Starting phenix.real_space_refine on Wed Feb 12 21:53:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5z1f_6875/02_2025/5z1f_6875.cif Found real_map, /net/cci-nas-00/data/ceres_data/5z1f_6875/02_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_6875/02_2025/5z1f_6875.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5z1f_6875/02_2025/5z1f_6875.map" model { file = "/net/cci-nas-00/data/ceres_data/5z1f_6875/02_2025/5z1f_6875.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5z1f_6875/02_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 7.31, per 1000 atoms: 0.86 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: 2.22 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: 0.87 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: 2.35 Time building geometry restraints manager: 2.54 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: 0.560 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.290 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.530 ------------------------------------------------------------------------------- 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 : 0.516 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: 0.1355 time to fit residues: 29.1881 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 : 0.440 ------------------------------------------------------------------------------- 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 = 41)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.074084 restraints weight = 17071.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.076106 restraints weight = 11896.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.077597 restraints weight = 8933.373| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- 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 19.747 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 B 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 : 0.466 Fit side-chains revert: symmetry clash REVERT: A 158 TRP cc_start: 0.7889 (t-100) cc_final: 0.7563 (t-100) REVERT: A 161 LEU cc_start: 0.9524 (mt) cc_final: 0.9270 (pp) REVERT: A 178 ARG cc_start: 0.9344 (ttt90) cc_final: 0.9070 (ttt-90) REVERT: A 180 GLN cc_start: 0.9285 (tp-100) cc_final: 0.8944 (tm-30) REVERT: A 209 LYS cc_start: 0.9188 (tttt) cc_final: 0.8852 (tptt) REVERT: A 315 PHE cc_start: 0.9319 (m-80) cc_final: 0.8540 (m-10) REVERT: A 354 ILE cc_start: 0.8275 (pt) cc_final: 0.8067 (pt) REVERT: A 563 MET cc_start: 0.9497 (mmp) cc_final: 0.9287 (mmm) REVERT: A 579 ILE cc_start: 0.9548 (pt) cc_final: 0.9315 (pt) REVERT: A 594 LEU cc_start: 0.9567 (pp) cc_final: 0.9219 (mp) outliers start: 1 outliers final: 1 residues processed: 132 average time/residue: 0.1188 time to fit residues: 20.9953 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 : 0.458 ------------------------------------------------------------------------------- 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: 0.0470 chunk 104 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 97 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 66 optimal weight: 0.0370 chunk 83 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 = 0.3502 r_free = 0.3502 target = 0.092027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.075138 restraints weight = 16736.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.077200 restraints weight = 11524.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.078701 restraints weight = 8594.942| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8694 Z= 0.223 Angle : 0.739 8.853 11948 Z= 0.382 Chirality : 0.042 0.160 1482 Planarity : 0.006 0.060 1484 Dihedral : 5.584 18.356 1248 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.92 % Favored : 93.74 % 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: -1.78 (0.25), residues: 1182 helix: -0.70 (0.18), residues: 780 sheet: -2.09 (0.99), residues: 34 loop : -1.87 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 61 HIS 0.003 0.001 HIS A 173 PHE 0.032 0.002 PHE B 514 TYR 0.032 0.002 TYR A 586 ARG 0.008 0.001 ARG A 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 134 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 132 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 TRP cc_start: 0.7710 (t-100) cc_final: 0.7380 (t-100) REVERT: A 178 ARG cc_start: 0.9322 (ttt90) cc_final: 0.9111 (ttt-90) REVERT: A 180 GLN cc_start: 0.9101 (tp-100) cc_final: 0.8734 (tm-30) REVERT: A 315 PHE cc_start: 0.9306 (m-80) cc_final: 0.8511 (m-10) REVERT: A 563 MET cc_start: 0.9466 (mmp) cc_final: 0.9265 (mmp) REVERT: A 594 LEU cc_start: 0.9494 (pp) cc_final: 0.9222 (mp) REVERT: A 656 PHE cc_start: 0.8725 (t80) cc_final: 0.8397 (t80) outliers start: 2 outliers final: 0 residues processed: 133 average time/residue: 0.1313 time to fit residues: 23.0624 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 : 0.520 ------------------------------------------------------------------------------- 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: 0.9980 chunk 89 optimal weight: 0.9980 chunk 92 optimal weight: 0.0980 chunk 9 optimal weight: 0.9990 chunk 108 optimal weight: 0.3980 chunk 87 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 15 optimal weight: 0.0670 chunk 77 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 58 optimal weight: 0.0370 overall best weight: 0.3196 ------------------------------------------------------------------------------- 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 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.093050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.075637 restraints weight = 17359.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.077728 restraints weight = 12082.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.079252 restraints weight = 8995.618| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.4606 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= 0.201 Angle : 0.713 8.582 11948 Z= 0.361 Chirality : 0.041 0.149 1482 Planarity : 0.005 0.058 1484 Dihedral : 5.197 17.176 1248 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.60 % Favored : 93.06 % Rotamer: Outliers : 0.53 % Allowed : 3.18 % Favored : 96.29 % 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: -1.21 (0.25), residues: 1182 helix: 0.01 (0.19), residues: 748 sheet: -2.19 (0.99), residues: 34 loop : -2.15 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 61 HIS 0.004 0.001 HIS B 447 PHE 0.020 0.001 PHE A 514 TYR 0.019 0.002 TYR B 164 ARG 0.003 0.001 ARG B 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: 2 poor density : 136 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLN cc_start: 0.9231 (tp-100) cc_final: 0.8831 (tm-30) REVERT: A 315 PHE cc_start: 0.9319 (m-80) cc_final: 0.8561 (m-10) REVERT: A 572 TYR cc_start: 0.8056 (m-10) cc_final: 0.7841 (m-10) REVERT: A 580 LEU cc_start: 0.9042 (mt) cc_final: 0.8834 (mt) REVERT: A 594 LEU cc_start: 0.9513 (pp) cc_final: 0.9129 (mp) REVERT: A 615 HIS cc_start: 0.7723 (t-90) cc_final: 0.6340 (t-90) REVERT: A 618 GLN cc_start: 0.8147 (pp30) cc_final: 0.6586 (pp30) REVERT: A 619 ARG cc_start: 0.8798 (mmt180) cc_final: 0.8495 (mmt-90) outliers start: 2 outliers final: 0 residues processed: 136 average time/residue: 0.1181 time to fit residues: 21.6706 Evaluate side-chains 104 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.455 ------------------------------------------------------------------------------- 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: 0.9980 chunk 117 optimal weight: 3.9990 chunk 4 optimal weight: 20.0000 chunk 12 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 90 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 chunk 46 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3463 r_free = 0.3463 target = 0.089561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.072957 restraints weight = 17902.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.074891 restraints weight = 12660.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.076303 restraints weight = 9537.547| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.5021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8694 Z= 0.240 Angle : 0.725 7.750 11948 Z= 0.373 Chirality : 0.041 0.137 1482 Planarity : 0.005 0.063 1484 Dihedral : 5.044 23.512 1248 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 14.22 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 : 0.00 % 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: -0.61 (0.26), residues: 1182 helix: 0.47 (0.20), residues: 768 sheet: -2.28 (0.98), residues: 34 loop : -1.97 (0.35), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 613 HIS 0.002 0.001 HIS A 615 PHE 0.018 0.002 PHE A 514 TYR 0.018 0.002 TYR B 164 ARG 0.009 0.001 ARG B 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 126 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 TRP cc_start: 0.8974 (p-90) cc_final: 0.8642 (p-90) REVERT: A 178 ARG cc_start: 0.9314 (ttt90) cc_final: 0.8809 (ttt-90) REVERT: A 180 GLN cc_start: 0.9246 (tp-100) cc_final: 0.8835 (tm-30) REVERT: A 222 GLU cc_start: 0.9253 (mm-30) cc_final: 0.8980 (mp0) REVERT: A 315 PHE cc_start: 0.9377 (m-80) cc_final: 0.8941 (m-10) REVERT: A 374 ILE cc_start: 0.9543 (pt) cc_final: 0.9337 (pt) REVERT: A 594 LEU cc_start: 0.9594 (pp) cc_final: 0.9200 (mp) outliers start: 1 outliers final: 0 residues processed: 126 average time/residue: 0.1204 time to fit residues: 20.5514 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 : 0.454 ------------------------------------------------------------------------------- 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: 0.5980 chunk 106 optimal weight: 0.9980 chunk 19 optimal weight: 0.0060 chunk 115 optimal weight: 6.9990 chunk 89 optimal weight: 0.0070 chunk 119 optimal weight: 10.0000 chunk 7 optimal weight: 0.6980 chunk 114 optimal weight: 0.4980 chunk 74 optimal weight: 0.9980 chunk 3 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 overall best weight: 0.3614 ------------------------------------------------------------------------------- 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 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.092382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.074964 restraints weight = 17687.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.076918 restraints weight = 12511.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.078344 restraints weight = 9497.839| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.5479 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= 0.184 Angle : 0.696 8.423 11948 Z= 0.350 Chirality : 0.041 0.156 1482 Planarity : 0.005 0.062 1484 Dihedral : 4.906 28.304 1248 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % 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: -0.53 (0.26), residues: 1182 helix: 0.59 (0.20), residues: 774 sheet: -2.41 (0.94), residues: 34 loop : -2.11 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 613 HIS 0.005 0.001 HIS A 447 PHE 0.024 0.001 PHE B 459 TYR 0.016 0.001 TYR A 164 ARG 0.002 0.000 ARG B 345 *********************** 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 128 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 ILE cc_start: 0.8924 (tp) cc_final: 0.8693 (pt) REVERT: A 178 ARG cc_start: 0.9321 (ttt90) cc_final: 0.8804 (ttt-90) REVERT: A 180 GLN cc_start: 0.9225 (tp-100) cc_final: 0.8862 (tm-30) REVERT: A 222 GLU cc_start: 0.9253 (mm-30) cc_final: 0.8999 (mp0) REVERT: A 315 PHE cc_start: 0.9348 (m-80) cc_final: 0.8421 (m-10) REVERT: A 354 ILE cc_start: 0.9016 (tp) cc_final: 0.8785 (tt) REVERT: A 361 ILE cc_start: 0.9387 (mt) cc_final: 0.9178 (mm) REVERT: A 374 ILE cc_start: 0.9486 (pt) cc_final: 0.9281 (pt) REVERT: A 594 LEU cc_start: 0.9540 (pp) cc_final: 0.9250 (mp) REVERT: A 606 TYR cc_start: 0.7797 (m-80) cc_final: 0.7568 (m-80) REVERT: A 618 GLN cc_start: 0.8242 (pp30) cc_final: 0.7708 (pp30) REVERT: A 659 VAL cc_start: 0.9359 (p) cc_final: 0.8992 (p) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1207 time to fit residues: 20.5815 Evaluate side-chains 108 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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: 0.0270 chunk 35 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 chunk 88 optimal weight: 0.3980 chunk 74 optimal weight: 0.1980 chunk 76 optimal weight: 2.9990 chunk 65 optimal weight: 0.0030 chunk 60 optimal weight: 30.0000 chunk 58 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.2648 ------------------------------------------------------------------------------- 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 = 0.3538 r_free = 0.3538 target = 0.093293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.075664 restraints weight = 17076.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.077654 restraints weight = 12126.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.079053 restraints weight = 9227.228| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.5776 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= 0.195 Angle : 0.706 8.462 11948 Z= 0.355 Chirality : 0.042 0.176 1482 Planarity : 0.005 0.060 1484 Dihedral : 4.852 27.513 1248 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % 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: -0.53 (0.26), residues: 1182 helix: 0.61 (0.20), residues: 774 sheet: -2.36 (0.97), residues: 34 loop : -2.15 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 613 HIS 0.004 0.001 HIS A 447 PHE 0.039 0.002 PHE A 514 TYR 0.021 0.002 TYR A 572 ARG 0.003 0.000 ARG B 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 130 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASN cc_start: 0.6632 (m-40) cc_final: 0.6365 (m-40) REVERT: A 178 ARG cc_start: 0.9284 (ttt90) cc_final: 0.8799 (ttt-90) REVERT: A 180 GLN cc_start: 0.9184 (tp-100) cc_final: 0.8929 (tm-30) REVERT: A 209 LYS cc_start: 0.9228 (tttt) cc_final: 0.8859 (tppt) REVERT: A 222 GLU cc_start: 0.9251 (mm-30) cc_final: 0.9039 (mp0) REVERT: A 315 PHE cc_start: 0.9247 (m-80) cc_final: 0.8929 (m-10) REVERT: A 361 ILE cc_start: 0.9392 (mt) cc_final: 0.9174 (mm) REVERT: A 447 HIS cc_start: 0.9007 (t-90) cc_final: 0.8775 (t-90) REVERT: A 572 TYR cc_start: 0.8113 (m-10) cc_final: 0.7855 (m-10) REVERT: A 594 LEU cc_start: 0.9528 (pp) cc_final: 0.9220 (mp) REVERT: A 619 ARG cc_start: 0.8967 (mmt180) cc_final: 0.8523 (mmp80) REVERT: A 627 PHE cc_start: 0.9446 (t80) cc_final: 0.9031 (t80) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.1181 time to fit residues: 20.7094 Evaluate side-chains 99 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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: 6.9990 chunk 112 optimal weight: 0.9990 chunk 65 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 9 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 100 optimal weight: 0.0040 chunk 111 optimal weight: 0.0270 overall best weight: 0.4452 ------------------------------------------------------------------------------- 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 = 0.3537 r_free = 0.3537 target = 0.093393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.075494 restraints weight = 17053.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.077469 restraints weight = 12136.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.078965 restraints weight = 9275.402| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.5991 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= 0.189 Angle : 0.694 8.906 11948 Z= 0.345 Chirality : 0.041 0.143 1482 Planarity : 0.005 0.059 1484 Dihedral : 4.653 24.660 1248 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % 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 : 0.00 % 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: -0.49 (0.26), residues: 1182 helix: 0.66 (0.20), residues: 782 sheet: -2.84 (0.72), residues: 46 loop : -2.14 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 613 HIS 0.003 0.001 HIS B 617 PHE 0.030 0.001 PHE B 514 TYR 0.016 0.001 TYR A 572 ARG 0.004 0.000 ARG A 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 132 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.509 Fit side-chains revert: symmetry clash REVERT: A 57 ASN cc_start: 0.6677 (m-40) cc_final: 0.6344 (m-40) REVERT: A 164 TYR cc_start: 0.8129 (m-80) cc_final: 0.7907 (m-80) REVERT: A 178 ARG cc_start: 0.9313 (ttt90) cc_final: 0.8762 (ttt-90) REVERT: A 180 GLN cc_start: 0.9206 (tp-100) cc_final: 0.8939 (tm-30) REVERT: A 209 LYS cc_start: 0.9214 (tttt) cc_final: 0.8793 (tppt) REVERT: A 222 GLU cc_start: 0.9271 (mm-30) cc_final: 0.9035 (mp0) REVERT: A 315 PHE cc_start: 0.9195 (m-80) cc_final: 0.8422 (m-10) REVERT: A 361 ILE cc_start: 0.9408 (mt) cc_final: 0.9182 (mm) REVERT: A 447 HIS cc_start: 0.9078 (t-90) cc_final: 0.8738 (t-90) REVERT: A 465 PHE cc_start: 0.8645 (t80) cc_final: 0.8135 (t80) REVERT: A 572 TYR cc_start: 0.8184 (m-10) cc_final: 0.7870 (m-10) REVERT: A 594 LEU cc_start: 0.9552 (pp) cc_final: 0.9174 (mp) REVERT: A 627 PHE cc_start: 0.9431 (t80) cc_final: 0.9093 (t80) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.1128 time to fit residues: 20.1706 Evaluate side-chains 99 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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: 2.9990 chunk 38 optimal weight: 4.9990 chunk 44 optimal weight: 0.1980 chunk 94 optimal weight: 0.9990 chunk 2 optimal weight: 0.0970 chunk 14 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3545 r_free = 0.3545 target = 0.093803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.076135 restraints weight = 17423.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.078107 restraints weight = 12503.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.079563 restraints weight = 9550.469| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.6321 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= 0.191 Angle : 0.684 7.706 11948 Z= 0.341 Chirality : 0.041 0.144 1482 Planarity : 0.005 0.057 1484 Dihedral : 4.672 30.255 1248 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.38 (0.26), residues: 1182 helix: 0.79 (0.20), residues: 784 sheet: -3.01 (0.68), residues: 48 loop : -2.19 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 613 HIS 0.004 0.001 HIS B 615 PHE 0.028 0.001 PHE A 668 TYR 0.017 0.001 TYR B 171 ARG 0.004 0.001 ARG A 661 *********************** 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 131 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: A 57 ASN cc_start: 0.6680 (m-40) cc_final: 0.6385 (m-40) REVERT: A 161 LEU cc_start: 0.9373 (mt) cc_final: 0.9136 (pp) REVERT: A 178 ARG cc_start: 0.9323 (ttt90) cc_final: 0.9038 (ttt180) REVERT: A 180 GLN cc_start: 0.9141 (tp-100) cc_final: 0.8921 (tm-30) REVERT: A 209 LYS cc_start: 0.9235 (tttt) cc_final: 0.8826 (tppt) REVERT: A 222 GLU cc_start: 0.9211 (mm-30) cc_final: 0.8975 (mp0) REVERT: A 315 PHE cc_start: 0.9082 (m-80) cc_final: 0.8870 (m-10) REVERT: A 361 ILE cc_start: 0.9405 (mt) cc_final: 0.9164 (mm) REVERT: A 447 HIS cc_start: 0.9062 (t-90) cc_final: 0.8733 (t-90) REVERT: A 465 PHE cc_start: 0.8604 (t80) cc_final: 0.7966 (t80) REVERT: A 572 TYR cc_start: 0.8096 (m-10) cc_final: 0.7771 (m-10) REVERT: A 594 LEU cc_start: 0.9573 (pp) cc_final: 0.9150 (mp) REVERT: A 627 PHE cc_start: 0.9457 (t80) cc_final: 0.9056 (t80) REVERT: A 668 PHE cc_start: 0.7566 (t80) cc_final: 0.7305 (t80) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1154 time to fit residues: 20.3374 Evaluate side-chains 99 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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: 0.7980 chunk 106 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 110 optimal weight: 0.0370 chunk 19 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- 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 = 0.3550 r_free = 0.3550 target = 0.094090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.076595 restraints weight = 17372.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.078466 restraints weight = 12621.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.079916 restraints weight = 9738.961| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.6565 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= 0.189 Angle : 0.675 7.831 11948 Z= 0.338 Chirality : 0.043 0.251 1482 Planarity : 0.005 0.059 1484 Dihedral : 4.540 28.663 1248 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.25 (0.26), residues: 1182 helix: 0.87 (0.20), residues: 786 sheet: -3.25 (0.85), residues: 38 loop : -2.15 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 613 HIS 0.002 0.001 HIS B 615 PHE 0.027 0.001 PHE A 668 TYR 0.011 0.001 TYR A 171 ARG 0.004 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 128 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.468 Fit side-chains revert: symmetry clash REVERT: A 178 ARG cc_start: 0.9348 (ttt90) cc_final: 0.8910 (ttm170) REVERT: A 209 LYS cc_start: 0.9240 (tttt) cc_final: 0.8898 (tppt) REVERT: A 222 GLU cc_start: 0.9229 (mm-30) cc_final: 0.8987 (mp0) REVERT: A 315 PHE cc_start: 0.9126 (m-80) cc_final: 0.8911 (m-10) REVERT: A 361 ILE cc_start: 0.9438 (mt) cc_final: 0.9222 (mm) REVERT: A 447 HIS cc_start: 0.9097 (t-90) cc_final: 0.8696 (t-90) REVERT: A 465 PHE cc_start: 0.8679 (t80) cc_final: 0.7926 (t80) REVERT: A 572 TYR cc_start: 0.8115 (m-10) cc_final: 0.7703 (m-10) REVERT: A 594 LEU cc_start: 0.9600 (pp) cc_final: 0.9211 (mp) REVERT: A 627 PHE cc_start: 0.9427 (t80) cc_final: 0.9130 (t80) REVERT: A 668 PHE cc_start: 0.7621 (t80) cc_final: 0.6961 (t80) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1138 time to fit residues: 19.8161 Evaluate side-chains 95 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.458 ------------------------------------------------------------------------------- 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: 0.0170 chunk 16 optimal weight: 1.9990 chunk 63 optimal weight: 40.0000 chunk 12 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 87 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 overall best weight: 1.3422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.092683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.075290 restraints weight = 17679.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.077123 restraints weight = 12826.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.078540 restraints weight = 9920.561| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.6862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8694 Z= 0.191 Angle : 0.677 7.377 11948 Z= 0.339 Chirality : 0.042 0.259 1482 Planarity : 0.005 0.058 1484 Dihedral : 4.490 29.264 1248 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.26), residues: 1182 helix: 0.96 (0.20), residues: 790 sheet: -3.02 (0.69), residues: 48 loop : -2.08 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 613 HIS 0.004 0.001 HIS B 615 PHE 0.025 0.001 PHE B 514 TYR 0.011 0.001 TYR A 377 ARG 0.003 0.000 ARG B 661 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1842.06 seconds wall clock time: 34 minutes 1.63 seconds (2041.63 seconds total)