Starting phenix.real_space_refine on Wed Mar 12 23:21:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5z1f_6875/03_2025/5z1f_6875.cif Found real_map, /net/cci-nas-00/data/ceres_data/5z1f_6875/03_2025/5z1f_6875.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5z1f_6875/03_2025/5z1f_6875.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5z1f_6875/03_2025/5z1f_6875.map" model { file = "/net/cci-nas-00/data/ceres_data/5z1f_6875/03_2025/5z1f_6875.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5z1f_6875/03_2025/5z1f_6875.cif" } resolution = 4.8 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= 0.002 sd= 0.009 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 24 5.16 5 C 5604 2.51 5 N 1364 2.21 5 O 1488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8480 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4240 Classifications: {'peptide': 601} Incomplete info: {'truncation_to_alanine': 145} Link IDs: {'PTRANS': 27, 'TRANS': 573} Chain breaks: 4 Unresolved non-hydrogen bonds: 634 Unresolved non-hydrogen angles: 792 Unresolved non-hydrogen dihedrals: 548 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 8, 'ASN:plan1': 5, 'TRP:plan': 4, 'ASP:plan': 4, 'PHE:plan': 10, 'GLU:plan': 21, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 384 Restraints were copied for chains: B Time building chain proxies: 7.61, per 1000 atoms: 0.90 Number of scatterers: 8480 At special positions: 0 Unit cell: (127.655, 81.235, 91.785, 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 24 16.00 O 1488 8.00 N 1364 7.00 C 5604 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.43 Conformation dependent library (CDL) restraints added in 1.1 seconds 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2296 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 2 sheets defined 70.9% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 4 through 24 removed outlier: 3.532A pdb=" N LEU A 22 " --> pdb=" O VAL A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 41 Processing helix chain 'A' and resid 61 through 68 Processing helix chain 'A' and resid 69 through 77 removed outlier: 3.507A pdb=" N VAL A 73 " --> pdb=" O SER A 69 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ASN A 75 " --> pdb=" O GLN A 71 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A 77 " --> pdb=" O VAL A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 97 removed outlier: 3.503A pdb=" N ALA A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 107 Proline residue: A 104 - end of helix Processing helix chain 'A' and resid 151 through 184 Processing helix chain 'A' and resid 188 through 191 removed outlier: 3.632A pdb=" N GLN A 191 " --> pdb=" O LYS A 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 188 through 191' Processing helix chain 'A' and resid 207 through 220 Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 240 through 247 Processing helix chain 'A' and resid 290 through 295 removed outlier: 3.949A pdb=" N LYS A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 305 Processing helix chain 'A' and resid 317 through 327 removed outlier: 3.548A pdb=" N SER A 327 " --> pdb=" O SER A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 377 removed outlier: 4.070A pdb=" N ILE A 361 " --> pdb=" O PHE A 357 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA A 371 " --> pdb=" O TYR A 367 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU A 375 " --> pdb=" O ALA A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 386 removed outlier: 4.340A pdb=" N ILE A 381 " --> pdb=" O TYR A 377 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 427 Proline residue: A 418 - end of helix Processing helix chain 'A' and resid 428 through 438 Processing helix chain 'A' and resid 444 through 463 removed outlier: 3.759A pdb=" N ARG A 450 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA A 451 " --> pdb=" O HIS A 447 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TYR A 458 " --> pdb=" O GLY A 454 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N PHE A 462 " --> pdb=" O TYR A 458 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN A 463 " --> pdb=" O PHE A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 475 Processing helix chain 'A' and resid 489 through 523 Proline residue: A 499 - end of helix removed outlier: 3.643A pdb=" N ILE A 515 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY A 516 " --> pdb=" O LYS A 512 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY A 518 " --> pdb=" O PHE A 514 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A 522 " --> pdb=" O GLY A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 537 removed outlier: 3.684A pdb=" N HIS A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 576 Proline residue: A 560 - end of helix removed outlier: 4.041A pdb=" N ILE A 565 " --> pdb=" O GLY A 561 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL A 574 " --> pdb=" O PHE A 570 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE A 575 " --> pdb=" O CYS A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 599 removed outlier: 3.587A pdb=" N ILE A 581 " --> pdb=" O PRO A 577 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR A 586 " --> pdb=" O PHE A 582 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE A 587 " --> pdb=" O GLY A 583 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU A 592 " --> pdb=" O GLY A 588 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG A 595 " --> pdb=" O TRP A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 639 removed outlier: 4.274A pdb=" N HIS A 615 " --> pdb=" O ARG A 611 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 637 " --> pdb=" O GLY A 633 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS A 638 " --> pdb=" O TYR A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 662 Proline residue: A 648 - end of helix Processing helix chain 'A' and resid 664 through 670 removed outlier: 4.005A pdb=" N HIS A 670 " --> pdb=" O GLY A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 680 Processing helix chain 'A' and resid 686 through 691 removed outlier: 3.887A pdb=" N PHE A 690 " --> pdb=" O LEU A 686 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG A 691 " --> pdb=" O GLU A 687 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 686 through 691' Processing helix chain 'B' and resid 4 through 24 removed outlier: 3.532A pdb=" N LEU B 22 " --> pdb=" O VAL B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 41 Processing helix chain 'B' and resid 61 through 68 Processing helix chain 'B' and resid 69 through 77 removed outlier: 3.507A pdb=" N VAL B 73 " --> pdb=" O SER B 69 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL B 74 " --> pdb=" O GLU B 70 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ASN B 75 " --> pdb=" O GLN B 71 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER B 77 " --> pdb=" O VAL B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 97 removed outlier: 3.503A pdb=" N ALA B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 107 Proline residue: B 104 - end of helix Processing helix chain 'B' and resid 151 through 184 Processing helix chain 'B' and resid 188 through 191 removed outlier: 3.631A pdb=" N GLN B 191 " --> pdb=" O LYS B 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 188 through 191' Processing helix chain 'B' and resid 207 through 220 Processing helix chain 'B' and resid 233 through 239 Processing helix chain 'B' and resid 240 through 247 Processing helix chain 'B' and resid 290 through 295 removed outlier: 3.949A pdb=" N LYS B 294 " --> pdb=" O GLU B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 305 Processing helix chain 'B' and resid 317 through 327 removed outlier: 3.548A pdb=" N SER B 327 " --> pdb=" O SER B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 377 removed outlier: 4.070A pdb=" N ILE B 361 " --> pdb=" O PHE B 357 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA B 371 " --> pdb=" O TYR B 367 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU B 375 " --> pdb=" O ALA B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 386 removed outlier: 4.341A pdb=" N ILE B 381 " --> pdb=" O TYR B 377 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA B 386 " --> pdb=" O ALA B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 427 Proline residue: B 418 - end of helix Processing helix chain 'B' and resid 428 through 438 Processing helix chain 'B' and resid 444 through 463 removed outlier: 3.759A pdb=" N ARG B 450 " --> pdb=" O SER B 446 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA B 451 " --> pdb=" O HIS B 447 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TYR B 458 " --> pdb=" O GLY B 454 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE B 462 " --> pdb=" O TYR B 458 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN B 463 " --> pdb=" O PHE B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 475 Processing helix chain 'B' and resid 489 through 523 Proline residue: B 499 - end of helix removed outlier: 3.643A pdb=" N ILE B 515 " --> pdb=" O LEU B 511 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY B 516 " --> pdb=" O LYS B 512 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY B 518 " --> pdb=" O PHE B 514 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER B 522 " --> pdb=" O GLY B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 537 removed outlier: 3.684A pdb=" N HIS B 531 " --> pdb=" O LEU B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 576 Proline residue: B 560 - end of helix removed outlier: 4.041A pdb=" N ILE B 565 " --> pdb=" O GLY B 561 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL B 574 " --> pdb=" O PHE B 570 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE B 575 " --> pdb=" O CYS B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 599 removed outlier: 3.587A pdb=" N ILE B 581 " --> pdb=" O PRO B 577 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR B 586 " --> pdb=" O PHE B 582 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE B 587 " --> pdb=" O GLY B 583 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU B 592 " --> pdb=" O GLY B 588 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG B 595 " --> pdb=" O TRP B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 639 removed outlier: 4.274A pdb=" N HIS B 615 " --> pdb=" O ARG B 611 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA B 637 " --> pdb=" O GLY B 633 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS B 638 " --> pdb=" O TYR B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 642 through 662 Proline residue: B 648 - end of helix Processing helix chain 'B' and resid 664 through 670 removed outlier: 4.005A pdb=" N HIS B 670 " --> pdb=" O GLY B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 680 Processing helix chain 'B' and resid 686 through 691 removed outlier: 3.887A pdb=" N PHE B 690 " --> pdb=" O LEU B 686 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG B 691 " --> pdb=" O GLU B 687 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 686 through 691' Processing sheet with id=AA1, first strand: chain 'A' and resid 224 through 229 removed outlier: 3.992A pdb=" N ARG A 226 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 224 through 229 removed outlier: 3.992A pdb=" N ARG B 226 " --> pdb=" O PHE B 314 " (cutoff:3.500A) 536 hydrogen bonds defined for protein. 1590 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: 2.56 Time building geometry restraints manager: 2.83 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: 2588 1.34 - 1.46: 2128 1.46 - 1.58: 3940 1.58 - 1.70: 2 1.70 - 1.82: 36 Bond restraints: 8694 Sorted by residual: bond pdb=" C ALA A 34 " pdb=" N PRO A 35 " ideal model delta sigma weight residual 1.334 1.594 -0.260 2.34e-02 1.83e+03 1.23e+02 bond pdb=" C ALA B 34 " pdb=" N PRO B 35 " ideal model delta sigma weight residual 1.334 1.593 -0.259 2.34e-02 1.83e+03 1.23e+02 bond pdb=" C PRO B 202 " pdb=" O PRO B 202 " ideal model delta sigma weight residual 1.243 1.231 0.013 8.50e-03 1.38e+04 2.18e+00 bond pdb=" C PRO A 202 " pdb=" O PRO A 202 " ideal model delta sigma weight residual 1.243 1.231 0.012 8.50e-03 1.38e+04 1.96e+00 bond pdb=" CG LEU A 422 " pdb=" CD2 LEU A 422 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.91e+00 ... (remaining 8689 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 11576 2.10 - 4.19: 301 4.19 - 6.29: 57 6.29 - 8.38: 10 8.38 - 10.48: 4 Bond angle restraints: 11948 Sorted by residual: angle pdb=" N GLU B 305 " pdb=" CA GLU B 305 " pdb=" C GLU B 305 " ideal model delta sigma weight residual 107.67 118.15 -10.48 2.09e+00 2.29e-01 2.51e+01 angle pdb=" N GLU A 305 " pdb=" CA GLU A 305 " pdb=" C GLU A 305 " ideal model delta sigma weight residual 107.67 118.13 -10.46 2.09e+00 2.29e-01 2.51e+01 angle pdb=" O PRO A 202 " pdb=" C PRO A 202 " pdb=" N PRO A 203 " ideal model delta sigma weight residual 121.15 123.42 -2.27 4.70e-01 4.53e+00 2.32e+01 angle pdb=" O PRO B 202 " pdb=" C PRO B 202 " pdb=" N PRO B 203 " ideal model delta sigma weight residual 121.15 123.39 -2.24 4.70e-01 4.53e+00 2.26e+01 angle pdb=" N THR A 297 " pdb=" CA THR A 297 " pdb=" C THR A 297 " ideal model delta sigma weight residual 111.07 115.54 -4.47 1.07e+00 8.73e-01 1.75e+01 ... (remaining 11943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.03: 4640 17.03 - 34.07: 262 34.07 - 51.10: 88 51.10 - 68.14: 10 68.14 - 85.17: 2 Dihedral angle restraints: 5002 sinusoidal: 1472 harmonic: 3530 Sorted by residual: dihedral pdb=" CA LEU B 46 " pdb=" C LEU B 46 " pdb=" N GLU B 47 " pdb=" CA GLU B 47 " ideal model delta harmonic sigma weight residual -180.00 -150.39 -29.61 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA LEU A 46 " pdb=" C LEU A 46 " pdb=" N GLU A 47 " pdb=" CA GLU A 47 " ideal model delta harmonic sigma weight residual -180.00 -150.45 -29.55 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA THR A 55 " pdb=" C THR A 55 " pdb=" N ARG A 56 " pdb=" CA ARG A 56 " ideal model delta harmonic sigma weight residual 180.00 154.98 25.02 0 5.00e+00 4.00e-02 2.50e+01 ... (remaining 4999 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1096 0.051 - 0.103: 298 0.103 - 0.154: 70 0.154 - 0.205: 14 0.205 - 0.257: 4 Chirality restraints: 1482 Sorted by residual: chirality pdb=" CA GLU B 305 " pdb=" N GLU B 305 " pdb=" C GLU B 305 " pdb=" CB GLU B 305 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA GLU A 305 " pdb=" N GLU A 305 " pdb=" C GLU A 305 " pdb=" CB GLU A 305 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA LYS B 300 " pdb=" N LYS B 300 " pdb=" C LYS B 300 " pdb=" CB LYS B 300 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1479 not shown) Planarity restraints: 1484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 107 " 0.059 5.00e-02 4.00e+02 8.87e-02 1.26e+01 pdb=" N PRO B 108 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO B 108 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 108 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 107 " -0.059 5.00e-02 4.00e+02 8.86e-02 1.26e+01 pdb=" N PRO A 108 " 0.153 5.00e-02 4.00e+02 pdb=" CA PRO A 108 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 108 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 202 " -0.056 5.00e-02 4.00e+02 8.59e-02 1.18e+01 pdb=" N PRO A 203 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO A 203 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 203 " -0.046 5.00e-02 4.00e+02 ... (remaining 1481 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1312 2.75 - 3.29: 9749 3.29 - 3.83: 14301 3.83 - 4.36: 16456 4.36 - 4.90: 25235 Nonbonded interactions: 67053 Sorted by model distance: nonbonded pdb=" O ASN B 492 " pdb=" OG1 THR B 496 " model vdw 2.213 3.040 nonbonded pdb=" O ASN A 492 " pdb=" OG1 THR A 496 " model vdw 2.213 3.040 nonbonded pdb=" O GLU A 232 " pdb=" CD GLU A 232 " model vdw 2.214 3.270 nonbonded pdb=" O GLU B 232 " pdb=" CD GLU B 232 " model vdw 2.214 3.270 nonbonded pdb=" O LEU A 635 " pdb=" OH TYR A 642 " model vdw 2.223 3.040 ... (remaining 67048 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 25.660 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 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 : 0.006 0.260 8694 Z= 0.418 Angle : 0.868 10.477 11948 Z= 0.490 Chirality : 0.052 0.257 1482 Planarity : 0.008 0.089 1484 Dihedral : 13.130 85.173 2706 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 25.36 Ramachandran Plot: Outliers : 1.02 % Allowed : 9.81 % Favored : 89.17 % Rotamer: Outliers : 5.04 % Allowed : 12.73 % Favored : 82.23 % 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: -4.90 (0.19), residues: 1182 helix: -3.32 (0.13), residues: 750 sheet: -2.20 (0.75), residues: 46 loop : -2.77 (0.28), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 61 HIS 0.006 0.002 HIS B 84 PHE 0.014 0.002 PHE A 668 TYR 0.019 0.002 TYR A 609 ARG 0.002 0.001 ARG B 178 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ARG cc_start: 0.9138 (ttt90) cc_final: 0.8859 (ttt-90) REVERT: A 180 GLN cc_start: 0.9136 (tp-100) cc_final: 0.8904 (tp40) REVERT: A 209 LYS cc_start: 0.9324 (tttt) cc_final: 0.8936 (tppt) REVERT: A 315 PHE cc_start: 0.9415 (m-80) cc_final: 0.9046 (m-10) REVERT: A 363 GLN cc_start: 0.9068 (tp-100) cc_final: 0.8750 (tp-100) REVERT: A 579 ILE cc_start: 0.9448 (pp) cc_final: 0.9079 (pt) REVERT: A 580 LEU cc_start: 0.9093 (mt) cc_final: 0.8809 (mt) REVERT: A 651 ILE cc_start: 0.9443 (OUTLIER) cc_final: 0.9092 (tp) REVERT: A 662 GLN cc_start: 0.8618 (mt0) cc_final: 0.8141 (mt0) outliers start: 19 outliers final: 4 residues processed: 168 average time/residue: 0.1451 time to fit residues: 31.4983 Evaluate side-chains 109 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 104 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 94 optimal weight: 0.0970 chunk 36 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 70 optimal weight: 20.0000 chunk 108 optimal weight: 6.9990 overall best weight: 1.2980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 ASN A 615 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.091039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.074088 restraints weight = 17071.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.076122 restraints weight = 11902.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.077541 restraints weight = 8932.242| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8694 Z= 0.241 Angle : 0.813 8.915 11948 Z= 0.430 Chirality : 0.046 0.353 1482 Planarity : 0.006 0.059 1484 Dihedral : 6.192 19.748 1248 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.41 % Favored : 94.25 % Rotamer: Outliers : 0.27 % Allowed : 5.57 % Favored : 94.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.23), residues: 1182 helix: -1.61 (0.17), residues: 780 sheet: -2.43 (0.76), residues: 46 loop : -2.17 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 61 HIS 0.013 0.002 HIS B 447 PHE 0.021 0.002 PHE B 664 TYR 0.036 0.002 TYR B 572 ARG 0.005 0.001 ARG A 345 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 131 time to evaluate : 0.450 Fit side-chains revert: symmetry clash REVERT: A 158 TRP cc_start: 0.7890 (t-100) cc_final: 0.7563 (t-100) REVERT: A 161 LEU cc_start: 0.9525 (mt) cc_final: 0.9271 (pp) REVERT: A 178 ARG cc_start: 0.9343 (ttt90) cc_final: 0.9068 (ttt-90) REVERT: A 180 GLN cc_start: 0.9288 (tp-100) cc_final: 0.8945 (tm-30) REVERT: A 209 LYS cc_start: 0.9187 (tttt) cc_final: 0.8852 (tptt) REVERT: A 315 PHE cc_start: 0.9319 (m-80) cc_final: 0.8538 (m-10) REVERT: A 354 ILE cc_start: 0.8274 (pt) cc_final: 0.8065 (pt) REVERT: A 563 MET cc_start: 0.9496 (mmp) cc_final: 0.9285 (mmm) REVERT: A 579 ILE cc_start: 0.9548 (pt) cc_final: 0.9315 (pt) REVERT: A 594 LEU cc_start: 0.9566 (pp) cc_final: 0.9218 (mp) outliers start: 1 outliers final: 1 residues processed: 132 average time/residue: 0.1219 time to fit residues: 21.4761 Evaluate side-chains 109 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 29 optimal weight: 0.0050 chunk 104 optimal weight: 0.0050 chunk 119 optimal weight: 0.2980 chunk 18 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 46 optimal weight: 0.0270 overall best weight: 0.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 615 HIS A 618 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.092817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.075705 restraints weight = 16757.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.077831 restraints weight = 11581.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.079302 restraints weight = 8631.914| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8694 Z= 0.225 Angle : 0.745 8.980 11948 Z= 0.383 Chirality : 0.043 0.161 1482 Planarity : 0.006 0.060 1484 Dihedral : 5.623 18.315 1248 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.26 % Favored : 93.40 % Rotamer: Outliers : 0.53 % Allowed : 3.45 % Favored : 96.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.24), residues: 1182 helix: -0.74 (0.18), residues: 778 sheet: -2.07 (1.00), residues: 34 loop : -1.89 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 61 HIS 0.003 0.001 HIS B 173 PHE 0.030 0.002 PHE A 514 TYR 0.031 0.002 TYR A 586 ARG 0.005 0.001 ARG B 450 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 133 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 TRP cc_start: 0.7756 (t-100) cc_final: 0.7422 (t-100) REVERT: A 161 LEU cc_start: 0.9470 (mt) cc_final: 0.9263 (pp) REVERT: A 180 GLN cc_start: 0.9114 (tp-100) cc_final: 0.8740 (tm-30) REVERT: A 315 PHE cc_start: 0.9297 (m-80) cc_final: 0.8537 (m-10) REVERT: A 563 MET cc_start: 0.9476 (mmp) cc_final: 0.9274 (mmp) REVERT: A 594 LEU cc_start: 0.9475 (pp) cc_final: 0.9205 (mp) outliers start: 2 outliers final: 0 residues processed: 134 average time/residue: 0.1237 time to fit residues: 22.0867 Evaluate side-chains 106 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 31 optimal weight: 5.9990 chunk 89 optimal weight: 0.0030 chunk 92 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 108 optimal weight: 0.0870 chunk 87 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 77 optimal weight: 0.0670 chunk 116 optimal weight: 1.9990 chunk 58 optimal weight: 0.0470 overall best weight: 0.4406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 ASN ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 618 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.092767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.075379 restraints weight = 17419.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.077436 restraints weight = 12124.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.078965 restraints weight = 9079.094| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8694 Z= 0.196 Angle : 0.716 8.694 11948 Z= 0.366 Chirality : 0.042 0.156 1482 Planarity : 0.005 0.058 1484 Dihedral : 5.364 30.875 1248 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.11 % Favored : 92.72 % Rotamer: Outliers : 0.80 % Allowed : 3.18 % Favored : 96.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.28 (0.25), residues: 1182 helix: -0.03 (0.19), residues: 748 sheet: -2.29 (0.98), residues: 34 loop : -2.19 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 61 HIS 0.006 0.001 HIS A 447 PHE 0.021 0.001 PHE A 514 TYR 0.020 0.002 TYR A 164 ARG 0.002 0.001 ARG A 619 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 135 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 TRP cc_start: 0.7677 (t-100) cc_final: 0.7350 (t-100) REVERT: A 161 LEU cc_start: 0.9459 (mt) cc_final: 0.9204 (pp) REVERT: A 180 GLN cc_start: 0.9205 (tp-100) cc_final: 0.8822 (tm-30) REVERT: A 315 PHE cc_start: 0.9308 (m-80) cc_final: 0.8566 (m-10) REVERT: A 580 LEU cc_start: 0.9019 (mt) cc_final: 0.8805 (mt) REVERT: A 594 LEU cc_start: 0.9529 (pp) cc_final: 0.9118 (mp) REVERT: A 615 HIS cc_start: 0.7727 (t-90) cc_final: 0.6458 (t-90) REVERT: A 618 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.6656 (pp30) REVERT: A 619 ARG cc_start: 0.8789 (mmt180) cc_final: 0.8502 (mmt-90) outliers start: 3 outliers final: 0 residues processed: 136 average time/residue: 0.1146 time to fit residues: 21.0490 Evaluate side-chains 104 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 3 optimal weight: 30.0000 chunk 88 optimal weight: 0.5980 chunk 117 optimal weight: 0.0170 chunk 4 optimal weight: 20.0000 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 5 optimal weight: 0.0770 chunk 90 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 ASN A 617 HIS A 618 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.093669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.076260 restraints weight = 17441.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.078252 restraints weight = 12309.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.079698 restraints weight = 9333.539| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.5048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8694 Z= 0.192 Angle : 0.713 8.578 11948 Z= 0.360 Chirality : 0.041 0.148 1482 Planarity : 0.005 0.059 1484 Dihedral : 5.119 30.732 1248 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 0.27 % Allowed : 2.39 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 (0.25), residues: 1182 helix: 0.24 (0.20), residues: 762 sheet: -2.47 (0.93), residues: 34 loop : -2.21 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 61 HIS 0.002 0.000 HIS A 173 PHE 0.018 0.001 PHE B 514 TYR 0.011 0.001 TYR A 164 ARG 0.008 0.001 ARG A 450 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 TRP cc_start: 0.7695 (t-100) cc_final: 0.7357 (t-100) REVERT: A 180 GLN cc_start: 0.9223 (tp-100) cc_final: 0.8801 (tm-30) REVERT: A 315 PHE cc_start: 0.9291 (m-80) cc_final: 0.9013 (m-10) REVERT: A 374 ILE cc_start: 0.9494 (pt) cc_final: 0.9280 (pt) REVERT: A 574 VAL cc_start: 0.8976 (p) cc_final: 0.8771 (p) REVERT: A 594 LEU cc_start: 0.9562 (pp) cc_final: 0.9168 (mp) REVERT: A 618 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7654 (pp30) outliers start: 1 outliers final: 0 residues processed: 133 average time/residue: 0.1257 time to fit residues: 22.3201 Evaluate side-chains 102 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 113 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 115 optimal weight: 0.2980 chunk 89 optimal weight: 0.3980 chunk 119 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 114 optimal weight: 0.0270 chunk 74 optimal weight: 0.9990 chunk 3 optimal weight: 30.0000 chunk 9 optimal weight: 8.9990 overall best weight: 0.7442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 308 GLN A 351 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.093316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.075858 restraints weight = 17154.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.077885 restraints weight = 12010.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.079361 restraints weight = 9053.266| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.5430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8694 Z= 0.189 Angle : 0.695 8.529 11948 Z= 0.349 Chirality : 0.041 0.168 1482 Planarity : 0.005 0.060 1484 Dihedral : 4.916 28.794 1248 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % 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: -0.71 (0.26), residues: 1182 helix: 0.49 (0.20), residues: 762 sheet: -2.53 (0.95), residues: 34 loop : -2.19 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 613 HIS 0.004 0.001 HIS B 615 PHE 0.018 0.001 PHE B 514 TYR 0.008 0.001 TYR B 225 ARG 0.002 0.001 ARG A 661 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASN cc_start: 0.6175 (m-40) cc_final: 0.5963 (m-40) REVERT: A 164 TYR cc_start: 0.8209 (m-80) cc_final: 0.7938 (m-80) REVERT: A 178 ARG cc_start: 0.9302 (ttt90) cc_final: 0.8636 (ttt-90) REVERT: A 180 GLN cc_start: 0.9245 (tp-100) cc_final: 0.8820 (tm-30) REVERT: A 222 GLU cc_start: 0.9226 (mm-30) cc_final: 0.8989 (mp0) REVERT: A 315 PHE cc_start: 0.9226 (m-80) cc_final: 0.8626 (m-10) REVERT: A 572 TYR cc_start: 0.8075 (m-10) cc_final: 0.7767 (m-10) REVERT: A 594 LEU cc_start: 0.9525 (pp) cc_final: 0.9168 (mp) REVERT: A 606 TYR cc_start: 0.7830 (m-80) cc_final: 0.7592 (m-80) REVERT: A 627 PHE cc_start: 0.9394 (t80) cc_final: 0.8941 (t80) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.1105 time to fit residues: 19.4562 Evaluate side-chains 102 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 117 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 88 optimal weight: 0.1980 chunk 74 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 65 optimal weight: 0.1980 chunk 60 optimal weight: 30.0000 chunk 58 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.092449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.075551 restraints weight = 16944.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.077363 restraints weight = 12108.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.078727 restraints weight = 9270.596| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.5733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8694 Z= 0.199 Angle : 0.688 8.893 11948 Z= 0.347 Chirality : 0.041 0.159 1482 Planarity : 0.005 0.060 1484 Dihedral : 4.769 25.786 1248 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % 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: -0.45 (0.26), residues: 1182 helix: 0.67 (0.20), residues: 766 sheet: -2.54 (0.94), residues: 34 loop : -2.04 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 613 HIS 0.005 0.001 HIS B 615 PHE 0.019 0.001 PHE A 504 TYR 0.024 0.002 TYR A 171 ARG 0.005 0.001 ARG A 661 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 LEU cc_start: 0.9387 (mt) cc_final: 0.9092 (pp) REVERT: A 178 ARG cc_start: 0.9222 (ttt90) cc_final: 0.8604 (ttt-90) REVERT: A 180 GLN cc_start: 0.9169 (tp-100) cc_final: 0.8874 (tm-30) REVERT: A 222 GLU cc_start: 0.9188 (mm-30) cc_final: 0.8953 (mp0) REVERT: A 315 PHE cc_start: 0.9193 (m-80) cc_final: 0.8903 (m-10) REVERT: A 419 GLN cc_start: 0.9060 (mt0) cc_final: 0.8775 (mt0) REVERT: A 447 HIS cc_start: 0.9030 (t70) cc_final: 0.8747 (t-90) REVERT: A 465 PHE cc_start: 0.8668 (t80) cc_final: 0.8251 (t80) REVERT: A 594 LEU cc_start: 0.9554 (pp) cc_final: 0.9166 (mp) REVERT: A 618 GLN cc_start: 0.8738 (tt0) cc_final: 0.8309 (tt0) REVERT: A 619 ARG cc_start: 0.8938 (mmt180) cc_final: 0.8661 (mmp80) REVERT: A 627 PHE cc_start: 0.9391 (t80) cc_final: 0.8999 (t80) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.1151 time to fit residues: 20.1747 Evaluate side-chains 100 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 2 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 65 optimal weight: 0.0670 chunk 18 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 83 optimal weight: 7.9990 chunk 17 optimal weight: 0.0270 chunk 9 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 100 optimal weight: 0.0030 chunk 111 optimal weight: 0.8980 overall best weight: 0.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 351 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.093939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.076575 restraints weight = 17139.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.078409 restraints weight = 12371.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.079783 restraints weight = 9521.690| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.5977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8694 Z= 0.175 Angle : 0.682 8.160 11948 Z= 0.341 Chirality : 0.041 0.155 1482 Planarity : 0.005 0.060 1484 Dihedral : 4.808 30.403 1248 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.46 (0.26), residues: 1182 helix: 0.69 (0.20), residues: 776 sheet: -3.14 (0.84), residues: 38 loop : -2.10 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 613 HIS 0.002 0.001 HIS B 173 PHE 0.036 0.001 PHE B 514 TYR 0.009 0.001 TYR A 572 ARG 0.003 0.001 ARG B 661 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 LEU cc_start: 0.9381 (mt) cc_final: 0.9110 (pp) REVERT: A 180 GLN cc_start: 0.9122 (tp-100) cc_final: 0.8855 (tm-30) REVERT: A 222 GLU cc_start: 0.9182 (mm-30) cc_final: 0.8973 (mp0) REVERT: A 315 PHE cc_start: 0.9098 (m-80) cc_final: 0.8492 (m-10) REVERT: A 594 LEU cc_start: 0.9565 (pp) cc_final: 0.9130 (mp) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.1131 time to fit residues: 20.5669 Evaluate side-chains 100 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 1 optimal weight: 0.3980 chunk 38 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 14 optimal weight: 0.0060 chunk 61 optimal weight: 0.0970 chunk 90 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 19 optimal weight: 0.0970 chunk 104 optimal weight: 0.0170 overall best weight: 0.1230 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 615 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.095941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.077662 restraints weight = 17074.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.079670 restraints weight = 12284.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.081149 restraints weight = 9402.255| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.6350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8694 Z= 0.185 Angle : 0.696 7.587 11948 Z= 0.347 Chirality : 0.041 0.148 1482 Planarity : 0.005 0.060 1484 Dihedral : 4.627 29.101 1248 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % 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: -0.38 (0.26), residues: 1182 helix: 0.79 (0.20), residues: 776 sheet: -3.32 (0.83), residues: 38 loop : -2.14 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 613 HIS 0.007 0.001 HIS A 447 PHE 0.031 0.001 PHE A 514 TYR 0.010 0.001 TYR B 572 ARG 0.006 0.001 ARG B 619 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: A 57 ASN cc_start: 0.6367 (m-40) cc_final: 0.6130 (m-40) REVERT: A 178 ARG cc_start: 0.9152 (ttt-90) cc_final: 0.8915 (ttm-80) REVERT: A 180 GLN cc_start: 0.9114 (tp-100) cc_final: 0.8895 (tm-30) REVERT: A 209 LYS cc_start: 0.9203 (tttt) cc_final: 0.8802 (tppt) REVERT: A 465 PHE cc_start: 0.8312 (t80) cc_final: 0.7653 (t80) REVERT: A 572 TYR cc_start: 0.8327 (m-10) cc_final: 0.8028 (m-10) REVERT: A 594 LEU cc_start: 0.9580 (pp) cc_final: 0.9171 (mp) REVERT: A 624 LEU cc_start: 0.9436 (tp) cc_final: 0.9152 (tt) REVERT: A 627 PHE cc_start: 0.9391 (t80) cc_final: 0.9102 (t80) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.1098 time to fit residues: 19.7718 Evaluate side-chains 98 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 12 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 106 optimal weight: 0.4980 chunk 90 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.095479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.077967 restraints weight = 17099.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.079800 restraints weight = 12549.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.081195 restraints weight = 9776.351| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.6530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8694 Z= 0.189 Angle : 0.702 7.592 11948 Z= 0.354 Chirality : 0.042 0.201 1482 Planarity : 0.005 0.058 1484 Dihedral : 4.712 34.474 1248 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.19 (0.26), residues: 1182 helix: 0.96 (0.20), residues: 776 sheet: -3.10 (0.83), residues: 38 loop : -2.16 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 61 HIS 0.001 0.000 HIS B 173 PHE 0.029 0.001 PHE B 514 TYR 0.017 0.001 TYR A 164 ARG 0.003 0.001 ARG B 661 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASN cc_start: 0.6543 (m-40) cc_final: 0.6264 (m-40) REVERT: A 141 ASN cc_start: 0.8394 (t0) cc_final: 0.8133 (m110) REVERT: A 180 GLN cc_start: 0.9116 (tp-100) cc_final: 0.8916 (tm-30) REVERT: A 209 LYS cc_start: 0.9229 (tttt) cc_final: 0.8837 (tppt) REVERT: A 222 GLU cc_start: 0.9130 (mm-30) cc_final: 0.8925 (mp0) REVERT: A 232 GLU cc_start: 0.7749 (pp20) cc_final: 0.7178 (mm-30) REVERT: A 465 PHE cc_start: 0.8514 (t80) cc_final: 0.7849 (t80) REVERT: A 572 TYR cc_start: 0.8164 (m-10) cc_final: 0.7783 (m-10) REVERT: A 594 LEU cc_start: 0.9591 (pp) cc_final: 0.9160 (mp) REVERT: A 627 PHE cc_start: 0.9388 (t80) cc_final: 0.9106 (t80) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.1123 time to fit residues: 20.0440 Evaluate side-chains 97 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 15 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 63 optimal weight: 30.0000 chunk 12 optimal weight: 0.9990 chunk 80 optimal weight: 0.0060 chunk 87 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 61 optimal weight: 0.0980 chunk 73 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.095882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.077845 restraints weight = 17207.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.079844 restraints weight = 12508.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.081282 restraints weight = 9594.460| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.6740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8694 Z= 0.187 Angle : 0.699 7.732 11948 Z= 0.346 Chirality : 0.042 0.220 1482 Planarity : 0.005 0.054 1484 Dihedral : 4.621 30.984 1248 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.14 (0.26), residues: 1182 helix: 0.99 (0.20), residues: 776 sheet: -2.91 (0.87), residues: 38 loop : -2.15 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 613 HIS 0.003 0.001 HIS B 615 PHE 0.027 0.002 PHE B 514 TYR 0.017 0.001 TYR A 164 ARG 0.003 0.001 ARG A 661 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1893.06 seconds wall clock time: 33 minutes 50.68 seconds (2030.68 seconds total)