Starting phenix.real_space_refine on Wed Nov 15 13:41:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wr4_21876/11_2023/6wr4_21876_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wr4_21876/11_2023/6wr4_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_21876/11_2023/6wr4_21876.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wr4_21876/11_2023/6wr4_21876.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wr4_21876/11_2023/6wr4_21876_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wr4_21876/11_2023/6wr4_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 1 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: 1 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: 1 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: 6.42, per 1000 atoms: 0.54 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: 4.14 Conformation dependent library (CDL) restraints added in 2.0 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: 2.22 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: 3.03 Time building geometry restraints manager: 4.51 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: 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 - 20.70: 6564 20.70 - 41.40: 378 41.40 - 62.09: 78 62.09 - 82.79: 21 82.79 - 103.49: 6 Dihedral angle restraints: 7047 sinusoidal: 2901 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 7044 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: 0.340 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: 0.010 Extract box with map and model: 2.230 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 32.020 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.240 ------------------------------------------------------------------------------- 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 : 14.492 103.490 4359 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 *********************** 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 : 1.274 Fit side-chains outliers start: 69 outliers final: 4 residues processed: 312 average time/residue: 1.0693 time to fit residues: 364.5784 Evaluate side-chains 153 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 149 time to evaluate : 1.302 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 1.6841 time to fit residues: 3.5485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 128 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 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 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: 0.6936 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12267 Z= 0.200 Angle : 0.744 8.107 16656 Z= 0.373 Chirality : 0.045 0.179 1908 Planarity : 0.006 0.060 2013 Dihedral : 11.384 69.827 1659 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.12 % Allowed : 10.42 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.67 % 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: -3.86 (0.19), residues: 1392 helix: -2.13 (0.14), residues: 948 sheet: -4.44 (0.57), residues: 30 loop : -3.03 (0.26), residues: 414 *********************** 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 210 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 171 time to evaluate : 1.392 Fit side-chains outliers start: 39 outliers final: 12 residues processed: 194 average time/residue: 1.0718 time to fit residues: 228.4754 Evaluate side-chains 153 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 141 time to evaluate : 1.286 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 0.1065 time to fit residues: 2.0085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 0.0970 chunk 39 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 87 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 127 optimal weight: 0.6980 chunk 43 optimal weight: 0.3980 chunk 102 optimal weight: 3.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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: 0.6909 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12267 Z= 0.156 Angle : 0.628 6.679 16656 Z= 0.314 Chirality : 0.043 0.165 1908 Planarity : 0.004 0.054 2013 Dihedral : 9.747 66.401 1659 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.53 % Allowed : 12.82 % Favored : 83.65 % 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: -2.44 (0.21), residues: 1392 helix: -0.86 (0.17), residues: 924 sheet: -4.18 (0.63), residues: 30 loop : -2.92 (0.24), residues: 438 *********************** 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 198 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 154 time to evaluate : 1.349 Fit side-chains revert: symmetry clash outliers start: 44 outliers final: 13 residues processed: 184 average time/residue: 0.9465 time to fit residues: 194.5462 Evaluate side-chains 148 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 135 time to evaluate : 1.338 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 10 residues processed: 4 average time/residue: 0.1573 time to fit residues: 3.2062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 14 optimal weight: 0.0010 chunk 61 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 128 optimal weight: 2.9990 chunk 136 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN B 54 HIS ** 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 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12267 Z= 0.172 Angle : 0.623 6.743 16656 Z= 0.309 Chirality : 0.043 0.190 1908 Planarity : 0.004 0.055 2013 Dihedral : 9.313 60.936 1659 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.37 % Allowed : 14.18 % Favored : 82.45 % 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: -1.85 (0.21), residues: 1392 helix: -0.42 (0.17), residues: 927 sheet: -4.00 (0.67), residues: 30 loop : -2.67 (0.24), residues: 435 *********************** 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 186 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 144 time to evaluate : 1.379 Fit side-chains outliers start: 42 outliers final: 20 residues processed: 173 average time/residue: 0.9021 time to fit residues: 174.6326 Evaluate side-chains 158 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 138 time to evaluate : 1.217 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 14 residues processed: 6 average time/residue: 0.5191 time to fit residues: 5.5598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0670 chunk 1 optimal weight: 0.5980 chunk 101 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 116 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 overall best weight: 2.3324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 145 HIS B 351 GLN B 355 ASN B 406 HIS ** B 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 HIS C 351 GLN ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 455 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.3113 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= 0.311 Angle : 0.730 7.907 16656 Z= 0.358 Chirality : 0.048 0.295 1908 Planarity : 0.005 0.055 2013 Dihedral : 9.422 65.582 1659 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.88 % Allowed : 15.46 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.01 (0.21), residues: 1392 helix: -0.58 (0.17), residues: 939 sheet: -4.14 (0.62), residues: 30 loop : -2.65 (0.26), residues: 423 *********************** 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 178 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 142 time to evaluate : 1.177 Fit side-chains outliers start: 36 outliers final: 21 residues processed: 170 average time/residue: 0.9576 time to fit residues: 180.6769 Evaluate side-chains 152 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 131 time to evaluate : 1.265 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 19 residues processed: 2 average time/residue: 0.9190 time to fit residues: 3.8640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 145 HIS ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12267 Z= 0.213 Angle : 0.647 7.403 16656 Z= 0.322 Chirality : 0.044 0.203 1908 Planarity : 0.004 0.055 2013 Dihedral : 8.954 66.060 1659 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.12 % Allowed : 16.75 % Favored : 80.13 % 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: -1.56 (0.22), residues: 1392 helix: -0.35 (0.17), residues: 918 sheet: -4.13 (0.63), residues: 30 loop : -2.10 (0.28), residues: 444 *********************** 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 178 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 139 time to evaluate : 1.397 Fit side-chains outliers start: 39 outliers final: 22 residues processed: 169 average time/residue: 0.9718 time to fit residues: 184.4949 Evaluate side-chains 145 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 123 time to evaluate : 1.298 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 21 residues processed: 2 average time/residue: 0.1425 time to fit residues: 2.2821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 3.9990 chunk 77 optimal weight: 0.0980 chunk 99 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 76 optimal weight: 0.5980 chunk 135 optimal weight: 0.6980 chunk 85 optimal weight: 0.0060 chunk 82 optimal weight: 0.0170 chunk 62 optimal weight: 6.9990 chunk 84 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 overall best weight: 0.2834 ------------------------------------------------------------------------------- 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 B 429 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: 0.6896 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12267 Z= 0.138 Angle : 0.570 6.597 16656 Z= 0.288 Chirality : 0.041 0.139 1908 Planarity : 0.004 0.048 2013 Dihedral : 8.108 67.098 1659 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.32 % Allowed : 17.79 % Favored : 79.89 % 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: -1.10 (0.22), residues: 1392 helix: 0.12 (0.18), residues: 921 sheet: None (None), residues: 0 loop : -2.39 (0.25), residues: 471 *********************** 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 178 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 149 time to evaluate : 1.247 Fit side-chains outliers start: 29 outliers final: 14 residues processed: 175 average time/residue: 0.9410 time to fit residues: 184.3147 Evaluate side-chains 145 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 131 time to evaluate : 1.682 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 14 residues processed: 2 average time/residue: 0.2163 time to fit residues: 2.5994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 0.3980 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 67 optimal weight: 0.0050 chunk 12 optimal weight: 4.9990 chunk 106 optimal weight: 0.0470 chunk 123 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 overall best weight: 0.6694 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.3671 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= 0.156 Angle : 0.589 6.860 16656 Z= 0.294 Chirality : 0.041 0.167 1908 Planarity : 0.004 0.051 2013 Dihedral : 7.983 72.065 1659 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.00 % Allowed : 18.59 % Favored : 79.41 % 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: -0.84 (0.22), residues: 1392 helix: 0.30 (0.18), residues: 903 sheet: None (None), residues: 0 loop : -2.16 (0.26), residues: 489 *********************** 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 161 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 136 time to evaluate : 1.202 Fit side-chains outliers start: 25 outliers final: 14 residues processed: 155 average time/residue: 0.9521 time to fit residues: 164.1872 Evaluate side-chains 146 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 132 time to evaluate : 1.275 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 13 residues processed: 2 average time/residue: 0.8043 time to fit residues: 3.5347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 38 optimal weight: 0.2980 chunk 114 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 133 optimal weight: 7.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.3751 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= 0.159 Angle : 0.592 8.061 16656 Z= 0.295 Chirality : 0.042 0.169 1908 Planarity : 0.004 0.046 2013 Dihedral : 7.846 73.648 1659 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.36 % Allowed : 19.39 % Favored : 79.25 % 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: -0.70 (0.22), residues: 1392 helix: 0.42 (0.18), residues: 903 sheet: None (None), residues: 0 loop : -2.14 (0.26), residues: 489 *********************** 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 154 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 137 time to evaluate : 1.377 Fit side-chains outliers start: 17 outliers final: 12 residues processed: 151 average time/residue: 0.9465 time to fit residues: 160.5008 Evaluate side-chains 140 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 128 time to evaluate : 1.391 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 1 average time/residue: 0.1400 time to fit residues: 1.8750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 chunk 140 optimal weight: 0.0370 chunk 129 optimal weight: 4.9990 chunk 111 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 overall best weight: 1.2062 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12267 Z= 0.197 Angle : 0.626 7.075 16656 Z= 0.310 Chirality : 0.043 0.199 1908 Planarity : 0.004 0.049 2013 Dihedral : 7.926 74.287 1659 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.04 % Allowed : 19.71 % Favored : 79.25 % 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: -0.77 (0.22), residues: 1392 helix: 0.36 (0.18), residues: 903 sheet: None (None), residues: 0 loop : -2.13 (0.26), residues: 489 ********************** 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 149 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 136 time to evaluate : 1.341 Fit side-chains outliers start: 13 outliers final: 11 residues processed: 148 average time/residue: 0.9270 time to fit residues: 155.5547 Evaluate side-chains 140 residues out of total 1251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 129 time to evaluate : 1.317 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 11 residues processed: 1 average time/residue: 0.1744 time to fit residues: 2.0651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 31 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.180534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.152592 restraints weight = 13329.153| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.07 r_work: 0.3449 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3453 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3453 r_free = 0.3453 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3452 r_free = 0.3452 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3452 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12267 Z= 0.209 Angle : 0.638 7.234 16656 Z= 0.316 Chirality : 0.044 0.208 1908 Planarity : 0.004 0.047 2013 Dihedral : 7.975 73.856 1659 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.36 % Allowed : 19.63 % Favored : 79.01 % 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: -0.88 (0.22), residues: 1392 helix: 0.25 (0.17), residues: 915 sheet: None (None), residues: 0 loop : -2.20 (0.26), residues: 477 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3788.16 seconds wall clock time: 68 minutes 36.98 seconds (4116.98 seconds total)