Starting phenix.real_space_refine on Thu Feb 15 18:15:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wjn_32546/02_2024/7wjn_32546.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wjn_32546/02_2024/7wjn_32546.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wjn_32546/02_2024/7wjn_32546.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wjn_32546/02_2024/7wjn_32546.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wjn_32546/02_2024/7wjn_32546.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wjn_32546/02_2024/7wjn_32546.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians Mn 2 7.51 5 P 4 5.49 5 S 74 5.16 5 C 8458 2.51 5 N 2170 2.21 5 O 2346 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13054 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 808, 6487 Classifications: {'peptide': 808} Link IDs: {'PTRANS': 30, 'TRANS': 777} Chain breaks: 2 Chain: "B" Number of atoms: 6487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 808, 6487 Classifications: {'peptide': 808} Link IDs: {'PTRANS': 30, 'TRANS': 777} Chain breaks: 2 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {' MN': 1, 'UD1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {' MN': 1, 'UD1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.26, per 1000 atoms: 0.56 Number of scatterers: 13054 At special positions: 0 Unit cell: (118.77, 112.35, 127.33, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 2 24.99 S 74 16.00 P 4 15.00 O 2346 8.00 N 2170 7.00 C 8458 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.19 Conformation dependent library (CDL) restraints added in 2.3 seconds 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3040 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 4 sheets defined 66.8% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 23 through 37 Processing helix chain 'A' and resid 66 through 74 removed outlier: 3.835A pdb=" N ASP A 70 " --> pdb=" O SER A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 89 removed outlier: 3.764A pdb=" N SER A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 110 Processing helix chain 'A' and resid 112 through 134 removed outlier: 4.146A pdb=" N GLU A 132 " --> pdb=" O ALA A 128 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ARG A 133 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN A 134 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 163 Processing helix chain 'A' and resid 194 through 199 Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 221 through 227 Processing helix chain 'A' and resid 242 through 262 removed outlier: 3.940A pdb=" N LEU A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 282 Processing helix chain 'A' and resid 297 through 307 Processing helix chain 'A' and resid 311 through 319 Processing helix chain 'A' and resid 357 through 374 Processing helix chain 'A' and resid 390 through 403 removed outlier: 3.560A pdb=" N HIS A 403 " --> pdb=" O PHE A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 447 removed outlier: 3.562A pdb=" N SER A 427 " --> pdb=" O ASN A 423 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 479 removed outlier: 5.156A pdb=" N THR A 476 " --> pdb=" O ALA A 472 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LEU A 477 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 485 removed outlier: 3.666A pdb=" N LEU A 484 " --> pdb=" O GLU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 493 removed outlier: 3.695A pdb=" N GLY A 489 " --> pdb=" O GLY A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 505 Processing helix chain 'A' and resid 528 through 554 Processing helix chain 'A' and resid 555 through 560 Processing helix chain 'A' and resid 564 through 587 removed outlier: 3.650A pdb=" N PHE A 587 " --> pdb=" O ALA A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 605 Processing helix chain 'A' and resid 621 through 646 removed outlier: 4.235A pdb=" N VAL A 626 " --> pdb=" O LEU A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 681 Processing helix chain 'A' and resid 684 through 706 removed outlier: 5.302A pdb=" N VAL A 697 " --> pdb=" O LEU A 693 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N TYR A 698 " --> pdb=" O THR A 694 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE A 699 " --> pdb=" O VAL A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 720 removed outlier: 5.368A pdb=" N THR A 716 " --> pdb=" O PHE A 712 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N HIS A 717 " --> pdb=" O MET A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 735 Processing helix chain 'A' and resid 764 through 819 removed outlier: 3.581A pdb=" N PHE A 818 " --> pdb=" O PHE A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 853 Processing helix chain 'A' and resid 854 through 858 removed outlier: 3.779A pdb=" N GLY A 857 " --> pdb=" O GLY A 854 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ARG A 858 " --> pdb=" O LEU A 855 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 854 through 858' Processing helix chain 'B' and resid 24 through 37 Processing helix chain 'B' and resid 66 through 74 removed outlier: 3.835A pdb=" N ASP B 70 " --> pdb=" O SER B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 89 removed outlier: 3.763A pdb=" N SER B 80 " --> pdb=" O LYS B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 110 Processing helix chain 'B' and resid 112 through 134 removed outlier: 4.145A pdb=" N GLU B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ARG B 133 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN B 134 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 163 Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 210 through 214 Processing helix chain 'B' and resid 221 through 227 Processing helix chain 'B' and resid 242 through 262 removed outlier: 3.941A pdb=" N LEU B 246 " --> pdb=" O GLY B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 282 Processing helix chain 'B' and resid 297 through 307 Processing helix chain 'B' and resid 311 through 319 Processing helix chain 'B' and resid 357 through 374 Processing helix chain 'B' and resid 390 through 403 removed outlier: 3.561A pdb=" N HIS B 403 " --> pdb=" O PHE B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 447 removed outlier: 3.561A pdb=" N SER B 427 " --> pdb=" O ASN B 423 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE B 447 " --> pdb=" O LEU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 479 removed outlier: 5.156A pdb=" N THR B 476 " --> pdb=" O ALA B 472 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LEU B 477 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 485 removed outlier: 3.665A pdb=" N LEU B 484 " --> pdb=" O GLU B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 493 removed outlier: 3.694A pdb=" N GLY B 489 " --> pdb=" O GLY B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 505 Processing helix chain 'B' and resid 528 through 554 Processing helix chain 'B' and resid 555 through 560 Processing helix chain 'B' and resid 564 through 587 removed outlier: 3.650A pdb=" N PHE B 587 " --> pdb=" O ALA B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 605 Processing helix chain 'B' and resid 621 through 646 removed outlier: 4.235A pdb=" N VAL B 626 " --> pdb=" O LEU B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 681 Processing helix chain 'B' and resid 684 through 706 removed outlier: 5.301A pdb=" N VAL B 697 " --> pdb=" O LEU B 693 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N TYR B 698 " --> pdb=" O THR B 694 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE B 699 " --> pdb=" O VAL B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 720 removed outlier: 5.367A pdb=" N THR B 716 " --> pdb=" O PHE B 712 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N HIS B 717 " --> pdb=" O MET B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 735 Processing helix chain 'B' and resid 764 through 819 removed outlier: 3.580A pdb=" N PHE B 818 " --> pdb=" O PHE B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 824 through 853 Processing helix chain 'B' and resid 854 through 858 removed outlier: 3.779A pdb=" N GLY B 857 " --> pdb=" O GLY B 854 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ARG B 858 " --> pdb=" O LEU B 855 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 854 through 858' Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 56 removed outlier: 6.049A pdb=" N HIS B 175 " --> pdb=" O PRO B 205 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N ARG B 200 " --> pdb=" O THR B 332 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N THR B 332 " --> pdb=" O ARG B 200 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLN B 346 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS B 352 " --> pdb=" O ALA B 290 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU B 232 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N CYS B 287 " --> pdb=" O LEU B 232 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE B 234 " --> pdb=" O CYS B 287 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N VAL B 289 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE B 236 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N MET B 233 " --> pdb=" O ALA B 379 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N MET B 381 " --> pdb=" O MET B 233 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N CYS B 235 " --> pdb=" O MET B 381 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG B 461 " --> pdb=" O GLY B 406 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N GLY B 406 " --> pdb=" O ARG B 461 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N HIS B 514 " --> pdb=" O GLY B 406 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ALA B 408 " --> pdb=" O HIS B 514 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL B 516 " --> pdb=" O ALA B 408 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N GLY B 410 " --> pdb=" O VAL B 516 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ASP B 518 " --> pdb=" O GLY B 410 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N LEU B 412 " --> pdb=" O ASP B 518 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N VAL B 520 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 9.251A pdb=" N VAL B 414 " --> pdb=" O VAL B 520 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ARG B 522 " --> pdb=" O VAL B 414 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 386 through 387 removed outlier: 7.645A pdb=" N HIS A 514 " --> pdb=" O GLY A 406 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ALA A 408 " --> pdb=" O HIS A 514 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL A 516 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N GLY A 410 " --> pdb=" O VAL A 516 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ASP A 518 " --> pdb=" O GLY A 410 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N LEU A 412 " --> pdb=" O ASP A 518 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N VAL A 520 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 9.251A pdb=" N VAL A 414 " --> pdb=" O VAL A 520 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ARG A 522 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N GLY A 406 " --> pdb=" O ARG A 461 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG A 461 " --> pdb=" O GLY A 406 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N MET A 233 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N MET A 381 " --> pdb=" O MET A 233 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N CYS A 235 " --> pdb=" O MET A 381 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU A 232 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N CYS A 287 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE A 234 " --> pdb=" O CYS A 287 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N VAL A 289 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE A 236 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLN A 346 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS A 352 " --> pdb=" O ALA A 290 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N THR A 332 " --> pdb=" O ARG A 200 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ARG A 200 " --> pdb=" O THR A 332 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N HIS A 175 " --> pdb=" O PRO A 205 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL A 174 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N SER B 55 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LYS A 176 " --> pdb=" O SER B 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 336 through 337 Processing sheet with id=AA4, first strand: chain 'B' and resid 336 through 337 855 hydrogen bonds defined for protein. 2517 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: 4.45 Time building geometry restraints manager: 5.62 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: 4088 1.34 - 1.46: 2260 1.46 - 1.57: 6932 1.57 - 1.69: 6 1.69 - 1.81: 118 Bond restraints: 13404 Sorted by residual: bond pdb=" O1' UD1 A1001 " pdb=" PB UD1 A1001 " ideal model delta sigma weight residual 1.658 1.563 0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" O1' UD1 B1001 " pdb=" PB UD1 B1001 " ideal model delta sigma weight residual 1.658 1.563 0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" O5B UD1 B1001 " pdb=" PA UD1 B1001 " ideal model delta sigma weight residual 1.645 1.582 0.063 2.00e-02 2.50e+03 1.00e+01 bond pdb=" O5B UD1 A1001 " pdb=" PA UD1 A1001 " ideal model delta sigma weight residual 1.645 1.582 0.063 2.00e-02 2.50e+03 9.81e+00 bond pdb=" O3A UD1 B1001 " pdb=" PA UD1 B1001 " ideal model delta sigma weight residual 1.642 1.586 0.056 2.00e-02 2.50e+03 7.89e+00 ... (remaining 13399 not shown) Histogram of bond angle deviations from ideal: 99.99 - 107.46: 485 107.46 - 114.92: 7772 114.92 - 122.38: 8532 122.38 - 129.85: 1309 129.85 - 137.31: 108 Bond angle restraints: 18206 Sorted by residual: angle pdb=" O1' UD1 A1001 " pdb=" PB UD1 A1001 " pdb=" O3A UD1 A1001 " ideal model delta sigma weight residual 92.88 112.10 -19.22 3.00e+00 1.11e-01 4.10e+01 angle pdb=" O1' UD1 B1001 " pdb=" PB UD1 B1001 " pdb=" O3A UD1 B1001 " ideal model delta sigma weight residual 92.88 112.10 -19.22 3.00e+00 1.11e-01 4.10e+01 angle pdb=" PA UD1 B1001 " pdb=" O3A UD1 B1001 " pdb=" PB UD1 B1001 " ideal model delta sigma weight residual 122.84 137.31 -14.47 3.00e+00 1.11e-01 2.33e+01 angle pdb=" PA UD1 A1001 " pdb=" O3A UD1 A1001 " pdb=" PB UD1 A1001 " ideal model delta sigma weight residual 122.84 137.29 -14.45 3.00e+00 1.11e-01 2.32e+01 angle pdb=" C SER A 615 " pdb=" N GLU A 616 " pdb=" CA GLU A 616 " ideal model delta sigma weight residual 121.71 116.60 5.11 1.39e+00 5.18e-01 1.35e+01 ... (remaining 18201 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.93: 7316 14.93 - 29.86: 467 29.86 - 44.80: 89 44.80 - 59.73: 18 59.73 - 74.66: 6 Dihedral angle restraints: 7896 sinusoidal: 3162 harmonic: 4734 Sorted by residual: dihedral pdb=" CA GLN A 602 " pdb=" C GLN A 602 " pdb=" N GLY A 603 " pdb=" CA GLY A 603 " ideal model delta harmonic sigma weight residual 180.00 161.36 18.64 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA GLN B 602 " pdb=" C GLN B 602 " pdb=" N GLY B 603 " pdb=" CA GLY B 603 " ideal model delta harmonic sigma weight residual 180.00 161.43 18.57 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA ASN A 607 " pdb=" CB ASN A 607 " pdb=" CG ASN A 607 " pdb=" OD1 ASN A 607 " ideal model delta sinusoidal sigma weight residual -90.00 -153.48 63.48 2 2.00e+01 2.50e-03 9.61e+00 ... (remaining 7893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1623 0.047 - 0.095: 314 0.095 - 0.142: 63 0.142 - 0.189: 0 0.189 - 0.237: 2 Chirality restraints: 2002 Sorted by residual: chirality pdb=" C1B UD1 A1001 " pdb=" C2B UD1 A1001 " pdb=" N1 UD1 A1001 " pdb=" O4B UD1 A1001 " both_signs ideal model delta sigma weight residual False 2.20 2.44 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" C1B UD1 B1001 " pdb=" C2B UD1 B1001 " pdb=" N1 UD1 B1001 " pdb=" O4B UD1 B1001 " both_signs ideal model delta sigma weight residual False 2.20 2.44 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" C1' UD1 A1001 " pdb=" C2' UD1 A1001 " pdb=" O1' UD1 A1001 " pdb=" O5' UD1 A1001 " both_signs ideal model delta sigma weight residual False -2.21 -2.34 0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 1999 not shown) Planarity restraints: 2292 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 437 " -0.012 2.00e-02 2.50e+03 2.50e-02 6.23e+00 pdb=" C ASN A 437 " 0.043 2.00e-02 2.50e+03 pdb=" O ASN A 437 " -0.016 2.00e-02 2.50e+03 pdb=" N ILE A 438 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 437 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.17e+00 pdb=" C ASN B 437 " -0.043 2.00e-02 2.50e+03 pdb=" O ASN B 437 " 0.016 2.00e-02 2.50e+03 pdb=" N ILE B 438 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 598 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.09e+00 pdb=" C PHE A 598 " 0.039 2.00e-02 2.50e+03 pdb=" O PHE A 598 " -0.015 2.00e-02 2.50e+03 pdb=" N ILE A 599 " -0.013 2.00e-02 2.50e+03 ... (remaining 2289 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2328 2.77 - 3.30: 12056 3.30 - 3.83: 21093 3.83 - 4.37: 22778 4.37 - 4.90: 42685 Nonbonded interactions: 100940 Sorted by model distance: nonbonded pdb=" OH TYR A 52 " pdb=" OE2 GLU B 225 " model vdw 2.235 2.440 nonbonded pdb=" OD1 ASN A 109 " pdb=" NH2 ARG A 171 " model vdw 2.249 2.520 nonbonded pdb=" OD1 ASN B 109 " pdb=" NH2 ARG B 171 " model vdw 2.249 2.520 nonbonded pdb=" O GLU A 241 " pdb=" OG1 THR A 300 " model vdw 2.303 2.440 nonbonded pdb=" O GLU B 241 " pdb=" OG1 THR B 300 " model vdw 2.303 2.440 ... (remaining 100935 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.440 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: 0.020 Extract box with map and model: 6.100 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 36.900 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 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 : 0.004 0.095 13404 Z= 0.229 Angle : 0.586 19.220 18206 Z= 0.286 Chirality : 0.039 0.237 2002 Planarity : 0.004 0.043 2292 Dihedral : 10.438 74.658 4856 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.58 % Allowed : 5.33 % Favored : 94.09 % 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: 2.06 (0.22), residues: 1604 helix: 2.65 (0.17), residues: 1006 sheet: -0.26 (0.41), residues: 166 loop : -1.19 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 804 HIS 0.002 0.001 HIS B 578 PHE 0.012 0.001 PHE A 601 TYR 0.008 0.001 TYR A 365 ARG 0.003 0.000 ARG B 608 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 250 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 ILE cc_start: 0.6431 (OUTLIER) cc_final: 0.6085 (mt) REVERT: A 327 HIS cc_start: 0.8676 (OUTLIER) cc_final: 0.8239 (m-70) REVERT: A 738 GLN cc_start: 0.8155 (pm20) cc_final: 0.7368 (pm20) REVERT: A 785 ARG cc_start: 0.7497 (ttm110) cc_final: 0.7020 (ttp80) REVERT: B 183 ASN cc_start: 0.7150 (m-40) cc_final: 0.6804 (p0) REVERT: B 403 HIS cc_start: 0.6931 (t-90) cc_final: 0.6641 (t-90) REVERT: B 552 TRP cc_start: 0.7593 (t-100) cc_final: 0.5244 (m-10) REVERT: B 790 LYS cc_start: 0.8149 (tttt) cc_final: 0.7920 (tttp) outliers start: 8 outliers final: 5 residues processed: 258 average time/residue: 0.2556 time to fit residues: 94.6289 Evaluate side-chains 157 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 150 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 617 TYR Chi-restraints excluded: chain B residue 651 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.5980 chunk 121 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 81 optimal weight: 0.0980 chunk 64 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 93 optimal weight: 0.0470 chunk 145 optimal weight: 0.7980 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN A 478 ASN ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 372 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13404 Z= 0.150 Angle : 0.483 6.865 18206 Z= 0.254 Chirality : 0.037 0.132 2002 Planarity : 0.004 0.044 2292 Dihedral : 6.709 59.957 1898 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.31 % Allowed : 8.93 % Favored : 88.76 % 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: 2.19 (0.22), residues: 1604 helix: 2.69 (0.17), residues: 1014 sheet: -0.35 (0.42), residues: 170 loop : -0.93 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 804 HIS 0.002 0.000 HIS A 709 PHE 0.014 0.001 PHE B 397 TYR 0.008 0.001 TYR A 732 ARG 0.005 0.000 ARG B 199 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 163 time to evaluate : 1.550 Fit side-chains revert: symmetry clash REVERT: A 37 ILE cc_start: 0.6244 (OUTLIER) cc_final: 0.5901 (mt) REVERT: A 71 MET cc_start: 0.0818 (ttm) cc_final: 0.0337 (mtt) REVERT: A 738 GLN cc_start: 0.8290 (pm20) cc_final: 0.7390 (pm20) REVERT: A 785 ARG cc_start: 0.7514 (ttm110) cc_final: 0.7033 (ttp80) REVERT: B 75 MET cc_start: 0.3096 (mpp) cc_final: 0.2324 (tpp) REVERT: B 183 ASN cc_start: 0.7116 (m-40) cc_final: 0.6814 (p0) REVERT: B 229 ARG cc_start: 0.7657 (OUTLIER) cc_final: 0.7301 (mtm-85) REVERT: B 552 TRP cc_start: 0.7600 (t-100) cc_final: 0.5223 (m-10) REVERT: B 780 ARG cc_start: 0.7001 (mtm110) cc_final: 0.6494 (ptp-110) REVERT: B 790 LYS cc_start: 0.8102 (tttt) cc_final: 0.7884 (tttp) outliers start: 32 outliers final: 12 residues processed: 191 average time/residue: 0.2547 time to fit residues: 71.4957 Evaluate side-chains 160 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 146 time to evaluate : 2.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 651 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 0.1980 chunk 45 optimal weight: 0.0170 chunk 120 optimal weight: 2.9990 chunk 98 optimal weight: 0.0980 chunk 40 optimal weight: 2.9990 chunk 145 optimal weight: 0.7980 chunk 157 optimal weight: 0.9980 chunk 129 optimal weight: 0.0980 chunk 144 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 overall best weight: 0.2418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13404 Z= 0.128 Angle : 0.456 11.356 18206 Z= 0.237 Chirality : 0.036 0.130 2002 Planarity : 0.004 0.045 2292 Dihedral : 6.345 63.049 1892 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.80 % Allowed : 10.37 % Favored : 87.82 % 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: 2.40 (0.22), residues: 1604 helix: 2.95 (0.17), residues: 984 sheet: -0.39 (0.41), residues: 174 loop : -0.80 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP A 552 HIS 0.001 0.000 HIS A 578 PHE 0.014 0.001 PHE B 397 TYR 0.007 0.001 TYR B 125 ARG 0.006 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 167 time to evaluate : 1.719 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 ILE cc_start: 0.6420 (OUTLIER) cc_final: 0.6138 (mt) REVERT: A 71 MET cc_start: 0.0701 (ttm) cc_final: 0.0321 (mtt) REVERT: A 148 PHE cc_start: 0.7671 (m-10) cc_final: 0.7463 (m-10) REVERT: A 161 ILE cc_start: 0.8420 (tp) cc_final: 0.8096 (tt) REVERT: A 229 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.7297 (mtm-85) REVERT: A 371 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7523 (mm-30) REVERT: A 651 HIS cc_start: 0.6682 (OUTLIER) cc_final: 0.5284 (p-80) REVERT: A 738 GLN cc_start: 0.8258 (pm20) cc_final: 0.7352 (pm20) REVERT: A 785 ARG cc_start: 0.7495 (ttm110) cc_final: 0.6744 (ttp80) REVERT: B 133 ARG cc_start: 0.6034 (mtt180) cc_final: 0.5737 (mtm-85) REVERT: B 183 ASN cc_start: 0.7154 (m-40) cc_final: 0.6879 (p0) REVERT: B 229 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.7311 (mtm-85) REVERT: B 552 TRP cc_start: 0.7462 (t-100) cc_final: 0.5065 (m-10) REVERT: B 651 HIS cc_start: 0.6403 (OUTLIER) cc_final: 0.5326 (p-80) REVERT: B 790 LYS cc_start: 0.8101 (tttt) cc_final: 0.7874 (tttp) outliers start: 25 outliers final: 10 residues processed: 187 average time/residue: 0.2852 time to fit residues: 78.9211 Evaluate side-chains 158 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 143 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 617 TYR Chi-restraints excluded: chain B residue 651 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 146 optimal weight: 0.9990 chunk 154 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 138 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 GLN B 263 GLN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13404 Z= 0.251 Angle : 0.515 9.329 18206 Z= 0.271 Chirality : 0.039 0.138 2002 Planarity : 0.004 0.046 2292 Dihedral : 6.355 63.623 1892 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.61 % Favored : 94.26 % Rotamer: Outliers : 3.03 % Allowed : 11.02 % Favored : 85.95 % 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: 2.03 (0.22), residues: 1604 helix: 2.62 (0.17), residues: 1000 sheet: -0.47 (0.41), residues: 174 loop : -1.00 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 804 HIS 0.004 0.001 HIS A 578 PHE 0.014 0.001 PHE A 601 TYR 0.010 0.001 TYR A 219 ARG 0.007 0.001 ARG A 164 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 143 time to evaluate : 1.592 Fit side-chains REVERT: A 37 ILE cc_start: 0.6288 (OUTLIER) cc_final: 0.5953 (mt) REVERT: A 71 MET cc_start: 0.0829 (ttm) cc_final: 0.0420 (mtt) REVERT: A 229 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7343 (mtm-85) REVERT: A 371 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7590 (mm-30) REVERT: A 496 ASP cc_start: 0.7577 (t0) cc_final: 0.7368 (t0) REVERT: A 651 HIS cc_start: 0.6918 (OUTLIER) cc_final: 0.5485 (p-80) REVERT: A 738 GLN cc_start: 0.8423 (pm20) cc_final: 0.7398 (pm20) REVERT: B 75 MET cc_start: 0.3051 (mpp) cc_final: 0.2654 (tpt) REVERT: B 133 ARG cc_start: 0.6213 (mtt180) cc_final: 0.5959 (mtm-85) REVERT: B 183 ASN cc_start: 0.7239 (m-40) cc_final: 0.6956 (p0) REVERT: B 229 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.7293 (mtm-85) REVERT: B 371 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7707 (mt-10) REVERT: B 552 TRP cc_start: 0.7656 (t-100) cc_final: 0.5020 (m-10) REVERT: B 647 ASN cc_start: 0.8519 (p0) cc_final: 0.8304 (p0) REVERT: B 651 HIS cc_start: 0.6669 (OUTLIER) cc_final: 0.5478 (p-80) REVERT: B 780 ARG cc_start: 0.6830 (mtm110) cc_final: 0.6427 (ptp-110) outliers start: 42 outliers final: 29 residues processed: 172 average time/residue: 0.2574 time to fit residues: 65.0256 Evaluate side-chains 171 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 137 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 617 TYR Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 263 GLN Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 617 TYR Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 848 VAL Chi-restraints excluded: chain B residue 852 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 138 optimal weight: 0.0010 chunk 39 optimal weight: 0.9980 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 GLN B 263 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13404 Z= 0.218 Angle : 0.498 10.848 18206 Z= 0.260 Chirality : 0.038 0.132 2002 Planarity : 0.004 0.047 2292 Dihedral : 6.261 63.324 1892 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.05 % Favored : 94.83 % Rotamer: Outliers : 2.95 % Allowed : 12.03 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.22), residues: 1604 helix: 2.57 (0.17), residues: 1000 sheet: -0.41 (0.42), residues: 174 loop : -1.01 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 804 HIS 0.003 0.001 HIS B 578 PHE 0.013 0.001 PHE A 601 TYR 0.010 0.001 TYR A 219 ARG 0.006 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 141 time to evaluate : 1.367 Fit side-chains revert: symmetry clash REVERT: A 37 ILE cc_start: 0.6309 (OUTLIER) cc_final: 0.5968 (mt) REVERT: A 161 ILE cc_start: 0.8532 (tp) cc_final: 0.8207 (tt) REVERT: A 229 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.7361 (mtm-85) REVERT: A 371 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7664 (mm-30) REVERT: A 496 ASP cc_start: 0.7603 (t0) cc_final: 0.7350 (t0) REVERT: A 651 HIS cc_start: 0.6914 (OUTLIER) cc_final: 0.5549 (p-80) REVERT: A 738 GLN cc_start: 0.8418 (pm20) cc_final: 0.7245 (pm20) REVERT: B 183 ASN cc_start: 0.7201 (m-40) cc_final: 0.6960 (p0) REVERT: B 229 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.7324 (mtm-85) REVERT: B 371 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7717 (mt-10) REVERT: B 552 TRP cc_start: 0.7661 (t-100) cc_final: 0.5075 (m-10) REVERT: B 651 HIS cc_start: 0.6736 (OUTLIER) cc_final: 0.5575 (p-80) outliers start: 41 outliers final: 26 residues processed: 169 average time/residue: 0.2429 time to fit residues: 60.2127 Evaluate side-chains 163 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 132 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 617 TYR Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 617 TYR Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 671 SER Chi-restraints excluded: chain B residue 852 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 154 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 GLN B 607 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13404 Z= 0.218 Angle : 0.499 8.757 18206 Z= 0.262 Chirality : 0.038 0.129 2002 Planarity : 0.004 0.047 2292 Dihedral : 6.189 62.616 1892 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.31 % Allowed : 11.96 % Favored : 84.73 % 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: 1.97 (0.22), residues: 1604 helix: 2.55 (0.17), residues: 1000 sheet: -0.39 (0.42), residues: 174 loop : -1.03 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 804 HIS 0.003 0.001 HIS B 578 PHE 0.013 0.001 PHE A 601 TYR 0.012 0.001 TYR B 492 ARG 0.007 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 142 time to evaluate : 1.500 Fit side-chains revert: symmetry clash REVERT: A 37 ILE cc_start: 0.6317 (OUTLIER) cc_final: 0.5981 (mt) REVERT: A 161 ILE cc_start: 0.8507 (tp) cc_final: 0.8193 (tt) REVERT: A 229 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.7370 (mtm-85) REVERT: A 496 ASP cc_start: 0.7615 (t0) cc_final: 0.7353 (t0) REVERT: A 651 HIS cc_start: 0.6850 (OUTLIER) cc_final: 0.5784 (p-80) REVERT: A 738 GLN cc_start: 0.8355 (pm20) cc_final: 0.7108 (pm20) REVERT: B 183 ASN cc_start: 0.7189 (m-40) cc_final: 0.6965 (p0) REVERT: B 229 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.7339 (mtm-85) REVERT: B 371 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7720 (mt-10) REVERT: B 552 TRP cc_start: 0.7617 (t-100) cc_final: 0.4860 (m-10) REVERT: B 647 ASN cc_start: 0.8561 (p0) cc_final: 0.8275 (p0) REVERT: B 651 HIS cc_start: 0.6819 (OUTLIER) cc_final: 0.5542 (p-80) REVERT: B 780 ARG cc_start: 0.6806 (mtm110) cc_final: 0.6406 (ptp-110) outliers start: 46 outliers final: 36 residues processed: 175 average time/residue: 0.2489 time to fit residues: 64.2397 Evaluate side-chains 178 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 137 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 617 TYR Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 851 HIS Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 617 TYR Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 671 SER Chi-restraints excluded: chain B residue 848 VAL Chi-restraints excluded: chain B residue 852 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 130 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 154 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 ASN B 263 GLN B 607 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13404 Z= 0.205 Angle : 0.499 10.686 18206 Z= 0.260 Chirality : 0.038 0.134 2002 Planarity : 0.004 0.046 2292 Dihedral : 6.105 61.911 1892 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.39 % Allowed : 12.46 % Favored : 84.15 % 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: 2.00 (0.22), residues: 1604 helix: 2.58 (0.17), residues: 1000 sheet: -0.37 (0.42), residues: 174 loop : -1.03 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 804 HIS 0.003 0.001 HIS B 578 PHE 0.014 0.001 PHE B 545 TYR 0.010 0.001 TYR A 492 ARG 0.007 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 135 time to evaluate : 1.721 Fit side-chains revert: symmetry clash REVERT: A 37 ILE cc_start: 0.6360 (OUTLIER) cc_final: 0.6042 (mt) REVERT: A 161 ILE cc_start: 0.8494 (tp) cc_final: 0.8187 (tt) REVERT: A 229 ARG cc_start: 0.7689 (OUTLIER) cc_final: 0.7367 (mtm-85) REVERT: A 496 ASP cc_start: 0.7659 (t0) cc_final: 0.7384 (t0) REVERT: A 651 HIS cc_start: 0.6814 (OUTLIER) cc_final: 0.5972 (p-80) REVERT: A 738 GLN cc_start: 0.8342 (pm20) cc_final: 0.7111 (pm20) REVERT: B 183 ASN cc_start: 0.7279 (m-40) cc_final: 0.7023 (p0) REVERT: B 229 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.7366 (mtm-85) REVERT: B 238 MET cc_start: 0.8658 (ttp) cc_final: 0.8330 (ptm) REVERT: B 371 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7690 (mt-10) REVERT: B 552 TRP cc_start: 0.7667 (t-100) cc_final: 0.5000 (m-10) REVERT: B 647 ASN cc_start: 0.8561 (p0) cc_final: 0.8288 (p0) REVERT: B 651 HIS cc_start: 0.6769 (OUTLIER) cc_final: 0.5509 (p-80) REVERT: B 667 MET cc_start: 0.7958 (tpp) cc_final: 0.7583 (tpt) outliers start: 47 outliers final: 34 residues processed: 170 average time/residue: 0.2339 time to fit residues: 59.6473 Evaluate side-chains 170 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 131 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 617 TYR Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 851 HIS Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 617 TYR Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 671 SER Chi-restraints excluded: chain B residue 848 VAL Chi-restraints excluded: chain B residue 851 HIS Chi-restraints excluded: chain B residue 852 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 121 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 ASN ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13404 Z= 0.192 Angle : 0.494 9.629 18206 Z= 0.257 Chirality : 0.038 0.130 2002 Planarity : 0.004 0.046 2292 Dihedral : 6.026 61.274 1892 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.24 % Allowed : 12.46 % Favored : 84.29 % 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: 2.02 (0.22), residues: 1604 helix: 2.60 (0.17), residues: 1000 sheet: -0.40 (0.42), residues: 174 loop : -1.03 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 804 HIS 0.002 0.001 HIS B 578 PHE 0.015 0.001 PHE A 545 TYR 0.009 0.001 TYR A 492 ARG 0.007 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 135 time to evaluate : 1.538 Fit side-chains REVERT: A 37 ILE cc_start: 0.6513 (OUTLIER) cc_final: 0.6209 (mt) REVERT: A 229 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.7371 (mtm-85) REVERT: A 238 MET cc_start: 0.8677 (ttp) cc_final: 0.8409 (ptm) REVERT: A 325 GLN cc_start: 0.7747 (mm-40) cc_final: 0.7523 (mm-40) REVERT: A 496 ASP cc_start: 0.7655 (t0) cc_final: 0.7386 (t0) REVERT: A 651 HIS cc_start: 0.6856 (OUTLIER) cc_final: 0.6061 (p-80) REVERT: A 738 GLN cc_start: 0.8334 (pm20) cc_final: 0.7129 (pm20) REVERT: B 75 MET cc_start: 0.3485 (mpp) cc_final: 0.2999 (tpt) REVERT: B 183 ASN cc_start: 0.7288 (m-40) cc_final: 0.7032 (p0) REVERT: B 229 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.7334 (mtm-85) REVERT: B 238 MET cc_start: 0.8729 (ttp) cc_final: 0.8406 (ptm) REVERT: B 371 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7670 (mt-10) REVERT: B 552 TRP cc_start: 0.7661 (t-100) cc_final: 0.5002 (m-10) REVERT: B 647 ASN cc_start: 0.8570 (p0) cc_final: 0.8341 (p0) REVERT: B 651 HIS cc_start: 0.6853 (OUTLIER) cc_final: 0.5683 (p-80) outliers start: 45 outliers final: 32 residues processed: 169 average time/residue: 0.2405 time to fit residues: 60.8651 Evaluate side-chains 166 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 129 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 617 TYR Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 851 HIS Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 617 TYR Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 851 HIS Chi-restraints excluded: chain B residue 852 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 0.6980 chunk 147 optimal weight: 5.9990 chunk 134 optimal weight: 0.6980 chunk 143 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 135 optimal weight: 0.7980 chunk 94 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 ASN B 263 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13404 Z= 0.191 Angle : 0.501 8.928 18206 Z= 0.261 Chirality : 0.038 0.131 2002 Planarity : 0.004 0.046 2292 Dihedral : 5.996 60.746 1892 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.10 % Allowed : 12.97 % Favored : 83.93 % 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: 2.06 (0.22), residues: 1604 helix: 2.66 (0.17), residues: 992 sheet: -0.40 (0.41), residues: 174 loop : -1.00 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 804 HIS 0.002 0.001 HIS B 578 PHE 0.014 0.001 PHE B 545 TYR 0.011 0.001 TYR B 492 ARG 0.007 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 136 time to evaluate : 1.509 Fit side-chains REVERT: A 37 ILE cc_start: 0.6507 (OUTLIER) cc_final: 0.6212 (mt) REVERT: A 229 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.7370 (mtm-85) REVERT: A 496 ASP cc_start: 0.7656 (t0) cc_final: 0.7387 (t0) REVERT: A 651 HIS cc_start: 0.6809 (OUTLIER) cc_final: 0.5991 (p-80) REVERT: A 738 GLN cc_start: 0.8330 (pm20) cc_final: 0.7121 (pm20) REVERT: B 75 MET cc_start: 0.3711 (mpp) cc_final: 0.3074 (tpt) REVERT: B 183 ASN cc_start: 0.7294 (m-40) cc_final: 0.7042 (p0) REVERT: B 229 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.7363 (mtm-85) REVERT: B 238 MET cc_start: 0.8721 (ttp) cc_final: 0.8398 (ptm) REVERT: B 371 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7676 (mt-10) REVERT: B 552 TRP cc_start: 0.7643 (t-100) cc_final: 0.4837 (m-10) REVERT: B 651 HIS cc_start: 0.6822 (OUTLIER) cc_final: 0.5754 (p-80) REVERT: B 667 MET cc_start: 0.7899 (tpp) cc_final: 0.7568 (tpt) outliers start: 43 outliers final: 34 residues processed: 167 average time/residue: 0.2336 time to fit residues: 59.1108 Evaluate side-chains 167 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 128 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 617 TYR Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 851 HIS Chi-restraints excluded: chain A residue 852 THR Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 263 GLN Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 617 TYR Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 671 SER Chi-restraints excluded: chain B residue 848 VAL Chi-restraints excluded: chain B residue 851 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 159 optimal weight: 0.4980 chunk 146 optimal weight: 0.5980 chunk 126 optimal weight: 0.7980 chunk 13 optimal weight: 0.0270 chunk 98 optimal weight: 0.0030 chunk 77 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.3848 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 ASN B 263 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13404 Z= 0.144 Angle : 0.492 10.498 18206 Z= 0.254 Chirality : 0.037 0.136 2002 Planarity : 0.004 0.044 2292 Dihedral : 5.873 60.227 1892 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.52 % Allowed : 13.76 % Favored : 83.72 % 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: 2.18 (0.22), residues: 1604 helix: 2.75 (0.17), residues: 992 sheet: -0.38 (0.41), residues: 174 loop : -0.93 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 804 HIS 0.003 0.000 HIS A 327 PHE 0.017 0.001 PHE B 545 TYR 0.008 0.001 TYR A 239 ARG 0.008 0.000 ARG A 199 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 133 time to evaluate : 1.560 Fit side-chains REVERT: A 37 ILE cc_start: 0.6549 (OUTLIER) cc_final: 0.6244 (mt) REVERT: A 229 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.7338 (mtm-85) REVERT: A 238 MET cc_start: 0.8683 (ttp) cc_final: 0.8390 (ptm) REVERT: A 371 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7613 (mm-30) REVERT: A 496 ASP cc_start: 0.7622 (t0) cc_final: 0.7351 (t0) REVERT: A 651 HIS cc_start: 0.6694 (OUTLIER) cc_final: 0.5874 (p-80) REVERT: A 738 GLN cc_start: 0.8298 (pm20) cc_final: 0.7099 (pm20) REVERT: A 785 ARG cc_start: 0.7834 (ttm110) cc_final: 0.7142 (ttp80) REVERT: B 75 MET cc_start: 0.3632 (mpp) cc_final: 0.2991 (tpt) REVERT: B 183 ASN cc_start: 0.7268 (m-40) cc_final: 0.7032 (p0) REVERT: B 238 MET cc_start: 0.8667 (ttp) cc_final: 0.8334 (ptm) REVERT: B 552 TRP cc_start: 0.7653 (t-100) cc_final: 0.4929 (m-10) REVERT: B 651 HIS cc_start: 0.6774 (OUTLIER) cc_final: 0.5810 (p-80) REVERT: B 667 MET cc_start: 0.7855 (tpp) cc_final: 0.7516 (tpt) outliers start: 35 outliers final: 24 residues processed: 160 average time/residue: 0.2421 time to fit residues: 57.9835 Evaluate side-chains 153 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 125 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 617 TYR Chi-restraints excluded: chain A residue 651 HIS Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 851 HIS Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 617 TYR Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 851 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 127 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 130 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 ASN B 129 ASN B 263 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.145755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.112753 restraints weight = 15638.422| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.88 r_work: 0.3119 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13404 Z= 0.256 Angle : 0.538 10.115 18206 Z= 0.280 Chirality : 0.039 0.137 2002 Planarity : 0.004 0.047 2292 Dihedral : 6.049 59.774 1892 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.45 % Allowed : 13.83 % Favored : 83.72 % 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: 1.94 (0.22), residues: 1604 helix: 2.53 (0.17), residues: 1002 sheet: -0.47 (0.41), residues: 174 loop : -1.04 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 804 HIS 0.003 0.001 HIS B 578 PHE 0.028 0.001 PHE A 487 TYR 0.010 0.001 TYR A 492 ARG 0.006 0.000 ARG A 199 =============================================================================== Job complete usr+sys time: 2812.76 seconds wall clock time: 52 minutes 1.35 seconds (3121.35 seconds total)