5, 124.02, 85.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 2037 8.00 N 1941 7.00 C 7896 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.44 Conformation dependent library (CDL) restraints added in 2.3 seconds 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2688 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 75 helices and 6 sheets defined 60.6% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.29 Creating SS restraints... Processing helix chain 'A' and resid 43 through 55 removed outlier: 3.671A pdb=" N PHE A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 85 removed outlier: 3.649A pdb=" N PHE A 68 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 70 " --> pdb=" O GLU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'A' and resid 112 through 115 No H-bonds generated for 'chain 'A' and resid 112 through 115' Processing helix chain 'A' and resid 119 through 122 No H-bonds generated for 'chain 'A' and resid 119 through 122' Processing helix chain 'A' and resid 130 through 166 removed outlier: 3.886A pdb=" N GLU A 159 " --> pdb=" O CYS A 155 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE A 160 " --> pdb=" O CYS A 156 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE A 163 " --> pdb=" O GLU A 159 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 165 " --> pdb=" O HIS A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 180 through 189 removed outlier: 3.532A pdb=" N ALA A 185 " --> pdb=" O GLN A 181 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 212 No H-bonds generated for 'chain 'A' and resid 209 through 212' Processing helix chain 'A' and resid 217 through 224 removed outlier: 3.789A pdb=" N ALA A 221 " --> pdb=" O ASN A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 255 removed outlier: 3.821A pdb=" N ASN A 250 " --> pdb=" O GLY A 246 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 274 No H-bonds generated for 'chain 'A' and resid 272 through 274' Processing helix chain 'A' and resid 280 through 299 removed outlier: 3.830A pdb=" N LEU A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU A 291 " --> pdb=" O SER A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 322 removed outlier: 3.569A pdb=" N TRP A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA A 317 " --> pdb=" O PHE A 313 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLU A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N VAL A 319 " --> pdb=" O SER A 315 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS A 321 " --> pdb=" O ALA A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 339 Processing helix chain 'A' and resid 347 through 354 removed outlier: 3.580A pdb=" N GLN A 351 " --> pdb=" O GLU A 347 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG A 353 " --> pdb=" O GLU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 364 removed outlier: 3.820A pdb=" N LYS A 363 " --> pdb=" O LYS A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 368 No H-bonds generated for 'chain 'A' and resid 366 through 368' Processing helix chain 'A' and resid 371 through 398 removed outlier: 3.541A pdb=" N PHE A 383 " --> pdb=" O ASN A 379 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE A 387 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 424 Processing helix chain 'A' and resid 438 through 444 removed outlier: 3.751A pdb=" N ALA A 443 " --> pdb=" O ARG A 439 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N HIS A 444 " --> pdb=" O VAL A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 468 No H-bonds generated for 'chain 'A' and resid 465 through 468' Processing helix chain 'A' and resid 472 through 480 Processing helix chain 'A' and resid 482 through 491 Proline residue: A 487 - end of helix Processing helix chain 'A' and resid 495 through 507 removed outlier: 4.683A pdb=" N LEU A 499 " --> pdb=" O PRO A 496 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE A 502 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP A 503 " --> pdb=" O GLU A 500 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE A 505 " --> pdb=" O ILE A 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 55 removed outlier: 3.671A pdb=" N PHE B 47 " --> pdb=" O LEU B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 85 removed outlier: 3.649A pdb=" N PHE B 68 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU B 69 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 70 " --> pdb=" O GLU B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 93 Processing helix chain 'B' and resid 112 through 115 No H-bonds generated for 'chain 'B' and resid 112 through 115' Processing helix chain 'B' and resid 119 through 122 No H-bonds generated for 'chain 'B' and resid 119 through 122' Processing helix chain 'B' and resid 130 through 166 removed outlier: 3.886A pdb=" N GLU B 159 " --> pdb=" O CYS B 155 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE B 160 " --> pdb=" O CYS B 156 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE B 163 " --> pdb=" O GLU B 159 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 165 " --> pdb=" O HIS B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 180 through 189 removed outlier: 3.531A pdb=" N ALA B 185 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN B 189 " --> pdb=" O ALA B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 212 No H-bonds generated for 'chain 'B' and resid 209 through 212' Processing helix chain 'B' and resid 217 through 224 removed outlier: 3.789A pdb=" N ALA B 221 " --> pdb=" O ASN B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 255 removed outlier: 3.821A pdb=" N ASN B 250 " --> pdb=" O GLY B 246 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU B 252 " --> pdb=" O LYS B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 274 No H-bonds generated for 'chain 'B' and resid 272 through 274' Processing helix chain 'B' and resid 280 through 299 removed outlier: 3.831A pdb=" N LEU B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU B 291 " --> pdb=" O SER B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 322 removed outlier: 3.568A pdb=" N TRP B 307 " --> pdb=" O LEU B 303 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA B 317 " --> pdb=" O PHE B 313 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLU B 318 " --> pdb=" O PHE B 314 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N VAL B 319 " --> pdb=" O SER B 315 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS B 321 " --> pdb=" O ALA B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 339 Processing helix chain 'B' and resid 347 through 354 removed outlier: 3.580A pdb=" N GLN B 351 " --> pdb=" O GLU B 347 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG B 353 " --> pdb=" O GLU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 364 removed outlier: 3.820A pdb=" N LYS B 363 " --> pdb=" O LYS B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 368 No H-bonds generated for 'chain 'B' and resid 366 through 368' Processing helix chain 'B' and resid 371 through 398 removed outlier: 3.541A pdb=" N PHE B 383 " --> pdb=" O ASN B 379 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE B 387 " --> pdb=" O PHE B 383 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP B 398 " --> pdb=" O LEU B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 424 Processing helix chain 'B' and resid 438 through 444 removed outlier: 3.752A pdb=" N ALA B 443 " --> pdb=" O ARG B 439 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N HIS B 444 " --> pdb=" O VAL B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 468 No H-bonds generated for 'chain 'B' and resid 465 through 468' Processing helix chain 'B' and resid 472 through 480 Processing helix chain 'B' and resid 482 through 491 Proline residue: B 487 - end of helix Processing helix chain 'B' and resid 495 through 507 removed outlier: 4.683A pdb=" N LEU B 499 " --> pdb=" O PRO B 496 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE B 502 " --> pdb=" O LEU B 499 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP B 503 " --> pdb=" O GLU B 500 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE B 505 " --> pdb=" O ILE B 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 55 removed outlier: 3.671A pdb=" N PHE C 47 " --> pdb=" O LEU C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 85 removed outlier: 3.650A pdb=" N PHE C 68 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU C 69 " --> pdb=" O GLY C 65 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU C 70 " --> pdb=" O GLU C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 93 Processing helix chain 'C' and resid 112 through 115 No H-bonds generated for 'chain 'C' and resid 112 through 115' Processing helix chain 'C' and resid 119 through 122 No H-bonds generated for 'chain 'C' and resid 119 through 122' Processing helix chain 'C' and resid 130 through 166 removed outlier: 3.887A pdb=" N GLU C 159 " --> pdb=" O CYS C 155 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE C 160 " --> pdb=" O CYS C 156 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE C 163 " --> pdb=" O GLU C 159 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU C 165 " --> pdb=" O HIS C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 180 through 189 removed outlier: 3.531A pdb=" N ALA C 185 " --> pdb=" O GLN C 181 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN C 189 " --> pdb=" O ALA C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 212 No H-bonds generated for 'chain 'C' and resid 209 through 212' Processing helix chain 'C' and resid 217 through 224 removed outlier: 3.789A pdb=" N ALA C 221 " --> pdb=" O ASN C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 255 removed outlier: 3.822A pdb=" N ASN C 250 " --> pdb=" O GLY C 246 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU C 252 " --> pdb=" O LYS C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 274 No H-bonds generated for 'chain 'C' and resid 272 through 274' Processing helix chain 'C' and resid 280 through 299 removed outlier: 3.831A pdb=" N LEU C 286 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU C 291 " --> pdb=" O SER C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 322 removed outlier: 3.568A pdb=" N TRP C 307 " --> pdb=" O LEU C 303 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA C 317 " --> pdb=" O PHE C 313 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLU C 318 " --> pdb=" O PHE C 314 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N VAL C 319 " --> pdb=" O SER C 315 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS C 321 " --> pdb=" O ALA C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 339 Processing helix chain 'C' and resid 347 through 354 removed outlier: 3.580A pdb=" N GLN C 351 " --> pdb=" O GLU C 347 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG C 353 " --> pdb=" O GLU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 364 removed outlier: 3.819A pdb=" N LYS C 363 " --> pdb=" O LYS C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 368 No H-bonds generated for 'chain 'C' and resid 366 through 368' Processing helix chain 'C' and resid 371 through 398 removed outlier: 3.541A pdb=" N PHE C 383 " --> pdb=" O ASN C 379 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE C 387 " --> pdb=" O PHE C 383 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP C 398 " --> pdb=" O LEU C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 424 Processing helix chain 'C' and resid 438 through 444 removed outlier: 3.752A pdb=" N ALA C 443 " --> pdb=" O ARG C 439 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N HIS C 444 " --> pdb=" O VAL C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 468 No H-bonds generated for 'chain 'C' and resid 465 through 468' Processing helix chain 'C' and resid 472 through 480 Processing helix chain 'C' and resid 482 through 491 Proline residue: C 487 - end of helix Processing helix chain 'C' and resid 495 through 507 removed outlier: 4.683A pdb=" N LEU C 499 " --> pdb=" O PRO C 496 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE C 502 " --> pdb=" O LEU C 499 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASP C 503 " --> pdb=" O GLU C 500 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE C 505 " --> pdb=" O ILE C 502 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 231 through 234 removed outlier: 3.532A pdb=" N GLY A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 510 through 512 Processing sheet with id= C, first strand: chain 'B' and resid 231 through 234 removed outlier: 3.533A pdb=" N GLY B 238 " --> pdb=" O LEU B 234 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 510 through 512 Processing sheet with id= E, first strand: chain 'C' and resid 231 through 234 removed outlier: 3.532A pdb=" N GLY C 238 " --> pdb=" O LEU C 234 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 510 through 512 480 hydrogen bonds defined for protein. 1368 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: 3.25 Time building geometry restraints manager: 4.81 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: 3471 1.34 - 1.46: 2483 1.46 - 1.58: 6173 1.58 - 1.69: 62 1.69 - 1.81: 78 Bond restraints: 12267 Sorted by residual: bond pdb=" C1 LMN A 902 " pdb=" O5 LMN A 902 " ideal model delta sigma weight residual 1.403 1.562 -0.159 2.00e-02 2.50e+03 6.35e+01 bond pdb=" C1 LMN C 902 " pdb=" O5 LMN C 902 " ideal model delta sigma weight residual 1.403 1.562 -0.159 2.00e-02 2.50e+03 6.33e+01 bond pdb=" C1 LMN B 902 " pdb=" O5 LMN B 902 " ideal model delta sigma weight residual 1.403 1.561 -0.158 2.00e-02 2.50e+03 6.28e+01 bond pdb=" C1 LMN A 901 " pdb=" O5 LMN A 901 " ideal model delta sigma weight residual 1.403 1.551 -0.148 2.00e-02 2.50e+03 5.49e+01 bond pdb=" C1 LMN C 901 " pdb=" O5 LMN C 901 " ideal model delta sigma weight residual 1.403 1.551 -0.148 2.00e-02 2.50e+03 5.48e+01 ... (remaining 12262 not shown) Histogram of bond angle deviations from ideal: 97.48 - 104.79: 174 104.79 - 112.10: 5816 112.10 - 119.41: 4355 119.41 - 126.72: 6094 126.72 - 134.04: 217 Bond angle restraints: 16656 Sorted by residual: angle pdb=" N THR C 461 " pdb=" CA THR C 461 " pdb=" C THR C 461 " ideal model delta sigma weight residual 114.75 106.70 8.05 1.26e+00 6.30e-01 4.08e+01 angle pdb=" N THR B 461 " pdb=" CA THR B 461 " pdb=" C THR B 461 " ideal model delta sigma weight residual 114.75 106.72 8.03 1.26e+00 6.30e-01 4.07e+01 angle pdb=" N THR A 461 " pdb=" CA THR A 461 " pdb=" C THR A 461 " ideal model delta sigma weight residual 114.75 106.75 8.00 1.26e+00 6.30e-01 4.03e+01 angle pdb=" C LEU A 203 " pdb=" N THR A 204 " pdb=" CA THR A 204 " ideal model delta sigma weight residual 121.54 131.51 -9.97 1.91e+00 2.74e-01 2.73e+01 angle pdb=" C LEU C 203 " pdb=" N THR C 204 " pdb=" CA THR C 204 " ideal model delta sigma weight residual 121.54 131.45 -9.91 1.91e+00 2.74e-01 2.69e+01 ... (remaining 16651 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.18: 6954 24.18 - 48.36: 387 48.36 - 72.54: 84 72.54 - 96.72: 57 96.72 - 120.90: 51 Dihedral angle restraints: 7533 sinusoidal: 3387 harmonic: 4146 Sorted by residual: dihedral pdb=" CA PRO B 36 " pdb=" C PRO B 36 " pdb=" N TRP B 37 " pdb=" CA TRP B 37 " ideal model delta harmonic sigma weight residual -180.00 -138.41 -41.59 0 5.00e+00 4.00e-02 6.92e+01 dihedral pdb=" CA PRO C 36 " pdb=" C PRO C 36 " pdb=" N TRP C 37 " pdb=" CA TRP C 37 " ideal model delta harmonic sigma weight residual -180.00 -138.42 -41.58 0 5.00e+00 4.00e-02 6.91e+01 dihedral pdb=" CA GLN C 436 " pdb=" C GLN C 436 " pdb=" N LEU C 437 " pdb=" CA LEU C 437 " ideal model delta harmonic sigma weight residual 180.00 138.43 41.57 0 5.00e+00 4.00e-02 6.91e+01 ... (remaining 7530 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1658 0.096 - 0.191: 223 0.191 - 0.287: 12 0.287 - 0.382: 12 0.382 - 0.478: 3 Chirality restraints: 1908 Sorted by residual: chirality pdb=" CA ARG C 279 " pdb=" N ARG C 279 " pdb=" C ARG C 279 " pdb=" CB ARG C 279 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.71e+00 chirality pdb=" CA ARG B 279 " pdb=" N ARG B 279 " pdb=" C ARG B 279 " pdb=" CB ARG B 279 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.68e+00 chirality pdb=" CA ARG A 279 " pdb=" N ARG A 279 " pdb=" C ARG A 279 " pdb=" CB ARG A 279 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.65e+00 ... (remaining 1905 not shown) Planarity restraints: 2013 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET C 448 " -0.043 5.00e-02 4.00e+02 6.51e-02 6.78e+00 pdb=" N PRO C 449 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO C 449 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 449 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 448 " -0.043 5.00e-02 4.00e+02 6.48e-02 6.72e+00 pdb=" N PRO B 449 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 449 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 449 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 448 " 0.043 5.00e-02 4.00e+02 6.48e-02 6.71e+00 pdb=" N PRO A 449 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 449 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 449 " 0.035 5.00e-02 4.00e+02 ... (remaining 2010 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3130 2.80 - 3.32: 10488 3.32 - 3.85: 19193 3.85 - 4.37: 23687 4.37 - 4.90: 38320 Nonbonded interactions: 94818 Sorted by model distance: nonbonded pdb=" OG SER B 261 " pdb=" O LEU B 262 " model vdw 2.272 2.440 nonbonded pdb=" OG SER C 261 " pdb=" O LEU C 262 " model vdw 2.272 2.440 nonbonded pdb=" OG SER A 261 " pdb=" O LEU A 262 " model vdw 2.272 2.440 nonbonded pdb=" O ILE C 254 " pdb=" NH1 ARG C 289 " model vdw 2.298 2.520 nonbonded pdb=" O ILE B 254 " pdb=" NH1 ARG B 289 " model vdw 2.298 2.520 ... (remaining 94813 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 2.170 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 33.640 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.070 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:12.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 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 : 0.012 0.159 12267 Z= 0.726 Angle : 1.398 10.956 16656 Z= 0.735 Chirality : 0.070 0.478 1908 Planarity : 0.007 0.065 2013 Dihedral : 20.663 120.896 4845 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.17 % Favored : 94.40 % Rotamer: Outliers : 5.53 % Allowed : 2.64 % Favored : 91.83 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.89 % 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: -6.12 (0.14), residues: 1392 helix: -4.16 (0.08), residues: 921 sheet: None (None), residues: 0 loop : -3.37 (0.22), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 257 HIS 0.011 0.002 HIS C 406 PHE 0.034 0.003 PHE A 243 TYR 0.020 0.003 TYR B 218 ARG 0.027 0.002 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 252 time to evaluate : 1.268 Fit side-chains REVERT: A 172 MET cc_start: 0.6909 (mmp) cc_final: 0.6696 (mmt) REVERT: A 245 ARG cc_start: 0.7000 (ttt-90) cc_final: 0.6784 (ttt180) REVERT: A 448 MET cc_start: 0.6421 (mmt) cc_final: 0.5882 (mmt) REVERT: B 504 PHE cc_start: 0.7359 (t80) cc_final: 0.7081 (t80) REVERT: C 245 ARG cc_start: 0.6834 (ttt-90) cc_final: 0.6544 (ttt180) outliers start: 69 outliers final: 4 residues processed: 312 average time/residue: 1.0725 time to fit residues: 365.5582 Evaluate side-chains 153 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 149 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain B residue 288 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 0.9990 chunk 106 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 110 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 128 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 191 GLN A 217 ASN ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 GLN A 348 HIS ** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN A 451 HIS A 457 HIS B 57 ASN B 191 GLN B 217 ASN ** B 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 GLN B 348 HIS ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 HIS B 455 ASN B 457 HIS C 57 ASN C 191 GLN C 217 ASN ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 GLN C 348 HIS ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 HIS C 457 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12267 Z= 0.192 Angle : 0.776 8.076 16656 Z= 0.376 Chirality : 0.046 0.225 1908 Planarity : 0.006 0.057 2013 Dihedral : 18.574 103.522 2153 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.72 % Allowed : 10.02 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.84 (0.19), residues: 1392 helix: -2.12 (0.14), residues: 948 sheet: -4.43 (0.57), residues: 30 loop : -3.00 (0.26), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 180 HIS 0.005 0.001 HIS B 406 PHE 0.012 0.001 PHE A 79 TYR 0.017 0.001 TYR A 177 ARG 0.005 0.001 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 178 time to evaluate : 1.204 Fit side-chains REVERT: A 43 LEU cc_start: 0.7843 (mt) cc_final: 0.7550 (tp) REVERT: B 422 ARG cc_start: 0.7441 (mmt-90) cc_final: 0.7238 (mmt180) outliers start: 34 outliers final: 11 residues processed: 197 average time/residue: 1.0733 time to fit residues: 231.9469 Evaluate side-chains 151 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 140 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PRO Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain B residue 36 PRO Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain C residue 36 PRO Chi-restraints excluded: chain C residue 145 HIS Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 423 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 127 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 102 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN B 250 ASN ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 ASN ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12267 Z= 0.173 Angle : 0.686 8.309 16656 Z= 0.331 Chirality : 0.046 0.356 1908 Planarity : 0.005 0.054 2013 Dihedral : 13.644 74.823 2145 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.37 % Allowed : 13.22 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.21), residues: 1392 helix: -1.03 (0.16), residues: 948 sheet: -4.17 (0.62), residues: 30 loop : -2.96 (0.25), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 37 HIS 0.005 0.001 HIS B 406 PHE 0.012 0.001 PHE C 79 TYR 0.017 0.001 TYR A 177 ARG 0.005 0.001 ARG C 245 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 151 time to evaluate : 1.320 Fit side-chains REVERT: A 43 LEU cc_start: 0.7799 (mt) cc_final: 0.7524 (tp) REVERT: A 477 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7674 (tp) REVERT: A 484 ILE cc_start: 0.7845 (mm) cc_final: 0.7644 (mm) REVERT: C 477 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7839 (tp) outliers start: 42 outliers final: 15 residues processed: 177 average time/residue: 0.9579 time to fit residues: 188.5557 Evaluate side-chains 149 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 132 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PRO Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain B residue 178 CYS Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain C residue 36 PRO Chi-restraints excluded: chain C residue 145 HIS Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 489 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 14 optimal weight: 0.0060 chunk 61 optimal weight: 0.3980 chunk 86 optimal weight: 9.9990 chunk 128 optimal weight: 5.9990 chunk 136 optimal weight: 0.9980 chunk 67 optimal weight: 0.0010 chunk 122 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 overall best weight: 0.4602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 429 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12267 Z= 0.141 Angle : 0.618 6.650 16656 Z= 0.301 Chirality : 0.044 0.320 1908 Planarity : 0.004 0.053 2013 Dihedral : 11.893 70.735 2145 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.21 % Allowed : 14.10 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.22), residues: 1392 helix: -0.39 (0.17), residues: 927 sheet: -3.95 (0.68), residues: 30 loop : -2.65 (0.25), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 37 HIS 0.005 0.001 HIS B 406 PHE 0.009 0.001 PHE A 383 TYR 0.015 0.001 TYR A 177 ARG 0.007 0.001 ARG A 462 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 155 time to evaluate : 1.358 Fit side-chains revert: symmetry clash REVERT: A 128 GLU cc_start: 0.6379 (OUTLIER) cc_final: 0.5887 (pm20) REVERT: A 477 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7714 (tp) REVERT: A 484 ILE cc_start: 0.7828 (mm) cc_final: 0.7616 (mm) REVERT: B 477 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7559 (tp) outliers start: 40 outliers final: 13 residues processed: 181 average time/residue: 0.9414 time to fit residues: 188.9105 Evaluate side-chains 154 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 138 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 145 HIS Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 245 ARG Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 145 HIS Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 178 CYS Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 490 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 101 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 116 optimal weight: 0.3980 chunk 94 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 69 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 HIS B 54 HIS ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 HIS ** B 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 455 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12267 Z= 0.180 Angle : 0.631 6.393 16656 Z= 0.308 Chirality : 0.044 0.260 1908 Planarity : 0.004 0.052 2013 Dihedral : 11.223 67.562 2145 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.40 % Allowed : 15.87 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.22), residues: 1392 helix: -0.21 (0.17), residues: 927 sheet: -4.00 (0.68), residues: 30 loop : -2.48 (0.25), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 37 HIS 0.007 0.001 HIS B 145 PHE 0.022 0.001 PHE C 73 TYR 0.015 0.001 TYR C 177 ARG 0.005 0.000 ARG A 462 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 143 time to evaluate : 1.314 Fit side-chains REVERT: A 477 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7739 (tp) REVERT: B 477 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7551 (tp) REVERT: C 69 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7246 (mp0) REVERT: C 128 GLU cc_start: 0.6258 (OUTLIER) cc_final: 0.5830 (pm20) outliers start: 30 outliers final: 17 residues processed: 162 average time/residue: 0.9447 time to fit residues: 170.4885 Evaluate side-chains 151 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 130 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 245 ARG Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 145 HIS Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 178 CYS Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 490 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 HIS B 145 HIS B 351 GLN B 355 ASN C 54 HIS C 284 GLN C 351 GLN ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 12267 Z= 0.307 Angle : 0.745 8.091 16656 Z= 0.360 Chirality : 0.049 0.305 1908 Planarity : 0.005 0.053 2013 Dihedral : 11.479 71.443 2145 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.04 % Allowed : 15.79 % Favored : 81.17 % 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: -1.91 (0.22), residues: 1392 helix: -0.55 (0.17), residues: 954 sheet: -4.11 (0.63), residues: 30 loop : -2.55 (0.27), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 180 HIS 0.009 0.001 HIS B 145 PHE 0.022 0.002 PHE A 243 TYR 0.017 0.002 TYR C 177 ARG 0.007 0.001 ARG C 341 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 137 time to evaluate : 1.211 Fit side-chains REVERT: A 43 LEU cc_start: 0.7861 (mt) cc_final: 0.7611 (tp) REVERT: A 477 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7780 (tp) REVERT: B 477 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7492 (tp) outliers start: 38 outliers final: 17 residues processed: 163 average time/residue: 1.0405 time to fit residues: 187.3384 Evaluate side-chains 141 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 122 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 178 CYS Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 408 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 99 optimal weight: 0.0980 chunk 114 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 135 optimal weight: 0.0770 chunk 85 optimal weight: 0.8980 chunk 82 optimal weight: 0.0770 chunk 62 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 HIS B 145 HIS B 429 HIS ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12267 Z= 0.142 Angle : 0.596 7.824 16656 Z= 0.295 Chirality : 0.042 0.175 1908 Planarity : 0.004 0.048 2013 Dihedral : 10.736 67.323 2145 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.08 % Allowed : 18.43 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.22), residues: 1392 helix: 0.05 (0.18), residues: 906 sheet: None (None), residues: 0 loop : -2.29 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 180 HIS 0.010 0.001 HIS B 145 PHE 0.018 0.001 PHE C 73 TYR 0.011 0.001 TYR C 177 ARG 0.007 0.000 ARG A 506 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 140 time to evaluate : 1.333 Fit side-chains REVERT: A 69 GLU cc_start: 0.7676 (mp0) cc_final: 0.7441 (mp0) REVERT: A 477 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7767 (tp) REVERT: B 477 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7583 (tp) REVERT: C 203 LEU cc_start: 0.2212 (OUTLIER) cc_final: 0.1958 (mt) outliers start: 26 outliers final: 11 residues processed: 158 average time/residue: 0.9710 time to fit residues: 170.1165 Evaluate side-chains 147 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 133 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain C residue 178 CYS Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 408 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 0.0770 chunk 40 optimal weight: 9.9990 chunk 26 optimal weight: 0.7980 chunk 86 optimal weight: 0.2980 chunk 92 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 118 optimal weight: 4.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 HIS B 145 HIS ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 12267 Z= 0.146 Angle : 0.598 6.813 16656 Z= 0.296 Chirality : 0.042 0.163 1908 Planarity : 0.004 0.045 2013 Dihedral : 10.591 70.702 2145 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.00 % Allowed : 18.91 % Favored : 79.09 % 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: -0.83 (0.22), residues: 1392 helix: 0.27 (0.18), residues: 903 sheet: None (None), residues: 0 loop : -2.09 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 37 HIS 0.011 0.001 HIS B 145 PHE 0.015 0.001 PHE C 73 TYR 0.015 0.001 TYR C 177 ARG 0.005 0.000 ARG A 506 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 137 time to evaluate : 1.244 Fit side-chains REVERT: A 69 GLU cc_start: 0.7575 (mp0) cc_final: 0.7370 (mp0) REVERT: A 203 LEU cc_start: 0.3174 (OUTLIER) cc_final: 0.2873 (mt) REVERT: A 477 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7715 (tp) REVERT: B 477 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7595 (tp) REVERT: C 203 LEU cc_start: 0.2395 (OUTLIER) cc_final: 0.2106 (mt) outliers start: 25 outliers final: 9 residues processed: 155 average time/residue: 0.9519 time to fit residues: 164.1834 Evaluate side-chains 135 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 122 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 359 LYS Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 490 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 0.9990 chunk 130 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 55 optimal weight: 0.0470 chunk 99 optimal weight: 3.9990 chunk 38 optimal weight: 0.0060 chunk 114 optimal weight: 5.9990 chunk 119 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 81 optimal weight: 0.0970 overall best weight: 0.3092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 HIS ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN B 145 HIS ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 444 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12267 Z= 0.132 Angle : 0.572 9.073 16656 Z= 0.283 Chirality : 0.040 0.152 1908 Planarity : 0.004 0.046 2013 Dihedral : 10.354 69.176 2145 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.44 % Allowed : 19.47 % Favored : 79.09 % 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: -0.57 (0.23), residues: 1392 helix: 0.50 (0.18), residues: 903 sheet: None (None), residues: 0 loop : -2.03 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 37 HIS 0.011 0.001 HIS B 145 PHE 0.016 0.001 PHE C 73 TYR 0.015 0.001 TYR B 249 ARG 0.005 0.000 ARG A 506 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 146 time to evaluate : 1.444 Fit side-chains REVERT: A 69 GLU cc_start: 0.7509 (mp0) cc_final: 0.7304 (mp0) REVERT: A 188 VAL cc_start: 0.6505 (p) cc_final: 0.6254 (t) REVERT: B 477 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7580 (tp) outliers start: 18 outliers final: 8 residues processed: 159 average time/residue: 0.8859 time to fit residues: 158.1631 Evaluate side-chains 134 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 125 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 490 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 140 optimal weight: 7.9990 chunk 129 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 68 optimal weight: 0.3980 chunk 88 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 HIS ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 HIS C 355 ASN C 444 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12267 Z= 0.258 Angle : 0.680 8.751 16656 Z= 0.334 Chirality : 0.046 0.255 1908 Planarity : 0.005 0.047 2013 Dihedral : 10.678 72.190 2145 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.68 % Allowed : 19.95 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.22), residues: 1392 helix: 0.15 (0.17), residues: 915 sheet: -4.07 (0.63), residues: 30 loop : -2.06 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 257 HIS 0.011 0.001 HIS B 145 PHE 0.018 0.002 PHE B 73 TYR 0.022 0.002 TYR C 177 ARG 0.005 0.001 ARG A 289 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2784 Ramachandran restraints generated. 1392 Oldfield, 0 Emsley, 1392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 130 time to evaluate : 1.248 Fit side-chains REVERT: A 188 VAL cc_start: 0.6671 (p) cc_final: 0.6394 (t) REVERT: B 69 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7442 (mp0) REVERT: B 477 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7472 (tp) outliers start: 21 outliers final: 10 residues processed: 145 average time/residue: 0.9446 time to fit residues: 153.1153 Evaluate side-chains 133 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 121 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 408 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 0.1980 chunk 112 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 115 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 HIS ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.185845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.158777 restraints weight = 13244.888| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 2.13 r_work: 0.3594 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3524 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3524 r_free = 0.3524 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3523 r_free = 0.3523 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3523 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12267 Z= 0.184 Angle : 0.629 8.410 16656 Z= 0.310 Chirality : 0.043 0.191 1908 Planarity : 0.004 0.047 2013 Dihedral : 10.515 69.970 2145 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.28 % Allowed : 20.59 % Favored : 78.12 % 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: -0.84 (0.22), residues: 1392 helix: 0.27 (0.17), residues: 912 sheet: None (None), residues: 0 loop : -2.14 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 257 HIS 0.012 0.001 HIS B 145 PHE 0.020 0.001 PHE B 73 TYR 0.015 0.001 TYR C 177 ARG 0.006 0.001 ARG C 289 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3774.83 seconds wall clock time: 67 minutes 43.07 seconds (4063.07 seconds total)