Starting phenix.real_space_refine on Fri Dec 8 17:52:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p6j_20264/12_2023/6p6j_20264_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p6j_20264/12_2023/6p6j_20264.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p6j_20264/12_2023/6p6j_20264_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p6j_20264/12_2023/6p6j_20264_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p6j_20264/12_2023/6p6j_20264_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p6j_20264/12_2023/6p6j_20264.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p6j_20264/12_2023/6p6j_20264.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p6j_20264/12_2023/6p6j_20264_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p6j_20264/12_2023/6p6j_20264_updated.pdb" } resolution = 3.4 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= 0.000 sd= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 32 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 1 7.16 5 S 46 5.16 5 C 5683 2.51 5 N 1554 2.21 5 O 1557 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 53": "NH1" <-> "NH2" Residue "A ARG 102": "NH1" <-> "NH2" Residue "A ASP 129": "OD1" <-> "OD2" Residue "A PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 217": "NH1" <-> "NH2" Residue "A PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "A PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 402": "NH1" <-> "NH2" Residue "A ASP 414": "OD1" <-> "OD2" Residue "A PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 461": "OD1" <-> "OD2" Residue "A PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 468": "OE1" <-> "OE2" Residue "A TYR 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 498": "OD1" <-> "OD2" Residue "A GLU 506": "OE1" <-> "OE2" Residue "A PHE 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 13": "NH1" <-> "NH2" Residue "B ARG 17": "NH1" <-> "NH2" Residue "B ARG 84": "NH1" <-> "NH2" Residue "B TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 93": "NH1" <-> "NH2" Residue "B ARG 113": "NH1" <-> "NH2" Residue "B ASP 167": "OD1" <-> "OD2" Residue "B ARG 221": "NH1" <-> "NH2" Residue "B TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 312": "OE1" <-> "OE2" Residue "B PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 343": "OD1" <-> "OD2" Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 347": "OD1" <-> "OD2" Residue "B GLU 355": "OE1" <-> "OE2" Residue "B ASP 357": "OD1" <-> "OD2" Residue "B TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 477": "OE1" <-> "OE2" Residue "B GLU 486": "OE1" <-> "OE2" Residue "B ASP 513": "OD1" <-> "OD2" Residue "B GLU 517": "OE1" <-> "OE2" Residue "B GLU 554": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 8841 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4413 Classifications: {'peptide': 571} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 25, 'TRANS': 545} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 4396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4396 Classifications: {'peptide': 569} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 19, 'TRANS': 549} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' FE': 1, 'O34': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.06, per 1000 atoms: 0.57 Number of scatterers: 8841 At special positions: 0 Unit cell: (77.76, 94.176, 132.192, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 1 26.01 S 46 16.00 O 1557 8.00 N 1554 7.00 C 5683 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.84 Conformation dependent library (CDL) restraints added in 1.8 seconds 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2130 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 4 sheets defined 62.6% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 25 through 57 removed outlier: 3.654A pdb=" N LEU A 29 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 107 Processing helix chain 'A' and resid 112 through 121 removed outlier: 3.683A pdb=" N SER A 120 " --> pdb=" O GLN A 116 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLY A 121 " --> pdb=" O GLN A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 138 removed outlier: 5.033A pdb=" N VAL A 131 " --> pdb=" O MET A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 162 Proline residue: A 152 - end of helix removed outlier: 4.430A pdb=" N ILE A 156 " --> pdb=" O PRO A 152 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N VAL A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 188 removed outlier: 3.648A pdb=" N SER A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 219 Proline residue: A 214 - end of helix Processing helix chain 'A' and resid 223 through 257 removed outlier: 3.980A pdb=" N ALA A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N SER A 250 " --> pdb=" O LYS A 246 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N PHE A 253 " --> pdb=" O PHE A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 276 removed outlier: 3.590A pdb=" N TRP A 269 " --> pdb=" O PHE A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 303 removed outlier: 4.431A pdb=" N ALA A 296 " --> pdb=" O GLY A 292 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLU A 297 " --> pdb=" O SER A 293 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA A 298 " --> pdb=" O GLY A 294 " (cutoff:3.500A) Proline residue: A 301 - end of helix Processing helix chain 'A' and resid 305 through 324 removed outlier: 4.170A pdb=" N GLN A 311 " --> pdb=" O ASN A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 330 No H-bonds generated for 'chain 'A' and resid 328 through 330' Processing helix chain 'A' and resid 385 through 390 Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 447 through 454 Processing helix chain 'A' and resid 460 through 464 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 484 through 497 Processing helix chain 'A' and resid 513 through 526 Processing helix chain 'A' and resid 539 through 542 No H-bonds generated for 'chain 'A' and resid 539 through 542' Processing helix chain 'A' and resid 562 through 568 Processing helix chain 'A' and resid 571 through 583 Processing helix chain 'B' and resid 13 through 22 Processing helix chain 'B' and resid 27 through 58 removed outlier: 4.196A pdb=" N TYR B 52 " --> pdb=" O PHE B 48 " (cutoff:3.500A) Proline residue: B 53 - end of helix Processing helix chain 'B' and resid 63 through 93 removed outlier: 4.356A pdb=" N ALA B 72 " --> pdb=" O ASN B 68 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLU B 91 " --> pdb=" O GLY B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 113 removed outlier: 3.561A pdb=" N GLU B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 121 Processing helix chain 'B' and resid 123 through 146 removed outlier: 4.280A pdb=" N MET B 127 " --> pdb=" O ARG B 123 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N GLU B 137 " --> pdb=" O GLY B 133 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ASN B 138 " --> pdb=" O SER B 134 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU B 139 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ASN B 140 " --> pdb=" O ASP B 136 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N TYR B 141 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N VAL B 142 " --> pdb=" O ASN B 138 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ILE B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ALA B 144 " --> pdb=" O ASN B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 166 Proline residue: B 156 - end of helix removed outlier: 4.418A pdb=" N TRP B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 177 removed outlier: 3.505A pdb=" N ILE B 177 " --> pdb=" O VAL B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 186 Processing helix chain 'B' and resid 189 through 215 removed outlier: 3.629A pdb=" N ALA B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 222 Processing helix chain 'B' and resid 226 through 250 removed outlier: 3.748A pdb=" N GLN B 250 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 259 Processing helix chain 'B' and resid 261 through 278 removed outlier: 4.013A pdb=" N VAL B 268 " --> pdb=" O LEU B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 294 Processing helix chain 'B' and resid 298 through 326 removed outlier: 5.469A pdb=" N SER B 309 " --> pdb=" O ILE B 305 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N VAL B 310 " --> pdb=" O SER B 306 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA B 326 " --> pdb=" O GLU B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 357 No H-bonds generated for 'chain 'B' and resid 355 through 357' Processing helix chain 'B' and resid 386 through 392 removed outlier: 4.014A pdb=" N MET B 392 " --> pdb=" O THR B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 411 No H-bonds generated for 'chain 'B' and resid 409 through 411' Processing helix chain 'B' and resid 414 through 418 Processing helix chain 'B' and resid 435 through 442 removed outlier: 5.673A pdb=" N ALA B 442 " --> pdb=" O ASN B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 457 removed outlier: 3.502A pdb=" N GLU B 452 " --> pdb=" O ARG B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 466 Processing helix chain 'B' and resid 484 through 497 Processing helix chain 'B' and resid 515 through 527 removed outlier: 3.685A pdb=" N ASN B 526 " --> pdb=" O LYS B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 544 Processing helix chain 'B' and resid 563 through 566 No H-bonds generated for 'chain 'B' and resid 563 through 566' Processing helix chain 'B' and resid 572 through 577 Processing sheet with id= A, first strand: chain 'A' and resid 365 through 367 Processing sheet with id= B, first strand: chain 'A' and resid 547 through 551 removed outlier: 3.563A pdb=" N VAL A 547 " --> pdb=" O ILE A 372 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL A 532 " --> pdb=" O VAL A 373 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N LEU A 375 " --> pdb=" O VAL A 532 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N MET A 534 " --> pdb=" O LEU A 375 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N GLY A 377 " --> pdb=" O MET A 534 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 344 through 347 Processing sheet with id= D, first strand: chain 'B' and resid 548 through 552 removed outlier: 6.039A pdb=" N VAL B 533 " --> pdb=" O SER B 374 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N LEU B 376 " --> pdb=" O VAL B 533 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE B 535 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N GLY B 378 " --> pdb=" O ILE B 535 " (cutoff:3.500A) 494 hydrogen bonds defined for protein. 1467 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: 2.43 Time building geometry restraints manager: 3.93 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: 2912 1.34 - 1.46: 1967 1.46 - 1.58: 4056 1.58 - 1.70: 0 1.70 - 1.82: 88 Bond restraints: 9023 Sorted by residual: bond pdb=" C11 O34 A 701 " pdb=" S2 O34 A 701 " ideal model delta sigma weight residual 1.442 1.817 -0.375 2.00e-02 2.50e+03 3.52e+02 bond pdb=" C7 O34 A 701 " pdb=" S1 O34 A 701 " ideal model delta sigma weight residual 1.495 1.786 -0.291 2.00e-02 2.50e+03 2.12e+02 bond pdb=" C7 O34 A 701 " pdb=" N1 O34 A 701 " ideal model delta sigma weight residual 1.536 1.263 0.273 2.00e-02 2.50e+03 1.87e+02 bond pdb=" C17 O34 A 701 " pdb=" N3 O34 A 701 " ideal model delta sigma weight residual 1.538 1.284 0.254 2.00e-02 2.50e+03 1.61e+02 bond pdb=" C17 O34 A 701 " pdb=" S3 O34 A 701 " ideal model delta sigma weight residual 1.501 1.742 -0.241 2.00e-02 2.50e+03 1.45e+02 ... (remaining 9018 not shown) Histogram of bond angle deviations from ideal: 88.30 - 98.02: 3 98.02 - 107.75: 412 107.75 - 117.47: 6215 117.47 - 127.19: 5528 127.19 - 136.91: 123 Bond angle restraints: 12281 Sorted by residual: angle pdb=" N ALA A 340 " pdb=" CA ALA A 340 " pdb=" CB ALA A 340 " ideal model delta sigma weight residual 114.17 106.64 7.53 1.14e+00 7.69e-01 4.36e+01 angle pdb=" C10 O34 A 701 " pdb=" S2 O34 A 701 " pdb=" C11 O34 A 701 " ideal model delta sigma weight residual 105.32 88.30 17.02 3.00e+00 1.11e-01 3.22e+01 angle pdb=" C VAL A 456 " pdb=" N ALA A 457 " pdb=" CA ALA A 457 " ideal model delta sigma weight residual 121.19 129.32 -8.13 1.59e+00 3.96e-01 2.61e+01 angle pdb=" C7 O34 A 701 " pdb=" S1 O34 A 701 " pdb=" C8 O34 A 701 " ideal model delta sigma weight residual 104.65 89.82 14.83 3.00e+00 1.11e-01 2.44e+01 angle pdb=" C LEU B 430 " pdb=" N PHE B 431 " pdb=" CA PHE B 431 " ideal model delta sigma weight residual 121.54 130.76 -9.22 1.91e+00 2.74e-01 2.33e+01 ... (remaining 12276 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.70: 4770 18.70 - 37.39: 497 37.39 - 56.09: 88 56.09 - 74.78: 17 74.78 - 93.48: 6 Dihedral angle restraints: 5378 sinusoidal: 2085 harmonic: 3293 Sorted by residual: dihedral pdb=" CA ASP A 432 " pdb=" C ASP A 432 " pdb=" N THR A 433 " pdb=" CA THR A 433 " ideal model delta harmonic sigma weight residual -180.00 -124.85 -55.15 0 5.00e+00 4.00e-02 1.22e+02 dihedral pdb=" CA VAL A 456 " pdb=" C VAL A 456 " pdb=" N ALA A 457 " pdb=" CA ALA A 457 " ideal model delta harmonic sigma weight residual -180.00 -140.58 -39.42 0 5.00e+00 4.00e-02 6.22e+01 dihedral pdb=" CA GLU A 339 " pdb=" C GLU A 339 " pdb=" N ALA A 340 " pdb=" CA ALA A 340 " ideal model delta harmonic sigma weight residual 180.00 145.13 34.87 0 5.00e+00 4.00e-02 4.86e+01 ... (remaining 5375 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1138 0.065 - 0.130: 241 0.130 - 0.194: 47 0.194 - 0.259: 9 0.259 - 0.324: 3 Chirality restraints: 1438 Sorted by residual: chirality pdb=" CA LEU B 430 " pdb=" N LEU B 430 " pdb=" C LEU B 430 " pdb=" CB LEU B 430 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" CB ILE B 514 " pdb=" CA ILE B 514 " pdb=" CG1 ILE B 514 " pdb=" CG2 ILE B 514 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CA THR A 142 " pdb=" N THR A 142 " pdb=" C THR A 142 " pdb=" CB THR A 142 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 1435 not shown) Planarity restraints: 1560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 126 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.93e+00 pdb=" C VAL A 126 " -0.049 2.00e-02 2.50e+03 pdb=" O VAL A 126 " 0.018 2.00e-02 2.50e+03 pdb=" N MET A 127 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 O34 A 701 " -0.008 2.00e-02 2.50e+03 1.83e-02 6.67e+00 pdb=" C2 O34 A 701 " -0.010 2.00e-02 2.50e+03 pdb=" C3 O34 A 701 " -0.014 2.00e-02 2.50e+03 pdb=" C4 O34 A 701 " 0.006 2.00e-02 2.50e+03 pdb=" C5 O34 A 701 " 0.031 2.00e-02 2.50e+03 pdb=" C6 O34 A 701 " -0.011 2.00e-02 2.50e+03 pdb=" C7 O34 A 701 " -0.021 2.00e-02 2.50e+03 pdb=" O1 O34 A 701 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 500 " -0.042 5.00e-02 4.00e+02 6.32e-02 6.39e+00 pdb=" N PRO B 501 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 501 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 501 " -0.035 5.00e-02 4.00e+02 ... (remaining 1557 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 38 2.50 - 3.10: 6041 3.10 - 3.70: 14069 3.70 - 4.30: 18450 4.30 - 4.90: 30418 Nonbonded interactions: 69016 Sorted by model distance: nonbonded pdb=" O2 O34 A 701 " pdb="FE FE A 702 " model vdw 1.901 2.260 nonbonded pdb=" O1 O34 A 701 " pdb="FE FE A 702 " model vdw 1.919 2.260 nonbonded pdb=" O3 O34 A 701 " pdb="FE FE A 702 " model vdw 2.078 2.260 nonbonded pdb=" N1 O34 A 701 " pdb="FE FE A 702 " model vdw 2.084 2.340 nonbonded pdb=" N3 O34 A 701 " pdb="FE FE A 702 " model vdw 2.131 2.340 ... (remaining 69011 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 8.350 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 27.060 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 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 : 0.011 0.375 9023 Z= 0.785 Angle : 1.148 17.019 12281 Z= 0.649 Chirality : 0.059 0.324 1438 Planarity : 0.008 0.063 1560 Dihedral : 15.764 93.480 3248 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.77 % Allowed : 13.06 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -4.33 (0.19), residues: 1136 helix: -2.64 (0.13), residues: 737 sheet: -1.54 (0.63), residues: 62 loop : -3.22 (0.29), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 17 HIS 0.005 0.002 HIS B 529 PHE 0.028 0.002 PHE B 431 TYR 0.019 0.002 TYR A 229 ARG 0.005 0.001 ARG B 410 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 276 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 279 average time/residue: 0.2367 time to fit residues: 89.1641 Evaluate side-chains 176 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 173 time to evaluate : 0.914 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0943 time to fit residues: 1.7207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 34 optimal weight: 0.0060 chunk 53 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 102 optimal weight: 0.0050 overall best weight: 0.4610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN A 335 GLN A 544 GLN A 568 GLN A 581 GLN B 18 GLN B 98 GLN B 248 HIS B 323 GLN ** B 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 9023 Z= 0.195 Angle : 0.694 10.314 12281 Z= 0.347 Chirality : 0.043 0.209 1438 Planarity : 0.005 0.068 1560 Dihedral : 6.808 74.785 1253 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 3.18 % Allowed : 22.61 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.23), residues: 1136 helix: -0.61 (0.18), residues: 731 sheet: -0.15 (0.64), residues: 73 loop : -2.69 (0.31), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 85 HIS 0.003 0.001 HIS A 460 PHE 0.025 0.002 PHE B 431 TYR 0.020 0.001 TYR A 145 ARG 0.006 0.000 ARG B 189 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 220 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 13 residues processed: 237 average time/residue: 0.2101 time to fit residues: 69.4359 Evaluate side-chains 195 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 182 time to evaluate : 1.049 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0859 time to fit residues: 3.4376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 0.0870 chunk 102 optimal weight: 2.9990 chunk 111 optimal weight: 0.0370 chunk 91 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN ** B 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 521 GLN ** B 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9023 Z= 0.182 Angle : 0.667 11.101 12281 Z= 0.329 Chirality : 0.042 0.187 1438 Planarity : 0.004 0.048 1560 Dihedral : 6.484 76.012 1253 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 3.84 % Allowed : 25.58 % Favored : 70.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.69 (0.25), residues: 1136 helix: 0.38 (0.19), residues: 726 sheet: 0.72 (0.68), residues: 66 loop : -2.48 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 85 HIS 0.003 0.001 HIS B 563 PHE 0.020 0.001 PHE B 297 TYR 0.019 0.001 TYR A 351 ARG 0.005 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 204 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 12 residues processed: 222 average time/residue: 0.2058 time to fit residues: 63.9637 Evaluate side-chains 193 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 181 time to evaluate : 0.925 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1031 time to fit residues: 3.5992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 109 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9023 Z= 0.205 Angle : 0.641 7.561 12281 Z= 0.318 Chirality : 0.041 0.165 1438 Planarity : 0.004 0.037 1560 Dihedral : 6.334 74.497 1253 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.96 % Allowed : 27.00 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.15 (0.26), residues: 1136 helix: 0.83 (0.19), residues: 725 sheet: 0.93 (0.69), residues: 66 loop : -2.34 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 85 HIS 0.003 0.001 HIS A 135 PHE 0.016 0.001 PHE B 297 TYR 0.010 0.001 TYR A 351 ARG 0.005 0.000 ARG B 17 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 188 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 13 residues processed: 204 average time/residue: 0.2055 time to fit residues: 59.0736 Evaluate side-chains 183 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 170 time to evaluate : 0.970 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0865 time to fit residues: 3.3614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 0.4980 chunk 1 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 36 optimal weight: 0.0070 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 GLN B 416 GLN ** B 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9023 Z= 0.188 Angle : 0.639 8.456 12281 Z= 0.311 Chirality : 0.041 0.210 1438 Planarity : 0.003 0.034 1560 Dihedral : 6.175 74.727 1253 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.74 % Allowed : 29.09 % Favored : 68.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.40 (0.26), residues: 1136 helix: 1.25 (0.20), residues: 718 sheet: 1.22 (0.70), residues: 66 loop : -2.06 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 85 HIS 0.003 0.001 HIS A 135 PHE 0.016 0.001 PHE A 428 TYR 0.010 0.001 TYR A 229 ARG 0.007 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 185 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 8 residues processed: 200 average time/residue: 0.1947 time to fit residues: 55.7415 Evaluate side-chains 176 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 168 time to evaluate : 0.997 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0946 time to fit residues: 2.6897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 0.4980 chunk 21 optimal weight: 3.9990 chunk 64 optimal weight: 0.0980 chunk 26 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9023 Z= 0.194 Angle : 0.643 8.097 12281 Z= 0.314 Chirality : 0.042 0.169 1438 Planarity : 0.003 0.037 1560 Dihedral : 6.088 73.862 1253 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.96 % Allowed : 28.87 % Favored : 68.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.61 (0.26), residues: 1136 helix: 1.40 (0.20), residues: 717 sheet: 1.68 (0.77), residues: 56 loop : -1.92 (0.35), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 85 HIS 0.003 0.001 HIS B 95 PHE 0.015 0.001 PHE B 297 TYR 0.017 0.002 TYR A 145 ARG 0.008 0.000 ARG B 189 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 180 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 11 residues processed: 197 average time/residue: 0.1940 time to fit residues: 54.1077 Evaluate side-chains 178 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 167 time to evaluate : 0.946 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0839 time to fit residues: 2.9578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.4980 chunk 62 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 43 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9023 Z= 0.206 Angle : 0.647 8.319 12281 Z= 0.315 Chirality : 0.042 0.163 1438 Planarity : 0.003 0.038 1560 Dihedral : 6.045 73.875 1253 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 1.54 % Allowed : 31.83 % Favored : 66.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.67 (0.26), residues: 1136 helix: 1.47 (0.20), residues: 718 sheet: 1.46 (0.73), residues: 61 loop : -1.93 (0.35), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 85 HIS 0.002 0.000 HIS A 135 PHE 0.021 0.001 PHE B 297 TYR 0.022 0.002 TYR A 145 ARG 0.005 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 176 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 183 average time/residue: 0.1828 time to fit residues: 48.2885 Evaluate side-chains 172 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 164 time to evaluate : 0.965 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0976 time to fit residues: 2.7610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN A 307 ASN ** B 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.4585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9023 Z= 0.221 Angle : 0.683 10.569 12281 Z= 0.332 Chirality : 0.042 0.166 1438 Planarity : 0.004 0.039 1560 Dihedral : 6.008 73.324 1253 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 1.87 % Allowed : 31.61 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.68 (0.27), residues: 1136 helix: 1.48 (0.20), residues: 714 sheet: 1.36 (0.73), residues: 61 loop : -1.89 (0.35), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 85 HIS 0.002 0.001 HIS B 570 PHE 0.023 0.001 PHE B 184 TYR 0.048 0.002 TYR A 145 ARG 0.005 0.000 ARG A 231 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 181 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 12 residues processed: 193 average time/residue: 0.1893 time to fit residues: 52.5068 Evaluate side-chains 179 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 167 time to evaluate : 0.908 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0832 time to fit residues: 3.0117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 44 optimal weight: 0.2980 chunk 79 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 91 optimal weight: 0.0570 chunk 95 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 107 optimal weight: 0.0970 chunk 65 optimal weight: 0.0870 overall best weight: 0.2074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 ASN ** B 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.4842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9023 Z= 0.180 Angle : 0.692 12.307 12281 Z= 0.329 Chirality : 0.041 0.159 1438 Planarity : 0.004 0.038 1560 Dihedral : 5.972 75.287 1253 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 0.77 % Allowed : 31.94 % Favored : 67.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.63 (0.27), residues: 1136 helix: 1.45 (0.20), residues: 722 sheet: 0.89 (0.70), residues: 67 loop : -1.94 (0.35), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 577 HIS 0.001 0.000 HIS A 135 PHE 0.024 0.001 PHE B 184 TYR 0.055 0.001 TYR A 145 ARG 0.007 0.000 ARG B 169 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 187 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 191 average time/residue: 0.1987 time to fit residues: 53.5770 Evaluate side-chains 177 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 172 time to evaluate : 0.986 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0906 time to fit residues: 2.1291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 112 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 89 optimal weight: 0.9990 chunk 9 optimal weight: 0.0170 chunk 69 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 71 optimal weight: 0.4980 chunk 95 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.9022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.4932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9023 Z= 0.230 Angle : 0.725 10.369 12281 Z= 0.345 Chirality : 0.043 0.168 1438 Planarity : 0.004 0.038 1560 Dihedral : 5.883 73.244 1253 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.55 % Allowed : 33.15 % Favored : 66.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.76 (0.27), residues: 1136 helix: 1.53 (0.20), residues: 717 sheet: 0.91 (0.71), residues: 67 loop : -1.81 (0.36), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 577 HIS 0.003 0.001 HIS A 537 PHE 0.021 0.001 PHE B 184 TYR 0.046 0.002 TYR A 145 ARG 0.008 0.000 ARG A 231 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 172 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 175 average time/residue: 0.1916 time to fit residues: 48.4169 Evaluate side-chains 174 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 170 time to evaluate : 0.884 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0879 time to fit residues: 1.9649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 0.0570 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.0770 chunk 78 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 ASN B 560 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.117521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.091788 restraints weight = 17641.109| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 4.34 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.5073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9023 Z= 0.197 Angle : 0.705 10.524 12281 Z= 0.332 Chirality : 0.042 0.163 1438 Planarity : 0.003 0.034 1560 Dihedral : 5.872 74.398 1253 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.88 % Allowed : 32.82 % Favored : 66.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.66 (0.27), residues: 1136 helix: 1.42 (0.20), residues: 725 sheet: 0.90 (0.71), residues: 67 loop : -1.82 (0.36), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 577 HIS 0.002 0.001 HIS A 135 PHE 0.021 0.001 PHE B 184 TYR 0.040 0.002 TYR A 145 ARG 0.007 0.000 ARG A 231 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2143.72 seconds wall clock time: 39 minutes 25.50 seconds (2365.50 seconds total)