Starting phenix.real_space_refine on Thu Feb 15 15:44:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ems_28263/02_2024/8ems_28263_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ems_28263/02_2024/8ems_28263.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ems_28263/02_2024/8ems_28263.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ems_28263/02_2024/8ems_28263.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ems_28263/02_2024/8ems_28263_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ems_28263/02_2024/8ems_28263_updated.pdb" } resolution = 2.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.055 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 56 5.16 5 C 8154 2.51 5 N 2152 2.21 5 O 2324 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: 12688 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 6329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 780, 6329 Classifications: {'peptide': 780} Link IDs: {'PTRANS': 29, 'TRANS': 750} Chain breaks: 3 Chain: "A" Number of atoms: 6329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 780, 6329 Classifications: {'peptide': 780} Link IDs: {'PTRANS': 29, 'TRANS': 750} Chain breaks: 3 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 6.44, per 1000 atoms: 0.51 Number of scatterers: 12688 At special positions: 0 Unit cell: (130.68, 102.6, 79.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 56 16.00 P 2 15.00 O 2324 8.00 N 2152 7.00 C 8154 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.59 Conformation dependent library (CDL) restraints added in 2.2 seconds 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2956 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 74 helices and 14 sheets defined 50.1% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.03 Creating SS restraints... Processing helix chain 'B' and resid 25 through 36 Processing helix chain 'B' and resid 48 through 71 removed outlier: 4.555A pdb=" N GLY B 65 " --> pdb=" O ASP B 61 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ARG B 66 " --> pdb=" O HIS B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 101 Processing helix chain 'B' and resid 106 through 115 Processing helix chain 'B' and resid 119 through 125 Processing helix chain 'B' and resid 135 through 149 Processing helix chain 'B' and resid 194 through 196 No H-bonds generated for 'chain 'B' and resid 194 through 196' Processing helix chain 'B' and resid 263 through 273 removed outlier: 3.870A pdb=" N ARG B 269 " --> pdb=" O ALA B 265 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ASN B 270 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LEU B 271 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA B 272 " --> pdb=" O ASP B 268 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU B 273 " --> pdb=" O ARG B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 312 Processing helix chain 'B' and resid 326 through 328 No H-bonds generated for 'chain 'B' and resid 326 through 328' Processing helix chain 'B' and resid 341 through 354 removed outlier: 4.650A pdb=" N LEU B 344 " --> pdb=" O HIS B 341 " (cutoff:3.500A) Proline residue: B 347 - end of helix removed outlier: 3.598A pdb=" N VAL B 354 " --> pdb=" O ARG B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 371 Processing helix chain 'B' and resid 381 through 383 No H-bonds generated for 'chain 'B' and resid 381 through 383' Processing helix chain 'B' and resid 389 through 395 Processing helix chain 'B' and resid 397 through 417 removed outlier: 3.645A pdb=" N LEU B 417 " --> pdb=" O ARG B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 427 Processing helix chain 'B' and resid 441 through 447 Processing helix chain 'B' and resid 457 through 465 Processing helix chain 'B' and resid 469 through 474 removed outlier: 3.678A pdb=" N LEU B 474 " --> pdb=" O ASP B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 491 No H-bonds generated for 'chain 'B' and resid 488 through 491' Processing helix chain 'B' and resid 497 through 507 removed outlier: 3.520A pdb=" N LYS B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 524 removed outlier: 3.591A pdb=" N SER B 523 " --> pdb=" O LYS B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 553 removed outlier: 3.603A pdb=" N THR B 551 " --> pdb=" O GLN B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 592 Processing helix chain 'B' and resid 614 through 631 Processing helix chain 'B' and resid 650 through 659 removed outlier: 3.639A pdb=" N LYS B 655 " --> pdb=" O SER B 651 " (cutoff:3.500A) Proline residue: B 658 - end of helix Processing helix chain 'B' and resid 677 through 683 Processing helix chain 'B' and resid 694 through 703 removed outlier: 3.709A pdb=" N VAL B 697 " --> pdb=" O GLY B 694 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA B 703 " --> pdb=" O ALA B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 707 No H-bonds generated for 'chain 'B' and resid 705 through 707' Processing helix chain 'B' and resid 715 through 724 Processing helix chain 'B' and resid 728 through 733 Processing helix chain 'B' and resid 736 through 746 Processing helix chain 'B' and resid 759 through 766 Processing helix chain 'B' and resid 774 through 791 removed outlier: 5.280A pdb=" N GLU B 778 " --> pdb=" O ALA B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 806 Processing helix chain 'B' and resid 809 through 811 No H-bonds generated for 'chain 'B' and resid 809 through 811' Processing helix chain 'B' and resid 813 through 823 Processing helix chain 'A' and resid 25 through 36 Processing helix chain 'A' and resid 48 through 71 removed outlier: 4.555A pdb=" N GLY A 65 " --> pdb=" O ASP A 61 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ARG A 66 " --> pdb=" O HIS A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 101 Processing helix chain 'A' and resid 106 through 115 Processing helix chain 'A' and resid 119 through 125 Processing helix chain 'A' and resid 135 through 149 Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 263 through 273 removed outlier: 3.870A pdb=" N ARG A 269 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ASN A 270 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N LEU A 271 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA A 272 " --> pdb=" O ASP A 268 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 312 Processing helix chain 'A' and resid 326 through 328 No H-bonds generated for 'chain 'A' and resid 326 through 328' Processing helix chain 'A' and resid 341 through 354 removed outlier: 4.650A pdb=" N LEU A 344 " --> pdb=" O HIS A 341 " (cutoff:3.500A) Proline residue: A 347 - end of helix removed outlier: 3.598A pdb=" N VAL A 354 " --> pdb=" O ARG A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 371 Processing helix chain 'A' and resid 381 through 383 No H-bonds generated for 'chain 'A' and resid 381 through 383' Processing helix chain 'A' and resid 389 through 395 Processing helix chain 'A' and resid 397 through 417 removed outlier: 3.644A pdb=" N LEU A 417 " --> pdb=" O ARG A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 427 Processing helix chain 'A' and resid 441 through 447 Processing helix chain 'A' and resid 457 through 465 Processing helix chain 'A' and resid 469 through 474 removed outlier: 3.678A pdb=" N LEU A 474 " --> pdb=" O ASP A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 491 No H-bonds generated for 'chain 'A' and resid 488 through 491' Processing helix chain 'A' and resid 497 through 507 removed outlier: 3.520A pdb=" N LYS A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 524 removed outlier: 3.591A pdb=" N SER A 523 " --> pdb=" O LYS A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 553 removed outlier: 3.602A pdb=" N THR A 551 " --> pdb=" O GLN A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 592 Processing helix chain 'A' and resid 614 through 631 Processing helix chain 'A' and resid 650 through 659 removed outlier: 3.640A pdb=" N LYS A 655 " --> pdb=" O SER A 651 " (cutoff:3.500A) Proline residue: A 658 - end of helix Processing helix chain 'A' and resid 677 through 683 Processing helix chain 'A' and resid 694 through 703 removed outlier: 3.709A pdb=" N VAL A 697 " --> pdb=" O GLY A 694 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA A 703 " --> pdb=" O ALA A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 707 No H-bonds generated for 'chain 'A' and resid 705 through 707' Processing helix chain 'A' and resid 715 through 724 Processing helix chain 'A' and resid 728 through 733 Processing helix chain 'A' and resid 736 through 746 Processing helix chain 'A' and resid 759 through 766 Processing helix chain 'A' and resid 774 through 791 removed outlier: 5.280A pdb=" N GLU A 778 " --> pdb=" O ALA A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 806 Processing helix chain 'A' and resid 809 through 811 No H-bonds generated for 'chain 'A' and resid 809 through 811' Processing helix chain 'A' and resid 813 through 823 Processing sheet with id= A, first strand: chain 'B' and resid 198 through 202 removed outlier: 7.922A pdb=" N ALA B 154 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N THR B 240 " --> pdb=" O ALA B 154 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL B 82 " --> pdb=" O TYR B 155 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N TYR B 157 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TYR B 84 " --> pdb=" O TYR B 157 " (cutoff:3.500A) removed outlier: 8.905A pdb=" N ILE B 159 " --> pdb=" O TYR B 84 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 167 through 171 Processing sheet with id= C, first strand: chain 'B' and resid 205 through 208 Processing sheet with id= D, first strand: chain 'B' and resid 386 through 388 Processing sheet with id= E, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.673A pdb=" N GLY B 454 " --> pdb=" O GLN B 480 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 562 through 567 removed outlier: 3.771A pdb=" N LYS B 641 " --> pdb=" O ARG B 601 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 662 through 665 removed outlier: 6.986A pdb=" N LEU B 687 " --> pdb=" O SER B 663 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N GLN B 665 " --> pdb=" O LEU B 687 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE B 689 " --> pdb=" O GLN B 665 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'A' and resid 198 through 202 removed outlier: 7.922A pdb=" N ALA A 154 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N THR A 240 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL A 82 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N TYR A 157 " --> pdb=" O VAL A 82 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TYR A 84 " --> pdb=" O TYR A 157 " (cutoff:3.500A) removed outlier: 8.906A pdb=" N ILE A 159 " --> pdb=" O TYR A 84 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 167 through 171 Processing sheet with id= J, first strand: chain 'A' and resid 205 through 208 Processing sheet with id= K, first strand: chain 'A' and resid 386 through 388 Processing sheet with id= L, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.672A pdb=" N GLY A 454 " --> pdb=" O GLN A 480 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 562 through 567 removed outlier: 3.771A pdb=" N LYS A 641 " --> pdb=" O ARG A 601 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 662 through 665 removed outlier: 6.986A pdb=" N LEU A 687 " --> pdb=" O SER A 663 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N GLN A 665 " --> pdb=" O LEU A 687 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE A 689 " --> pdb=" O GLN A 665 " (cutoff:3.500A) No H-bonds generated for sheet with id= N 548 hydrogen bonds defined for protein. 1428 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: 4.15 Time building geometry restraints manager: 5.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4110 1.34 - 1.46: 2483 1.46 - 1.58: 6269 1.58 - 1.69: 2 1.69 - 1.81: 100 Bond restraints: 12964 Sorted by residual: bond pdb=" CA VAL B 59 " pdb=" C VAL B 59 " ideal model delta sigma weight residual 1.524 1.535 -0.012 1.30e-02 5.92e+03 8.18e-01 bond pdb=" CA VAL A 59 " pdb=" C VAL A 59 " ideal model delta sigma weight residual 1.524 1.535 -0.012 1.30e-02 5.92e+03 8.18e-01 bond pdb=" N GLN B 480 " pdb=" CA GLN B 480 " ideal model delta sigma weight residual 1.456 1.469 -0.013 1.44e-02 4.82e+03 8.05e-01 bond pdb=" CA LYS B 482 " pdb=" C LYS B 482 " ideal model delta sigma weight residual 1.522 1.532 -0.010 1.14e-02 7.69e+03 8.00e-01 bond pdb=" N GLN A 480 " pdb=" CA GLN A 480 " ideal model delta sigma weight residual 1.456 1.468 -0.012 1.44e-02 4.82e+03 7.05e-01 ... (remaining 12959 not shown) Histogram of bond angle deviations from ideal: 100.38 - 107.11: 341 107.11 - 113.84: 7222 113.84 - 120.57: 5197 120.57 - 127.29: 4628 127.29 - 134.02: 140 Bond angle restraints: 17528 Sorted by residual: angle pdb=" C ILE A 165 " pdb=" N PHE A 166 " pdb=" CA PHE A 166 " ideal model delta sigma weight residual 121.54 127.46 -5.92 1.91e+00 2.74e-01 9.61e+00 angle pdb=" C ILE B 165 " pdb=" N PHE B 166 " pdb=" CA PHE B 166 " ideal model delta sigma weight residual 121.54 127.44 -5.90 1.91e+00 2.74e-01 9.55e+00 angle pdb=" N ARG B 292 " pdb=" CA ARG B 292 " pdb=" CB ARG B 292 " ideal model delta sigma weight residual 114.17 110.71 3.46 1.14e+00 7.69e-01 9.22e+00 angle pdb=" N ARG A 292 " pdb=" CA ARG A 292 " pdb=" CB ARG A 292 " ideal model delta sigma weight residual 114.17 110.73 3.44 1.14e+00 7.69e-01 9.09e+00 angle pdb=" N GLN A 480 " pdb=" CA GLN A 480 " pdb=" C GLN A 480 " ideal model delta sigma weight residual 109.18 113.23 -4.05 1.42e+00 4.96e-01 8.12e+00 ... (remaining 17523 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.62: 7027 16.62 - 33.24: 617 33.24 - 49.86: 132 49.86 - 66.48: 12 66.48 - 83.10: 10 Dihedral angle restraints: 7798 sinusoidal: 3224 harmonic: 4574 Sorted by residual: dihedral pdb=" CA ILE B 165 " pdb=" C ILE B 165 " pdb=" N PHE B 166 " pdb=" CA PHE B 166 " ideal model delta harmonic sigma weight residual 180.00 160.09 19.91 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA ILE A 165 " pdb=" C ILE A 165 " pdb=" N PHE A 166 " pdb=" CA PHE A 166 " ideal model delta harmonic sigma weight residual 180.00 160.12 19.88 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA ARG B 292 " pdb=" C ARG B 292 " pdb=" N LEU B 293 " pdb=" CA LEU B 293 " ideal model delta harmonic sigma weight residual 180.00 162.21 17.79 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 7795 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1771 0.072 - 0.144: 147 0.144 - 0.216: 2 0.216 - 0.288: 0 0.288 - 0.360: 2 Chirality restraints: 1922 Sorted by residual: chirality pdb=" CB ILE B 165 " pdb=" CA ILE B 165 " pdb=" CG1 ILE B 165 " pdb=" CG2 ILE B 165 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" CB ILE A 165 " pdb=" CA ILE A 165 " pdb=" CG1 ILE A 165 " pdb=" CG2 ILE A 165 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CA LYS B 482 " pdb=" N LYS B 482 " pdb=" C LYS B 482 " pdb=" CB LYS B 482 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.04e-01 ... (remaining 1919 not shown) Planarity restraints: 2240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 292 " 0.008 2.00e-02 2.50e+03 1.56e-02 2.42e+00 pdb=" C ARG B 292 " -0.027 2.00e-02 2.50e+03 pdb=" O ARG B 292 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU B 293 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 292 " -0.008 2.00e-02 2.50e+03 1.55e-02 2.41e+00 pdb=" C ARG A 292 " 0.027 2.00e-02 2.50e+03 pdb=" O ARG A 292 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU A 293 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 90 " 0.013 2.00e-02 2.50e+03 1.01e-02 2.05e+00 pdb=" CG TYR A 90 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR A 90 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR A 90 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 90 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 90 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 90 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 90 " 0.001 2.00e-02 2.50e+03 ... (remaining 2237 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1564 2.75 - 3.29: 12348 3.29 - 3.83: 21792 3.83 - 4.36: 27002 4.36 - 4.90: 45102 Nonbonded interactions: 107808 Sorted by model distance: nonbonded pdb=" O PHE B 311 " pdb=" OG SER B 314 " model vdw 2.217 2.440 nonbonded pdb=" O PHE A 311 " pdb=" OG SER A 314 " model vdw 2.218 2.440 nonbonded pdb=" OE1 GLN A 71 " pdb=" OG1 THR A 240 " model vdw 2.224 2.440 nonbonded pdb=" OE1 GLN B 71 " pdb=" OG1 THR B 240 " model vdw 2.225 2.440 nonbonded pdb=" OE1 GLU A 664 " pdb=" OH TYR A 780 " model vdw 2.278 2.440 ... (remaining 107803 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.410 Check model and map are aligned: 0.180 Set scattering table: 0.130 Process input model: 36.560 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.070 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:13.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 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 : 0.003 0.033 12964 Z= 0.171 Angle : 0.530 5.922 17528 Z= 0.294 Chirality : 0.042 0.360 1922 Planarity : 0.003 0.040 2240 Dihedral : 13.281 83.104 4842 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.15 % Allowed : 0.00 % Favored : 99.85 % 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: -0.04 (0.21), residues: 1544 helix: 0.99 (0.18), residues: 828 sheet: -0.70 (0.38), residues: 166 loop : -1.33 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 491 HIS 0.002 0.001 HIS A 614 PHE 0.015 0.001 PHE A 298 TYR 0.025 0.002 TYR A 90 ARG 0.003 0.000 ARG A 309 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 214 time to evaluate : 1.474 Fit side-chains REVERT: B 764 MET cc_start: 0.7291 (tmm) cc_final: 0.7063 (tmt) REVERT: B 827 VAL cc_start: 0.7493 (t) cc_final: 0.7105 (m) REVERT: A 547 GLN cc_start: 0.7020 (mm-40) cc_final: 0.6782 (mm-40) REVERT: A 827 VAL cc_start: 0.7492 (t) cc_final: 0.7111 (m) outliers start: 2 outliers final: 0 residues processed: 216 average time/residue: 1.3008 time to fit residues: 304.8230 Evaluate side-chains 176 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.6980 chunk 118 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 141 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12964 Z= 0.316 Angle : 0.637 6.920 17528 Z= 0.333 Chirality : 0.046 0.224 1922 Planarity : 0.005 0.054 2240 Dihedral : 5.288 46.673 1702 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.91 % Allowed : 11.07 % Favored : 87.02 % 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: -0.75 (0.20), residues: 1544 helix: 0.20 (0.17), residues: 830 sheet: -0.72 (0.35), residues: 190 loop : -1.40 (0.25), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 365 HIS 0.005 0.001 HIS A 34 PHE 0.020 0.002 PHE B 285 TYR 0.026 0.003 TYR B 297 ARG 0.004 0.001 ARG A 489 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 173 time to evaluate : 1.436 Fit side-chains REVERT: B 90 TYR cc_start: 0.7110 (OUTLIER) cc_final: 0.6475 (t80) REVERT: B 506 LYS cc_start: 0.6807 (OUTLIER) cc_final: 0.6503 (mptt) REVERT: B 764 MET cc_start: 0.7483 (tmm) cc_final: 0.7191 (tmt) REVERT: B 827 VAL cc_start: 0.7620 (t) cc_final: 0.7228 (m) REVERT: A 90 TYR cc_start: 0.7112 (OUTLIER) cc_final: 0.6479 (t80) REVERT: A 506 LYS cc_start: 0.6792 (OUTLIER) cc_final: 0.6481 (mptt) outliers start: 26 outliers final: 15 residues processed: 181 average time/residue: 1.2317 time to fit residues: 243.5638 Evaluate side-chains 180 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 161 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 90 TYR Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 506 LYS Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 635 MET Chi-restraints excluded: chain B residue 717 ASP Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 717 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12964 Z= 0.263 Angle : 0.591 6.210 17528 Z= 0.309 Chirality : 0.043 0.163 1922 Planarity : 0.004 0.036 2240 Dihedral : 5.230 49.362 1702 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.35 % Allowed : 13.49 % Favored : 84.16 % 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: -0.77 (0.20), residues: 1544 helix: 0.15 (0.17), residues: 844 sheet: -0.65 (0.35), residues: 190 loop : -1.41 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 365 HIS 0.004 0.001 HIS A 399 PHE 0.017 0.002 PHE B 166 TYR 0.024 0.002 TYR B 297 ARG 0.004 0.000 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 166 time to evaluate : 1.452 Fit side-chains REVERT: B 90 TYR cc_start: 0.6985 (OUTLIER) cc_final: 0.6370 (t80) REVERT: B 764 MET cc_start: 0.7519 (tmm) cc_final: 0.7205 (tmt) REVERT: A 90 TYR cc_start: 0.6985 (OUTLIER) cc_final: 0.6376 (t80) REVERT: A 827 VAL cc_start: 0.7667 (t) cc_final: 0.7287 (m) outliers start: 32 outliers final: 20 residues processed: 178 average time/residue: 1.1215 time to fit residues: 219.6657 Evaluate side-chains 174 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 152 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 90 TYR Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 635 MET Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 717 ASP Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 717 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 0.6980 chunk 106 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 142 optimal weight: 0.6980 chunk 150 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12964 Z= 0.184 Angle : 0.510 5.426 17528 Z= 0.268 Chirality : 0.040 0.139 1922 Planarity : 0.003 0.032 2240 Dihedral : 4.951 49.326 1702 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.98 % Allowed : 14.81 % Favored : 83.21 % 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: -0.22 (0.21), residues: 1544 helix: 0.59 (0.18), residues: 828 sheet: -0.37 (0.37), residues: 190 loop : -1.13 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 365 HIS 0.005 0.001 HIS A 399 PHE 0.015 0.001 PHE A 298 TYR 0.020 0.002 TYR B 297 ARG 0.003 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 157 time to evaluate : 1.437 Fit side-chains REVERT: B 29 LYS cc_start: 0.7336 (OUTLIER) cc_final: 0.6762 (mttp) REVERT: B 764 MET cc_start: 0.7496 (tmm) cc_final: 0.7174 (tmt) REVERT: B 827 VAL cc_start: 0.7620 (t) cc_final: 0.7224 (m) REVERT: A 29 LYS cc_start: 0.7334 (OUTLIER) cc_final: 0.6756 (mttp) REVERT: A 827 VAL cc_start: 0.7620 (t) cc_final: 0.7216 (m) outliers start: 27 outliers final: 14 residues processed: 169 average time/residue: 1.1936 time to fit residues: 221.1393 Evaluate side-chains 169 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 153 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 90 TYR Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 635 MET Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 635 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 112 optimal weight: 0.0670 chunk 62 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 38 optimal weight: 0.3980 overall best weight: 1.6722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 ASN ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12964 Z= 0.312 Angle : 0.635 6.513 17528 Z= 0.330 Chirality : 0.045 0.177 1922 Planarity : 0.005 0.044 2240 Dihedral : 5.336 52.384 1702 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.27 % Allowed : 16.06 % Favored : 81.67 % 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: -0.69 (0.21), residues: 1544 helix: 0.10 (0.17), residues: 842 sheet: -0.56 (0.36), residues: 190 loop : -1.18 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 365 HIS 0.004 0.001 HIS A 34 PHE 0.019 0.002 PHE B 285 TYR 0.044 0.003 TYR B 297 ARG 0.006 0.001 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 161 time to evaluate : 1.443 Fit side-chains REVERT: B 29 LYS cc_start: 0.7384 (OUTLIER) cc_final: 0.6803 (mttp) REVERT: B 165 ILE cc_start: 0.5815 (OUTLIER) cc_final: 0.5124 (tp) REVERT: B 205 LYS cc_start: 0.6636 (mmmt) cc_final: 0.6135 (mptt) REVERT: B 764 MET cc_start: 0.7569 (tmm) cc_final: 0.7226 (tmt) REVERT: A 29 LYS cc_start: 0.7384 (OUTLIER) cc_final: 0.6808 (mttp) REVERT: A 165 ILE cc_start: 0.5820 (OUTLIER) cc_final: 0.5129 (tp) REVERT: A 205 LYS cc_start: 0.6632 (mmmt) cc_final: 0.6132 (mptt) outliers start: 31 outliers final: 22 residues processed: 174 average time/residue: 1.1327 time to fit residues: 216.9557 Evaluate side-chains 179 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 153 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 90 TYR Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 635 MET Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 789 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 0.8980 chunk 135 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12964 Z= 0.244 Angle : 0.575 7.038 17528 Z= 0.300 Chirality : 0.042 0.180 1922 Planarity : 0.004 0.035 2240 Dihedral : 5.219 53.071 1702 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.79 % Allowed : 16.50 % Favored : 80.72 % 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: -0.57 (0.21), residues: 1544 helix: 0.22 (0.18), residues: 840 sheet: -0.48 (0.37), residues: 190 loop : -1.16 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 365 HIS 0.003 0.001 HIS B 34 PHE 0.016 0.002 PHE B 166 TYR 0.038 0.002 TYR A 297 ARG 0.005 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 163 time to evaluate : 1.454 Fit side-chains REVERT: B 29 LYS cc_start: 0.7353 (OUTLIER) cc_final: 0.6772 (mttp) REVERT: B 165 ILE cc_start: 0.5790 (OUTLIER) cc_final: 0.5115 (tp) REVERT: B 506 LYS cc_start: 0.6880 (OUTLIER) cc_final: 0.6659 (mptt) REVERT: B 764 MET cc_start: 0.7558 (tmm) cc_final: 0.7206 (tmt) REVERT: B 827 VAL cc_start: 0.7671 (t) cc_final: 0.7297 (m) REVERT: A 29 LYS cc_start: 0.7354 (OUTLIER) cc_final: 0.6772 (mttp) REVERT: A 165 ILE cc_start: 0.5794 (OUTLIER) cc_final: 0.5120 (tp) REVERT: A 506 LYS cc_start: 0.6872 (OUTLIER) cc_final: 0.6608 (mptt) REVERT: A 792 MET cc_start: 0.5664 (OUTLIER) cc_final: 0.5390 (mmp) REVERT: A 827 VAL cc_start: 0.7667 (t) cc_final: 0.7309 (m) outliers start: 38 outliers final: 23 residues processed: 182 average time/residue: 1.1678 time to fit residues: 233.4905 Evaluate side-chains 184 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 154 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 90 TYR Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 506 LYS Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 635 MET Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 722 ASP Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 789 GLN Chi-restraints excluded: chain A residue 792 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 150 optimal weight: 0.9980 chunk 94 optimal weight: 0.0470 chunk 91 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 93 optimal weight: 0.3980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 ASN ** B 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 ASN ** A 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 12964 Z= 0.188 Angle : 0.516 6.022 17528 Z= 0.272 Chirality : 0.041 0.175 1922 Planarity : 0.003 0.032 2240 Dihedral : 4.969 52.963 1702 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.49 % Allowed : 17.30 % Favored : 80.21 % 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: -0.20 (0.21), residues: 1544 helix: 0.53 (0.18), residues: 834 sheet: -0.22 (0.38), residues: 190 loop : -1.04 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 365 HIS 0.006 0.001 HIS B 399 PHE 0.015 0.001 PHE A 298 TYR 0.014 0.001 TYR B 90 ARG 0.004 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 161 time to evaluate : 1.516 Fit side-chains REVERT: B 29 LYS cc_start: 0.7310 (OUTLIER) cc_final: 0.6737 (mttp) REVERT: B 165 ILE cc_start: 0.5722 (OUTLIER) cc_final: 0.5060 (tp) REVERT: B 197 MET cc_start: 0.6893 (ttt) cc_final: 0.6621 (tmm) REVERT: B 205 LYS cc_start: 0.6538 (mmmt) cc_final: 0.6217 (mmmm) REVERT: B 506 LYS cc_start: 0.6863 (OUTLIER) cc_final: 0.6611 (mptt) REVERT: B 764 MET cc_start: 0.7522 (tmm) cc_final: 0.7261 (tmt) REVERT: B 778 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6456 (mp0) REVERT: B 792 MET cc_start: 0.5932 (OUTLIER) cc_final: 0.5648 (mmp) REVERT: B 827 VAL cc_start: 0.7634 (t) cc_final: 0.7250 (m) REVERT: A 29 LYS cc_start: 0.7314 (OUTLIER) cc_final: 0.6741 (mttp) REVERT: A 197 MET cc_start: 0.6868 (ttt) cc_final: 0.6597 (tmm) REVERT: A 205 LYS cc_start: 0.6495 (mmmt) cc_final: 0.6179 (mmmm) REVERT: A 506 LYS cc_start: 0.6855 (OUTLIER) cc_final: 0.6585 (mptt) REVERT: A 778 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6456 (mp0) REVERT: A 827 VAL cc_start: 0.7635 (t) cc_final: 0.7258 (m) outliers start: 34 outliers final: 20 residues processed: 180 average time/residue: 1.1960 time to fit residues: 236.3733 Evaluate side-chains 188 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 160 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 90 TYR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 350 MET Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 506 LYS Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 635 MET Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 792 MET Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 350 MET Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 789 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 95 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 136 optimal weight: 0.3980 chunk 144 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 ASN ** B 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12964 Z= 0.192 Angle : 0.519 5.986 17528 Z= 0.273 Chirality : 0.041 0.179 1922 Planarity : 0.003 0.032 2240 Dihedral : 4.933 53.277 1702 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.42 % Allowed : 17.89 % Favored : 79.69 % 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: -0.12 (0.21), residues: 1544 helix: 0.59 (0.18), residues: 834 sheet: -0.17 (0.38), residues: 190 loop : -1.00 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 365 HIS 0.003 0.001 HIS A 399 PHE 0.017 0.001 PHE B 298 TYR 0.014 0.001 TYR B 90 ARG 0.004 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 163 time to evaluate : 1.441 Fit side-chains REVERT: B 29 LYS cc_start: 0.7304 (OUTLIER) cc_final: 0.6731 (mttp) REVERT: B 165 ILE cc_start: 0.5724 (OUTLIER) cc_final: 0.5058 (tp) REVERT: B 171 ARG cc_start: 0.6615 (mpt-90) cc_final: 0.6374 (mpt-90) REVERT: B 197 MET cc_start: 0.6835 (ttt) cc_final: 0.6607 (tmm) REVERT: B 506 LYS cc_start: 0.6829 (OUTLIER) cc_final: 0.6556 (mptt) REVERT: B 764 MET cc_start: 0.7513 (tmm) cc_final: 0.7255 (tmt) REVERT: B 778 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.6591 (mp0) REVERT: B 827 VAL cc_start: 0.7638 (t) cc_final: 0.7250 (m) REVERT: A 29 LYS cc_start: 0.7304 (OUTLIER) cc_final: 0.6726 (mttp) REVERT: A 165 ILE cc_start: 0.5750 (OUTLIER) cc_final: 0.5019 (tp) REVERT: A 171 ARG cc_start: 0.6611 (mpt-90) cc_final: 0.6371 (mpt-90) REVERT: A 197 MET cc_start: 0.6838 (ttt) cc_final: 0.6608 (tmm) REVERT: A 506 LYS cc_start: 0.6824 (OUTLIER) cc_final: 0.6553 (mptt) REVERT: A 778 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6567 (mp0) REVERT: A 827 VAL cc_start: 0.7639 (t) cc_final: 0.7252 (m) outliers start: 33 outliers final: 18 residues processed: 183 average time/residue: 1.1985 time to fit residues: 240.4367 Evaluate side-chains 183 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 157 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 90 TYR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 506 LYS Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 635 MET Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 778 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.6980 chunk 140 optimal weight: 9.9990 chunk 144 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 92 optimal weight: 0.0980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 12964 Z= 0.247 Angle : 0.575 5.948 17528 Z= 0.301 Chirality : 0.043 0.189 1922 Planarity : 0.004 0.033 2240 Dihedral : 5.112 54.554 1702 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.71 % Allowed : 17.82 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.21), residues: 1544 helix: 0.37 (0.18), residues: 834 sheet: -0.32 (0.37), residues: 190 loop : -1.09 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 365 HIS 0.003 0.001 HIS A 399 PHE 0.016 0.002 PHE B 166 TYR 0.018 0.002 TYR B 90 ARG 0.005 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 162 time to evaluate : 1.427 Fit side-chains REVERT: B 29 LYS cc_start: 0.7329 (OUTLIER) cc_final: 0.6752 (mttp) REVERT: B 95 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.6989 (tp) REVERT: B 165 ILE cc_start: 0.5798 (OUTLIER) cc_final: 0.5117 (tp) REVERT: B 205 LYS cc_start: 0.6600 (mmmt) cc_final: 0.6279 (mmmm) REVERT: B 506 LYS cc_start: 0.6848 (OUTLIER) cc_final: 0.6578 (mptt) REVERT: B 764 MET cc_start: 0.7549 (tmm) cc_final: 0.7278 (tmt) REVERT: B 778 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6577 (mp0) REVERT: B 827 VAL cc_start: 0.7666 (t) cc_final: 0.7284 (m) REVERT: A 29 LYS cc_start: 0.7319 (OUTLIER) cc_final: 0.6751 (mttp) REVERT: A 95 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.6974 (tp) REVERT: A 165 ILE cc_start: 0.5754 (OUTLIER) cc_final: 0.5035 (tp) REVERT: A 197 MET cc_start: 0.6823 (ttt) cc_final: 0.6610 (tmm) REVERT: A 205 LYS cc_start: 0.6612 (mmmt) cc_final: 0.6296 (mmmm) REVERT: A 506 LYS cc_start: 0.6836 (OUTLIER) cc_final: 0.6568 (mptt) REVERT: A 778 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6578 (mp0) REVERT: A 827 VAL cc_start: 0.7666 (t) cc_final: 0.7287 (m) outliers start: 37 outliers final: 25 residues processed: 182 average time/residue: 1.1966 time to fit residues: 239.0017 Evaluate side-chains 195 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 160 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 90 TYR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 506 LYS Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 635 MET Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 789 GLN Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 778 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 0.3980 chunk 90 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 12964 Z= 0.210 Angle : 0.545 6.692 17528 Z= 0.286 Chirality : 0.042 0.188 1922 Planarity : 0.003 0.032 2240 Dihedral : 5.023 54.437 1702 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.35 % Allowed : 18.11 % Favored : 79.55 % 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: -0.24 (0.21), residues: 1544 helix: 0.48 (0.18), residues: 834 sheet: -0.21 (0.38), residues: 190 loop : -1.05 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 365 HIS 0.002 0.001 HIS A 399 PHE 0.015 0.001 PHE A 298 TYR 0.016 0.002 TYR B 90 ARG 0.004 0.000 ARG A 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 156 time to evaluate : 1.477 Fit side-chains REVERT: B 29 LYS cc_start: 0.7274 (OUTLIER) cc_final: 0.6711 (mttp) REVERT: B 205 LYS cc_start: 0.6595 (mmmt) cc_final: 0.6278 (mmmm) REVERT: B 506 LYS cc_start: 0.6839 (OUTLIER) cc_final: 0.6566 (mptt) REVERT: B 764 MET cc_start: 0.7536 (tmm) cc_final: 0.7269 (tmt) REVERT: B 778 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6589 (mp0) REVERT: B 827 VAL cc_start: 0.7649 (t) cc_final: 0.7267 (m) REVERT: A 29 LYS cc_start: 0.7300 (OUTLIER) cc_final: 0.6733 (mttp) REVERT: A 165 ILE cc_start: 0.5703 (OUTLIER) cc_final: 0.4993 (tp) REVERT: A 197 MET cc_start: 0.6950 (ttt) cc_final: 0.6586 (tmm) REVERT: A 205 LYS cc_start: 0.6592 (mmmt) cc_final: 0.6277 (mmmm) REVERT: A 506 LYS cc_start: 0.6822 (OUTLIER) cc_final: 0.6568 (mptt) REVERT: A 778 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6565 (mp0) REVERT: A 827 VAL cc_start: 0.7648 (t) cc_final: 0.7266 (m) outliers start: 32 outliers final: 25 residues processed: 177 average time/residue: 1.1959 time to fit residues: 232.2036 Evaluate side-chains 186 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 154 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 90 TYR Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 506 LYS Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 635 MET Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 789 GLN Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 778 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 114 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.193574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.176687 restraints weight = 12879.243| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 1.15 r_work: 0.3981 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3880 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 12964 Z= 0.211 Angle : 0.545 7.056 17528 Z= 0.287 Chirality : 0.042 0.188 1922 Planarity : 0.003 0.032 2240 Dihedral : 5.010 54.521 1702 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.42 % Allowed : 18.04 % Favored : 79.55 % 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: -0.23 (0.21), residues: 1544 helix: 0.49 (0.18), residues: 834 sheet: -0.21 (0.38), residues: 190 loop : -1.04 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 365 HIS 0.002 0.001 HIS B 450 PHE 0.016 0.002 PHE B 166 TYR 0.015 0.002 TYR B 90 ARG 0.004 0.000 ARG A 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4382.48 seconds wall clock time: 78 minutes 55.69 seconds (4735.69 seconds total)