Starting phenix.real_space_refine on Fri Dec 27 19:28:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8aqw_15592/12_2024/8aqw_15592.cif Found real_map, /net/cci-nas-00/data/ceres_data/8aqw_15592/12_2024/8aqw_15592.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8aqw_15592/12_2024/8aqw_15592.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8aqw_15592/12_2024/8aqw_15592.map" model { file = "/net/cci-nas-00/data/ceres_data/8aqw_15592/12_2024/8aqw_15592.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8aqw_15592/12_2024/8aqw_15592.cif" } resolution = 3.3 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= -0.001 sd= 0.021 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 37 5.16 5 C 4121 2.51 5 N 1083 2.21 5 O 1216 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6457 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1543 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 11, 'TRANS': 181} Chain: "A" Number of atoms: 4872 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 596, 4857 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 596, 4857 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 4982 Conformer: "C" Number of residues, atoms: 596, 4854 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Unresolved chain links: 2 Unresolved chain link angles: 6 Unresolved chain link dihedrals: 6 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 bond proxies already assigned to first conformer: 4982 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLN A 34 " occ=0.00 ... (22 atoms not shown) pdb=" NE2CGLN A 34 " occ=0.31 Time building chain proxies: 10.61, per 1000 atoms: 1.64 Number of scatterers: 6457 At special positions: 0 Unit cell: (87.2384, 87.2384, 115.642, 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 37 16.00 O 1216 8.00 N 1083 7.00 C 4121 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.02 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG B1301 " - " ASN B 343 " " NAG C 1 " - " ASN A 53 " Time building additional restraints: 1.84 Conformation dependent library (CDL) restraints added in 2.1 seconds 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1492 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 6 sheets defined 53.6% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.928A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE B 371 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.771A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.750A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 40 removed outlier: 3.599A pdb=" N THR A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE A 28 " --> pdb=" O ASN A 24 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N AGLN A 34 " --> pdb=" O ASN A 30 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU A 35 " --> pdb=" O ASN A 31 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ASP A 38 " --> pdb=" O AGLN A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 53 Processing helix chain 'A' and resid 56 through 81 removed outlier: 3.729A pdb=" N GLN A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 Processing helix chain 'A' and resid 109 through 129 removed outlier: 3.630A pdb=" N THR A 129 " --> pdb=" O THR A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 155 removed outlier: 4.016A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 172 removed outlier: 3.609A pdb=" N VAL A 172 " --> pdb=" O TRP A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 176 through 194 Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 221 through 231 removed outlier: 3.525A pdb=" N ASP A 225 " --> pdb=" O GLN A 221 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR A 229 " --> pdb=" O ASP A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 248 removed outlier: 3.702A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 301 removed outlier: 3.678A pdb=" N GLY A 301 " --> pdb=" O MET A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 319 removed outlier: 3.569A pdb=" N PHE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.934A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 385 removed outlier: 3.591A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 400 through 413 removed outlier: 4.212A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 466 removed outlier: 3.655A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR A 449 " --> pdb=" O THR A 445 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU A 450 " --> pdb=" O ILE A 446 " (cutoff:3.500A) Proline residue: A 451 - end of helix Processing helix chain 'A' and resid 472 through 485 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 4.409A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.671A pdb=" N LYS A 541 " --> pdb=" O SER A 538 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N CYS A 542 " --> pdb=" O LEU A 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 538 through 542' Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.875A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 4.129A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 599 Proline residue: A 590 - end of helix removed outlier: 3.901A pdb=" N ASP A 593 " --> pdb=" O GLN A 589 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 357 through 358 removed outlier: 3.518A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AA5, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.609A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.510A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) 269 hydrogen bonds defined for protein. 759 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: 1.97 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2081 1.34 - 1.46: 1685 1.46 - 1.58: 2814 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6638 Sorted by residual: bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.99e+00 bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.97e+00 bond pdb=" C5 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.24e+00 bond pdb=" C5 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.22e+00 bond pdb=" C5 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.06e+00 ... (remaining 6633 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 8888 2.10 - 4.20: 110 4.20 - 6.29: 14 6.29 - 8.39: 3 8.39 - 10.49: 2 Bond angle restraints: 9017 Sorted by residual: angle pdb=" N VAL B 341 " pdb=" CA VAL B 341 " pdb=" C VAL B 341 " ideal model delta sigma weight residual 113.53 108.46 5.07 9.80e-01 1.04e+00 2.67e+01 angle pdb=" N GLU A 35 " pdb=" CA GLU A 35 " pdb=" C GLU A 35 " ideal model delta sigma weight residual 113.43 107.81 5.62 1.26e+00 6.30e-01 1.99e+01 angle pdb=" C PHE B 371 " pdb=" N ALA B 372 " pdb=" CA ALA B 372 " ideal model delta sigma weight residual 121.80 132.29 -10.49 2.44e+00 1.68e-01 1.85e+01 angle pdb=" N ARG A 228 " pdb=" CA ARG A 228 " pdb=" C ARG A 228 " ideal model delta sigma weight residual 113.01 109.52 3.49 1.20e+00 6.94e-01 8.47e+00 angle pdb=" N ASP B 420 " pdb=" CA ASP B 420 " pdb=" C ASP B 420 " ideal model delta sigma weight residual 114.04 110.58 3.46 1.24e+00 6.50e-01 7.79e+00 ... (remaining 9012 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.46: 3644 21.46 - 42.91: 272 42.91 - 64.37: 36 64.37 - 85.82: 7 85.82 - 107.28: 9 Dihedral angle restraints: 3968 sinusoidal: 1643 harmonic: 2325 Sorted by residual: dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual -86.00 -22.20 -63.80 1 1.00e+01 1.00e-02 5.36e+01 dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual -86.00 -144.11 58.11 1 1.00e+01 1.00e-02 4.53e+01 dihedral pdb=" CA CYS B 432 " pdb=" C CYS B 432 " pdb=" N VAL B 433 " pdb=" CA VAL B 433 " ideal model delta harmonic sigma weight residual -180.00 -160.06 -19.94 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 3965 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 580 0.032 - 0.064: 253 0.064 - 0.096: 81 0.096 - 0.128: 26 0.128 - 0.160: 2 Chirality restraints: 942 Sorted by residual: chirality pdb=" CA ILE A 88 " pdb=" N ILE A 88 " pdb=" C ILE A 88 " pdb=" CB ILE A 88 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.36e-01 chirality pdb=" CA ILE B 434 " pdb=" N ILE B 434 " pdb=" C ILE B 434 " pdb=" CB ILE B 434 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.67e-01 chirality pdb=" CA PRO B 491 " pdb=" N PRO B 491 " pdb=" C PRO B 491 " pdb=" CB PRO B 491 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.90e-01 ... (remaining 939 not shown) Planarity restraints: 1173 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 478 " 0.039 5.00e-02 4.00e+02 5.87e-02 5.51e+00 pdb=" N PRO B 479 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO B 479 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 479 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 288 " -0.030 5.00e-02 4.00e+02 4.54e-02 3.30e+00 pdb=" N PRO A 289 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 289 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 289 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 594 " -0.011 2.00e-02 2.50e+03 1.09e-02 2.96e+00 pdb=" CG TRP A 594 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP A 594 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A 594 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 594 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 594 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 594 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 594 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 594 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 594 " -0.000 2.00e-02 2.50e+03 ... (remaining 1170 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 237 2.72 - 3.27: 6347 3.27 - 3.81: 9986 3.81 - 4.36: 11959 4.36 - 4.90: 21173 Nonbonded interactions: 49702 Sorted by model distance: nonbonded pdb=" O ASN B 439 " pdb=" OG SER B 443 " model vdw 2.177 3.040 nonbonded pdb=" OE1CGLN A 34 " pdb=" N GLU A 35 " model vdw 2.232 3.120 nonbonded pdb=" O ILE A 151 " pdb=" OG SER A 155 " model vdw 2.232 3.040 nonbonded pdb=" OG1 THR A 229 " pdb=" OH TYR A 516 " model vdw 2.249 3.040 nonbonded pdb=" O PHE A 327 " pdb=" OG SER A 331 " model vdw 2.257 3.040 ... (remaining 49697 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.00 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: 9.700 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 27.090 Find NCS groups from input model: 0.100 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 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 : 0.002 0.028 6638 Z= 0.161 Angle : 0.593 10.488 9017 Z= 0.321 Chirality : 0.040 0.160 942 Planarity : 0.005 0.059 1171 Dihedral : 15.582 107.280 2455 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.11 % Favored : 93.63 % Rotamer: Outliers : 0.15 % Allowed : 0.29 % Favored : 99.56 % 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: -0.74 (0.30), residues: 788 helix: 1.10 (0.28), residues: 364 sheet: -0.24 (0.69), residues: 52 loop : -2.27 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 594 HIS 0.004 0.001 HIS A 374 PHE 0.010 0.001 PHE A 400 TYR 0.016 0.001 TYR B 501 ARG 0.005 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.766 Fit side-chains REVERT: A 277 ASN cc_start: 0.7426 (m-40) cc_final: 0.7092 (m110) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.2319 time to fit residues: 34.7759 Evaluate side-chains 94 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 70 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 487 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 24 ASN A 34 GLN C ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6638 Z= 0.188 Angle : 0.632 10.350 9017 Z= 0.315 Chirality : 0.042 0.191 942 Planarity : 0.005 0.045 1171 Dihedral : 8.503 68.328 929 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.61 % Favored : 94.14 % Rotamer: Outliers : 0.44 % Allowed : 7.70 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.30), residues: 788 helix: 1.16 (0.28), residues: 366 sheet: -0.76 (0.69), residues: 53 loop : -2.33 (0.28), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 163 HIS 0.003 0.001 HIS A 374 PHE 0.027 0.001 PHE A 72 TYR 0.015 0.001 TYR A 183 ARG 0.005 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 99 time to evaluate : 0.697 Fit side-chains REVERT: B 516 GLU cc_start: 0.8478 (tt0) cc_final: 0.8246 (tt0) REVERT: A 102 GLN cc_start: 0.7308 (mm-40) cc_final: 0.7030 (mm-40) REVERT: A 249 MET cc_start: 0.5926 (tpt) cc_final: 0.2138 (ptm) REVERT: A 277 ASN cc_start: 0.7684 (m-40) cc_final: 0.7430 (m-40) outliers start: 3 outliers final: 1 residues processed: 100 average time/residue: 0.2183 time to fit residues: 28.6440 Evaluate side-chains 92 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 380 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 56 optimal weight: 0.1980 chunk 53 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 487 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 34 GLN C A 374 HIS A 508 ASN ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6638 Z= 0.205 Angle : 0.620 10.381 9017 Z= 0.311 Chirality : 0.042 0.154 942 Planarity : 0.005 0.045 1171 Dihedral : 5.732 38.183 929 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.50 % Favored : 93.25 % Rotamer: Outliers : 0.58 % Allowed : 10.90 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.30), residues: 788 helix: 1.07 (0.28), residues: 368 sheet: -0.87 (0.70), residues: 53 loop : -2.31 (0.29), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 163 HIS 0.002 0.001 HIS A 374 PHE 0.028 0.001 PHE A 72 TYR 0.016 0.001 TYR A 183 ARG 0.005 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 94 time to evaluate : 0.755 Fit side-chains REVERT: A 249 MET cc_start: 0.6074 (tpt) cc_final: 0.2157 (ptm) REVERT: A 455 MET cc_start: 0.6736 (tpp) cc_final: 0.6091 (tpp) outliers start: 4 outliers final: 2 residues processed: 96 average time/residue: 0.2190 time to fit residues: 27.3932 Evaluate side-chains 94 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 92 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 47 optimal weight: 0.0980 chunk 71 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 487 ASN ** A 34 GLN C ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6638 Z= 0.252 Angle : 0.651 10.370 9017 Z= 0.331 Chirality : 0.043 0.152 942 Planarity : 0.005 0.045 1171 Dihedral : 5.241 36.322 929 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.88 % Favored : 92.87 % Rotamer: Outliers : 1.31 % Allowed : 11.63 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.30), residues: 788 helix: 1.06 (0.28), residues: 362 sheet: -0.84 (0.72), residues: 53 loop : -2.40 (0.29), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 594 HIS 0.004 0.001 HIS A 374 PHE 0.023 0.002 PHE A 72 TYR 0.016 0.001 TYR A 183 ARG 0.004 0.001 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.733 Fit side-chains REVERT: A 249 MET cc_start: 0.6174 (tpt) cc_final: 0.5498 (tpt) REVERT: A 455 MET cc_start: 0.6815 (tpp) cc_final: 0.6159 (tpp) outliers start: 9 outliers final: 5 residues processed: 99 average time/residue: 0.2413 time to fit residues: 30.6654 Evaluate side-chains 95 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 285 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 0 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 0.0670 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 487 ASN A 34 GLN C ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6638 Z= 0.202 Angle : 0.614 10.471 9017 Z= 0.311 Chirality : 0.042 0.151 942 Planarity : 0.005 0.048 1171 Dihedral : 4.825 33.803 929 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.37 % Favored : 93.38 % Rotamer: Outliers : 1.45 % Allowed : 11.63 % Favored : 86.92 % 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: -0.86 (0.30), residues: 788 helix: 1.13 (0.28), residues: 361 sheet: -0.84 (0.71), residues: 53 loop : -2.37 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 594 HIS 0.002 0.001 HIS A 322 PHE 0.020 0.001 PHE A 72 TYR 0.016 0.001 TYR A 183 ARG 0.006 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.772 Fit side-chains REVERT: B 457 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.8062 (tpt-90) REVERT: A 249 MET cc_start: 0.5787 (tpt) cc_final: 0.4878 (tpt) REVERT: A 518 ARG cc_start: 0.7500 (ptm-80) cc_final: 0.7169 (ptm160) outliers start: 10 outliers final: 7 residues processed: 103 average time/residue: 0.2198 time to fit residues: 29.7881 Evaluate side-chains 100 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 285 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 487 ASN B 493 GLN A 34 GLN C A 374 HIS A 378 HIS ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6638 Z= 0.222 Angle : 0.624 10.459 9017 Z= 0.316 Chirality : 0.042 0.148 942 Planarity : 0.005 0.046 1171 Dihedral : 4.819 31.485 929 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.75 % Favored : 92.99 % Rotamer: Outliers : 1.74 % Allowed : 12.21 % Favored : 86.05 % 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: -0.92 (0.30), residues: 788 helix: 1.03 (0.28), residues: 369 sheet: -0.81 (0.72), residues: 53 loop : -2.42 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 594 HIS 0.003 0.001 HIS A 241 PHE 0.019 0.001 PHE A 72 TYR 0.016 0.001 TYR A 183 ARG 0.004 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.728 Fit side-chains REVERT: A 249 MET cc_start: 0.5805 (tpt) cc_final: 0.4714 (tpt) outliers start: 12 outliers final: 7 residues processed: 98 average time/residue: 0.2137 time to fit residues: 27.3053 Evaluate side-chains 98 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 285 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 47 optimal weight: 0.0060 chunk 45 optimal weight: 0.0970 chunk 34 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 487 ASN B 493 GLN A 34 GLN C A 378 HIS A 508 ASN ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6638 Z= 0.165 Angle : 0.589 10.598 9017 Z= 0.297 Chirality : 0.041 0.149 942 Planarity : 0.004 0.048 1171 Dihedral : 4.534 28.526 929 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.86 % Favored : 93.89 % Rotamer: Outliers : 1.60 % Allowed : 12.50 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.30), residues: 788 helix: 1.26 (0.28), residues: 360 sheet: -0.77 (0.71), residues: 52 loop : -2.43 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 594 HIS 0.002 0.001 HIS A 265 PHE 0.017 0.001 PHE A 72 TYR 0.022 0.001 TYR A 243 ARG 0.003 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.749 Fit side-chains REVERT: A 249 MET cc_start: 0.5748 (tpt) cc_final: 0.4813 (tpt) outliers start: 11 outliers final: 6 residues processed: 102 average time/residue: 0.2047 time to fit residues: 27.3731 Evaluate side-chains 96 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 473 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.0170 chunk 47 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 42 optimal weight: 0.0470 overall best weight: 0.5516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 487 ASN B 493 GLN A 34 GLN C A 378 HIS ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6638 Z= 0.164 Angle : 0.594 10.610 9017 Z= 0.299 Chirality : 0.041 0.151 942 Planarity : 0.004 0.045 1171 Dihedral : 4.418 26.195 929 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.11 % Favored : 93.63 % Rotamer: Outliers : 1.60 % Allowed : 12.79 % Favored : 85.61 % 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: -0.79 (0.30), residues: 788 helix: 1.20 (0.28), residues: 366 sheet: -0.78 (0.71), residues: 52 loop : -2.41 (0.29), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 594 HIS 0.002 0.001 HIS A 374 PHE 0.017 0.001 PHE A 72 TYR 0.022 0.001 TYR A 243 ARG 0.004 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.793 Fit side-chains REVERT: A 249 MET cc_start: 0.5788 (tpt) cc_final: 0.4897 (tpt) outliers start: 11 outliers final: 9 residues processed: 99 average time/residue: 0.2110 time to fit residues: 27.2854 Evaluate side-chains 101 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 473 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 35 optimal weight: 7.9990 chunk 51 optimal weight: 0.0970 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 487 ASN B 493 GLN A 34 GLN C A 378 HIS ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6638 Z= 0.184 Angle : 0.609 10.571 9017 Z= 0.308 Chirality : 0.042 0.209 942 Planarity : 0.004 0.046 1171 Dihedral : 4.455 25.162 929 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.24 % Favored : 93.50 % Rotamer: Outliers : 1.45 % Allowed : 13.08 % Favored : 85.47 % 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: -0.82 (0.30), residues: 788 helix: 1.17 (0.28), residues: 367 sheet: -0.87 (0.71), residues: 53 loop : -2.41 (0.29), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 594 HIS 0.003 0.001 HIS A 378 PHE 0.016 0.001 PHE A 72 TYR 0.022 0.001 TYR A 243 ARG 0.004 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.816 Fit side-chains REVERT: A 249 MET cc_start: 0.5878 (tpt) cc_final: 0.4789 (tpt) outliers start: 10 outliers final: 8 residues processed: 101 average time/residue: 0.2141 time to fit residues: 28.2696 Evaluate side-chains 100 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 473 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 61 optimal weight: 0.0170 chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 18 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.3424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 487 ASN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 34 GLN C ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 HIS ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6638 Z= 0.256 Angle : 0.664 10.415 9017 Z= 0.338 Chirality : 0.044 0.216 942 Planarity : 0.005 0.049 1171 Dihedral : 4.800 26.065 929 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.50 % Favored : 93.25 % Rotamer: Outliers : 1.16 % Allowed : 13.23 % Favored : 85.61 % 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: -0.98 (0.30), residues: 788 helix: 1.04 (0.28), residues: 367 sheet: -0.83 (0.72), residues: 53 loop : -2.51 (0.29), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 594 HIS 0.004 0.001 HIS A 241 PHE 0.017 0.002 PHE A 592 TYR 0.024 0.002 TYR A 243 ARG 0.004 0.001 ARG B 457 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.923 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 94 average time/residue: 0.2401 time to fit residues: 29.6974 Evaluate side-chains 93 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 501 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain A residue 473 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 0.0470 chunk 54 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 41 optimal weight: 0.3980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 487 ASN B 493 GLN A 34 GLN C A 378 HIS ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.182225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.158848 restraints weight = 25221.570| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 3.83 r_work: 0.3771 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3803 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3803 r_free = 0.3803 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3803 r_free = 0.3803 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3803 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6638 Z= 0.170 Angle : 0.622 10.693 9017 Z= 0.315 Chirality : 0.042 0.207 942 Planarity : 0.004 0.048 1171 Dihedral : 4.529 26.194 929 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.61 % Favored : 94.14 % Rotamer: Outliers : 1.16 % Allowed : 13.37 % Favored : 85.47 % 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: -0.82 (0.30), residues: 788 helix: 1.19 (0.28), residues: 363 sheet: -0.80 (0.72), residues: 53 loop : -2.41 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 594 HIS 0.003 0.001 HIS A 378 PHE 0.017 0.001 PHE A 72 TYR 0.022 0.001 TYR A 243 ARG 0.004 0.000 ARG B 457 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1820.76 seconds wall clock time: 34 minutes 11.67 seconds (2051.67 seconds total)