Starting phenix.real_space_refine on Tue Mar 19 22:50:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stn_25434/03_2024/7stn_25434_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stn_25434/03_2024/7stn_25434.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stn_25434/03_2024/7stn_25434.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stn_25434/03_2024/7stn_25434.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stn_25434/03_2024/7stn_25434_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stn_25434/03_2024/7stn_25434_trim_updated.pdb" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 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 P 8 5.49 5 S 56 5.16 5 C 8480 2.51 5 N 2062 2.21 5 O 2326 1.98 5 H 12256 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 991": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 991": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 25188 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 12400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 790, 12400 Classifications: {'peptide': 790} Link IDs: {'PTRANS': 24, 'TRANS': 765} Chain breaks: 3 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 5, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 60 Chain: "B" Number of atoms: 12400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 790, 12400 Classifications: {'peptide': 790} Link IDs: {'PTRANS': 24, 'TRANS': 765} Chain breaks: 3 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 5, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 60 Chain: "A" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 231 Unusual residues: {'3PE': 5, 'BGI': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 59 Chain: "B" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 157 Unusual residues: {'3PE': 3, 'BGI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Time building chain proxies: 11.07, per 1000 atoms: 0.44 Number of scatterers: 25188 At special positions: 0 Unit cell: (135, 76.68, 120.96, 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) S 56 16.00 P 8 15.00 O 2326 8.00 N 2062 7.00 C 8480 6.00 H 12256 1.00 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: 20.91 Conformation dependent library (CDL) restraints added in 2.6 seconds 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2976 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 62 helices and 6 sheets defined 53.4% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.31 Creating SS restraints... Processing helix chain 'A' and resid 147 through 154 removed outlier: 3.663A pdb=" N ARG A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 245 No H-bonds generated for 'chain 'A' and resid 243 through 245' Processing helix chain 'A' and resid 255 through 259 Processing helix chain 'A' and resid 275 through 278 No H-bonds generated for 'chain 'A' and resid 275 through 278' Processing helix chain 'A' and resid 300 through 302 No H-bonds generated for 'chain 'A' and resid 300 through 302' Processing helix chain 'A' and resid 323 through 342 Processing helix chain 'A' and resid 354 through 356 No H-bonds generated for 'chain 'A' and resid 354 through 356' Processing helix chain 'A' and resid 371 through 379 Processing helix chain 'A' and resid 440 through 450 Processing helix chain 'A' and resid 452 through 456 Processing helix chain 'A' and resid 474 through 484 Processing helix chain 'A' and resid 508 through 531 removed outlier: 4.747A pdb=" N LYS A 525 " --> pdb=" O ASN A 521 " (cutoff:3.500A) Proline residue: A 526 - end of helix Processing helix chain 'A' and resid 547 through 549 No H-bonds generated for 'chain 'A' and resid 547 through 549' Processing helix chain 'A' and resid 558 through 568 removed outlier: 4.002A pdb=" N GLY A 565 " --> pdb=" O LYS A 561 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLU A 566 " --> pdb=" O TYR A 562 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE A 567 " --> pdb=" O PHE A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 589 Processing helix chain 'A' and resid 594 through 601 removed outlier: 5.444A pdb=" N TYR A 600 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 612 Processing helix chain 'A' and resid 637 through 660 removed outlier: 4.138A pdb=" N ARG A 646 " --> pdb=" O LEU A 642 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TRP A 647 " --> pdb=" O GLN A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 666 Processing helix chain 'A' and resid 672 through 693 Processing helix chain 'A' and resid 695 through 711 removed outlier: 3.600A pdb=" N LEU A 710 " --> pdb=" O LEU A 706 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY A 711 " --> pdb=" O THR A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 744 Processing helix chain 'A' and resid 751 through 786 Processing helix chain 'A' and resid 792 through 797 Processing helix chain 'A' and resid 799 through 821 removed outlier: 4.092A pdb=" N ALA A 807 " --> pdb=" O ASP A 803 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N THR A 808 " --> pdb=" O LEU A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 830 removed outlier: 4.166A pdb=" N THR A 830 " --> pdb=" O HIS A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 852 Proline residue: A 840 - end of helix removed outlier: 3.842A pdb=" N LEU A 846 " --> pdb=" O TYR A 842 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN A 847 " --> pdb=" O VAL A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 903 Processing helix chain 'A' and resid 919 through 945 Processing helix chain 'A' and resid 949 through 953 Processing helix chain 'A' and resid 958 through 1001 Processing helix chain 'B' and resid 147 through 154 removed outlier: 3.663A pdb=" N ARG B 154 " --> pdb=" O GLU B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 245 No H-bonds generated for 'chain 'B' and resid 243 through 245' Processing helix chain 'B' and resid 255 through 259 Processing helix chain 'B' and resid 275 through 278 No H-bonds generated for 'chain 'B' and resid 275 through 278' Processing helix chain 'B' and resid 300 through 302 No H-bonds generated for 'chain 'B' and resid 300 through 302' Processing helix chain 'B' and resid 323 through 342 Processing helix chain 'B' and resid 354 through 356 No H-bonds generated for 'chain 'B' and resid 354 through 356' Processing helix chain 'B' and resid 371 through 379 Processing helix chain 'B' and resid 440 through 450 Processing helix chain 'B' and resid 452 through 456 Processing helix chain 'B' and resid 474 through 484 Processing helix chain 'B' and resid 508 through 531 removed outlier: 4.747A pdb=" N LYS B 525 " --> pdb=" O ASN B 521 " (cutoff:3.500A) Proline residue: B 526 - end of helix Processing helix chain 'B' and resid 547 through 549 No H-bonds generated for 'chain 'B' and resid 547 through 549' Processing helix chain 'B' and resid 558 through 568 removed outlier: 4.002A pdb=" N GLY B 565 " --> pdb=" O LYS B 561 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLU B 566 " --> pdb=" O TYR B 562 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE B 567 " --> pdb=" O PHE B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 589 Processing helix chain 'B' and resid 594 through 601 removed outlier: 5.444A pdb=" N TYR B 600 " --> pdb=" O THR B 596 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 612 Processing helix chain 'B' and resid 637 through 660 removed outlier: 4.139A pdb=" N ARG B 646 " --> pdb=" O LEU B 642 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TRP B 647 " --> pdb=" O GLN B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 666 Processing helix chain 'B' and resid 672 through 693 Processing helix chain 'B' and resid 695 through 711 removed outlier: 3.600A pdb=" N LEU B 710 " --> pdb=" O LEU B 706 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY B 711 " --> pdb=" O THR B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 744 Processing helix chain 'B' and resid 751 through 786 Processing helix chain 'B' and resid 792 through 797 Processing helix chain 'B' and resid 799 through 821 removed outlier: 4.093A pdb=" N ALA B 807 " --> pdb=" O ASP B 803 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N THR B 808 " --> pdb=" O LEU B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 826 through 830 removed outlier: 4.165A pdb=" N THR B 830 " --> pdb=" O HIS B 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 852 Proline residue: B 840 - end of helix removed outlier: 3.842A pdb=" N LEU B 846 " --> pdb=" O TYR B 842 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN B 847 " --> pdb=" O VAL B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 903 Processing helix chain 'B' and resid 919 through 945 Processing helix chain 'B' and resid 949 through 953 Processing helix chain 'B' and resid 958 through 1001 Processing sheet with id= A, first strand: chain 'A' and resid 248 through 252 removed outlier: 7.964A pdb=" N PHE A 279 " --> pdb=" O THR A 405 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N THR A 405 " --> pdb=" O PHE A 279 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ILE A 357 " --> pdb=" O GLN A 429 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N LEU A 431 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL A 359 " --> pdb=" O LEU A 431 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N CYS A 433 " --> pdb=" O VAL A 359 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE A 361 " --> pdb=" O CYS A 433 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LYS A 435 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N SER A 363 " --> pdb=" O LYS A 435 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU A 312 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N CYS A 360 " --> pdb=" O LEU A 312 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE A 314 " --> pdb=" O CYS A 360 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N VAL A 362 " --> pdb=" O ILE A 314 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ILE A 316 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL A 462 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N THR A 317 " --> pdb=" O VAL A 462 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LEU A 464 " --> pdb=" O THR A 317 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N PHE A 541 " --> pdb=" O GLY A 493 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY A 493 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N LEU A 620 " --> pdb=" O ALA A 489 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ALA A 491 " --> pdb=" O LEU A 620 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ARG A 622 " --> pdb=" O ALA A 491 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLY A 493 " --> pdb=" O ARG A 622 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N CYS A 624 " --> pdb=" O GLY A 493 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 494 through 497 Processing sheet with id= C, first strand: chain 'A' and resid 409 through 413 removed outlier: 7.188A pdb=" N LYS A 419 " --> pdb=" O SER A 411 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 248 through 252 removed outlier: 7.964A pdb=" N PHE B 279 " --> pdb=" O THR B 405 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N THR B 405 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ILE B 357 " --> pdb=" O GLN B 429 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N LEU B 431 " --> pdb=" O ILE B 357 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL B 359 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N CYS B 433 " --> pdb=" O VAL B 359 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE B 361 " --> pdb=" O CYS B 433 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LYS B 435 " --> pdb=" O ILE B 361 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N SER B 363 " --> pdb=" O LYS B 435 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU B 312 " --> pdb=" O VAL B 358 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N CYS B 360 " --> pdb=" O LEU B 312 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE B 314 " --> pdb=" O CYS B 360 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N VAL B 362 " --> pdb=" O ILE B 314 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ILE B 316 " --> pdb=" O VAL B 362 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL B 462 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N THR B 317 " --> pdb=" O VAL B 462 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LEU B 464 " --> pdb=" O THR B 317 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N PHE B 541 " --> pdb=" O GLY B 493 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY B 493 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N LEU B 620 " --> pdb=" O ALA B 489 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ALA B 491 " --> pdb=" O LEU B 620 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ARG B 622 " --> pdb=" O ALA B 491 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLY B 493 " --> pdb=" O ARG B 622 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N CYS B 624 " --> pdb=" O GLY B 493 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 494 through 497 Processing sheet with id= F, first strand: chain 'B' and resid 409 through 413 removed outlier: 7.187A pdb=" N LYS B 419 " --> pdb=" O SER B 411 " (cutoff:3.500A) 628 hydrogen bonds defined for protein. 1788 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: 8.93 Time building geometry restraints manager: 21.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12232 1.03 - 1.23: 46 1.23 - 1.42: 5654 1.42 - 1.61: 7460 1.61 - 1.81: 106 Bond restraints: 25498 Sorted by residual: bond pdb=" C28 BGI B1202 " pdb=" N27 BGI B1202 " ideal model delta sigma weight residual 1.371 1.518 -0.147 2.00e-02 2.50e+03 5.44e+01 bond pdb=" C28 BGI A1202 " pdb=" N27 BGI A1202 " ideal model delta sigma weight residual 1.371 1.518 -0.147 2.00e-02 2.50e+03 5.39e+01 bond pdb=" C28 BGI A1202 " pdb=" N22 BGI A1202 " ideal model delta sigma weight residual 1.382 1.515 -0.133 2.00e-02 2.50e+03 4.40e+01 bond pdb=" C28 BGI B1202 " pdb=" N22 BGI B1202 " ideal model delta sigma weight residual 1.382 1.514 -0.132 2.00e-02 2.50e+03 4.33e+01 bond pdb=" C13 BGI B1202 " pdb=" N15 BGI B1202 " ideal model delta sigma weight residual 1.343 1.472 -0.129 2.00e-02 2.50e+03 4.19e+01 ... (remaining 25493 not shown) Histogram of bond angle deviations from ideal: 100.39 - 107.11: 392 107.11 - 113.83: 29184 113.83 - 120.54: 9336 120.54 - 127.26: 6611 127.26 - 133.98: 129 Bond angle restraints: 45652 Sorted by residual: angle pdb=" O12 3PE A1203 " pdb=" P 3PE A1203 " pdb=" O14 3PE A1203 " ideal model delta sigma weight residual 123.79 109.39 14.40 3.00e+00 1.11e-01 2.30e+01 angle pdb=" O12 3PE B1203 " pdb=" P 3PE B1203 " pdb=" O14 3PE B1203 " ideal model delta sigma weight residual 123.79 109.42 14.37 3.00e+00 1.11e-01 2.30e+01 angle pdb=" O12 3PE A1206 " pdb=" P 3PE A1206 " pdb=" O14 3PE A1206 " ideal model delta sigma weight residual 123.79 109.44 14.35 3.00e+00 1.11e-01 2.29e+01 angle pdb=" O12 3PE A1204 " pdb=" P 3PE A1204 " pdb=" O14 3PE A1204 " ideal model delta sigma weight residual 123.79 109.47 14.32 3.00e+00 1.11e-01 2.28e+01 angle pdb=" O12 3PE B1204 " pdb=" P 3PE B1204 " pdb=" O14 3PE B1204 " ideal model delta sigma weight residual 123.79 109.48 14.31 3.00e+00 1.11e-01 2.28e+01 ... (remaining 45647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 11595 17.84 - 35.69: 448 35.69 - 53.53: 195 53.53 - 71.38: 50 71.38 - 89.22: 14 Dihedral angle restraints: 12302 sinusoidal: 6540 harmonic: 5762 Sorted by residual: dihedral pdb=" N TYR B 699 " pdb=" CA TYR B 699 " pdb=" CB TYR B 699 " pdb=" CG TYR B 699 " ideal model delta sinusoidal sigma weight residual -60.00 -114.31 54.31 3 1.50e+01 4.44e-03 9.27e+00 dihedral pdb=" N TYR A 699 " pdb=" CA TYR A 699 " pdb=" CB TYR A 699 " pdb=" CG TYR A 699 " ideal model delta sinusoidal sigma weight residual -60.00 -114.28 54.28 3 1.50e+01 4.44e-03 9.27e+00 dihedral pdb=" CB ARG A 645 " pdb=" CG ARG A 645 " pdb=" CD ARG A 645 " pdb=" NE ARG A 645 " ideal model delta sinusoidal sigma weight residual 60.00 111.47 -51.47 3 1.50e+01 4.44e-03 9.02e+00 ... (remaining 12299 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1896 0.099 - 0.199: 74 0.199 - 0.298: 2 0.298 - 0.398: 0 0.398 - 0.497: 2 Chirality restraints: 1974 Sorted by residual: chirality pdb=" C19 BGI A1202 " pdb=" C18 BGI A1202 " pdb=" C20 BGI A1202 " pdb=" O30 BGI A1202 " both_signs ideal model delta sigma weight residual False 2.48 2.97 -0.50 2.00e-01 2.50e+01 6.18e+00 chirality pdb=" C19 BGI B1202 " pdb=" C18 BGI B1202 " pdb=" C20 BGI B1202 " pdb=" O30 BGI B1202 " both_signs ideal model delta sigma weight residual False 2.48 2.97 -0.49 2.00e-01 2.50e+01 6.12e+00 chirality pdb=" C18 BGI B1202 " pdb=" C17 BGI B1202 " pdb=" C19 BGI B1202 " pdb=" O31 BGI B1202 " both_signs ideal model delta sigma weight residual False 2.72 2.92 -0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 1971 not shown) Planarity restraints: 3738 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 945 " 0.010 2.00e-02 2.50e+03 1.93e-02 3.71e+00 pdb=" N GLU B 946 " -0.033 2.00e-02 2.50e+03 pdb=" CA GLU B 946 " 0.009 2.00e-02 2.50e+03 pdb=" H GLU B 946 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 945 " 0.010 2.00e-02 2.50e+03 1.91e-02 3.65e+00 pdb=" N GLU A 946 " -0.033 2.00e-02 2.50e+03 pdb=" CA GLU A 946 " 0.009 2.00e-02 2.50e+03 pdb=" H GLU A 946 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 943 " 0.009 2.00e-02 2.50e+03 1.73e-02 3.01e+00 pdb=" N VAL A 944 " -0.030 2.00e-02 2.50e+03 pdb=" CA VAL A 944 " 0.008 2.00e-02 2.50e+03 pdb=" H VAL A 944 " 0.013 2.00e-02 2.50e+03 ... (remaining 3735 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 1100 2.21 - 2.80: 50951 2.80 - 3.40: 67250 3.40 - 4.00: 87591 4.00 - 4.60: 139745 Nonbonded interactions: 346637 Sorted by model distance: nonbonded pdb=" OE1 GLU A 341 " pdb=" HG SER A 353 " model vdw 1.608 1.850 nonbonded pdb=" OE1 GLU B 341 " pdb=" HG SER B 353 " model vdw 1.608 1.850 nonbonded pdb=" O GLY B 453 " pdb=" H ASP B 457 " model vdw 1.650 1.850 nonbonded pdb=" O GLY A 453 " pdb=" H ASP A 457 " model vdw 1.651 1.850 nonbonded pdb=" O VAL B 665 " pdb=" HG SER B 668 " model vdw 1.670 1.850 ... (remaining 346632 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' and (resid 135 through 1002 or resid 1201 through 1204)) 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: 0.730 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: 0.360 Extract box with map and model: 3.740 Check model and map are aligned: 0.380 Set scattering table: 0.230 Process input model: 80.130 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.147 13242 Z= 0.405 Angle : 0.776 14.398 17896 Z= 0.323 Chirality : 0.042 0.497 1974 Planarity : 0.002 0.030 2214 Dihedral : 11.717 89.221 4922 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.15 % Allowed : 1.67 % Favored : 98.18 % 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: 2.30 (0.22), residues: 1564 helix: 3.01 (0.17), residues: 828 sheet: 1.12 (0.45), residues: 140 loop : -0.60 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 933 HIS 0.002 0.000 HIS A 679 PHE 0.008 0.001 PHE B 984 TYR 0.007 0.001 TYR B 731 ARG 0.002 0.000 ARG B 926 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 142 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 140 time to evaluate : 1.993 Fit side-chains REVERT: A 699 TYR cc_start: 0.8326 (OUTLIER) cc_final: 0.7690 (m-80) REVERT: B 699 TYR cc_start: 0.8306 (OUTLIER) cc_final: 0.7592 (m-80) outliers start: 2 outliers final: 0 residues processed: 142 average time/residue: 0.6723 time to fit residues: 133.1609 Evaluate side-chains 63 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 61 time to evaluate : 2.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain B residue 699 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 66 optimal weight: 30.0000 chunk 40 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 GLN A 797 GLN B 582 GLN B 598 ASN B 797 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13242 Z= 0.333 Angle : 0.508 5.518 17896 Z= 0.271 Chirality : 0.040 0.149 1974 Planarity : 0.003 0.038 2214 Dihedral : 11.478 91.911 2110 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.06 % Allowed : 4.47 % Favored : 94.47 % 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: 1.92 (0.21), residues: 1564 helix: 2.58 (0.17), residues: 846 sheet: 0.98 (0.46), residues: 140 loop : -0.69 (0.24), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 933 HIS 0.003 0.001 HIS A 679 PHE 0.016 0.001 PHE B 984 TYR 0.010 0.001 TYR B 151 ARG 0.004 0.001 ARG B 281 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 76 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 62 time to evaluate : 1.881 Fit side-chains REVERT: A 147 ASP cc_start: 0.5961 (OUTLIER) cc_final: 0.5607 (p0) REVERT: A 699 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.7801 (m-80) REVERT: B 699 TYR cc_start: 0.8476 (OUTLIER) cc_final: 0.7782 (m-80) outliers start: 14 outliers final: 9 residues processed: 74 average time/residue: 0.6285 time to fit residues: 66.3690 Evaluate side-chains 69 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 57 time to evaluate : 1.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 699 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 97 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 13242 Z= 0.226 Angle : 0.424 5.046 17896 Z= 0.228 Chirality : 0.038 0.151 1974 Planarity : 0.003 0.033 2214 Dihedral : 10.918 91.876 2110 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.83 % Allowed : 5.15 % Favored : 94.02 % 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: 2.04 (0.21), residues: 1564 helix: 2.72 (0.18), residues: 832 sheet: 1.03 (0.45), residues: 140 loop : -0.62 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 933 HIS 0.003 0.001 HIS B 679 PHE 0.012 0.001 PHE B 984 TYR 0.008 0.001 TYR B 842 ARG 0.007 0.000 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 69 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 58 time to evaluate : 2.043 Fit side-chains REVERT: A 699 TYR cc_start: 0.8439 (OUTLIER) cc_final: 0.7729 (m-80) REVERT: B 699 TYR cc_start: 0.8458 (OUTLIER) cc_final: 0.7777 (m-80) outliers start: 11 outliers final: 7 residues processed: 65 average time/residue: 0.6797 time to fit residues: 63.4889 Evaluate side-chains 65 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 56 time to evaluate : 2.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 715 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 68 optimal weight: 20.0000 chunk 96 optimal weight: 4.9990 chunk 144 optimal weight: 10.0000 chunk 152 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 136 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 429 GLN B 429 GLN ** B 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13242 Z= 0.351 Angle : 0.491 5.326 17896 Z= 0.268 Chirality : 0.040 0.156 1974 Planarity : 0.004 0.035 2214 Dihedral : 11.305 90.176 2110 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.29 % Allowed : 5.08 % Favored : 93.64 % 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: 1.62 (0.21), residues: 1564 helix: 2.33 (0.17), residues: 842 sheet: 0.86 (0.45), residues: 130 loop : -0.76 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 693 HIS 0.004 0.001 HIS B 679 PHE 0.018 0.002 PHE B 984 TYR 0.011 0.001 TYR A 404 ARG 0.004 0.000 ARG B 644 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 76 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 59 time to evaluate : 2.109 Fit side-chains REVERT: A 699 TYR cc_start: 0.8523 (OUTLIER) cc_final: 0.7826 (m-80) REVERT: B 699 TYR cc_start: 0.8529 (OUTLIER) cc_final: 0.7808 (m-80) outliers start: 17 outliers final: 12 residues processed: 71 average time/residue: 0.6455 time to fit residues: 65.4577 Evaluate side-chains 72 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 58 time to evaluate : 2.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 645 ARG Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 645 ARG Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 715 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 2.9990 chunk 86 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13242 Z= 0.266 Angle : 0.442 5.143 17896 Z= 0.241 Chirality : 0.038 0.150 1974 Planarity : 0.003 0.031 2214 Dihedral : 11.039 90.868 2110 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.98 % Allowed : 5.61 % Favored : 93.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.21), residues: 1564 helix: 2.50 (0.18), residues: 830 sheet: 0.90 (0.46), residues: 130 loop : -0.66 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 933 HIS 0.003 0.001 HIS A 679 PHE 0.014 0.001 PHE A 984 TYR 0.009 0.001 TYR B 842 ARG 0.002 0.000 ARG B 644 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 70 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 57 time to evaluate : 1.925 Fit side-chains REVERT: A 699 TYR cc_start: 0.8474 (OUTLIER) cc_final: 0.7768 (m-80) REVERT: B 699 TYR cc_start: 0.8471 (OUTLIER) cc_final: 0.7773 (m-80) outliers start: 13 outliers final: 11 residues processed: 65 average time/residue: 0.6694 time to fit residues: 61.3560 Evaluate side-chains 67 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 54 time to evaluate : 1.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 645 ARG Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 645 ARG Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 715 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 0.8980 chunk 137 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 80 optimal weight: 20.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13242 Z= 0.275 Angle : 0.447 5.107 17896 Z= 0.242 Chirality : 0.038 0.135 1974 Planarity : 0.003 0.033 2214 Dihedral : 10.944 89.329 2110 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.14 % Allowed : 5.68 % Favored : 93.18 % 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: 1.75 (0.21), residues: 1564 helix: 2.48 (0.18), residues: 830 sheet: 0.78 (0.46), residues: 130 loop : -0.67 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 933 HIS 0.003 0.001 HIS B 679 PHE 0.014 0.001 PHE B 984 TYR 0.009 0.001 TYR A 842 ARG 0.002 0.000 ARG B 644 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 72 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 57 time to evaluate : 2.072 Fit side-chains REVERT: A 699 TYR cc_start: 0.8490 (OUTLIER) cc_final: 0.7779 (m-80) REVERT: B 699 TYR cc_start: 0.8485 (OUTLIER) cc_final: 0.7778 (m-80) outliers start: 15 outliers final: 13 residues processed: 67 average time/residue: 0.6761 time to fit residues: 64.0452 Evaluate side-chains 70 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 55 time to evaluate : 1.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 645 ARG Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 645 ARG Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 715 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 128 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 152 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13242 Z= 0.285 Angle : 0.452 5.161 17896 Z= 0.245 Chirality : 0.038 0.130 1974 Planarity : 0.003 0.033 2214 Dihedral : 10.934 89.625 2110 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.06 % Allowed : 6.06 % Favored : 92.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.21), residues: 1564 helix: 2.45 (0.18), residues: 830 sheet: 0.67 (0.46), residues: 130 loop : -0.66 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 693 HIS 0.003 0.001 HIS B 679 PHE 0.014 0.001 PHE A 984 TYR 0.009 0.001 TYR B 842 ARG 0.003 0.000 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 69 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 55 time to evaluate : 1.961 Fit side-chains REVERT: A 699 TYR cc_start: 0.8491 (OUTLIER) cc_final: 0.7778 (m-80) REVERT: B 699 TYR cc_start: 0.8489 (OUTLIER) cc_final: 0.7783 (m-80) REVERT: B 800 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7539 (tt0) outliers start: 14 outliers final: 10 residues processed: 64 average time/residue: 0.6194 time to fit residues: 57.6094 Evaluate side-chains 68 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 55 time to evaluate : 1.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 645 ARG Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 645 ARG Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 800 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 94 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 96 optimal weight: 9.9990 chunk 103 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 13242 Z= 0.302 Angle : 0.458 5.162 17896 Z= 0.249 Chirality : 0.039 0.132 1974 Planarity : 0.003 0.033 2214 Dihedral : 10.971 89.063 2110 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.67 % Favored : 95.27 % Rotamer: Outliers : 1.36 % Allowed : 5.83 % Favored : 92.80 % 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: 1.65 (0.21), residues: 1564 helix: 2.39 (0.18), residues: 830 sheet: 0.54 (0.45), residues: 130 loop : -0.66 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 693 HIS 0.004 0.001 HIS B 679 PHE 0.015 0.001 PHE B 984 TYR 0.009 0.001 TYR A 842 ARG 0.003 0.000 ARG B 366 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 73 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 55 time to evaluate : 1.969 Fit side-chains REVERT: A 699 TYR cc_start: 0.8500 (OUTLIER) cc_final: 0.7788 (m-80) REVERT: A 800 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7546 (tt0) REVERT: B 699 TYR cc_start: 0.8498 (OUTLIER) cc_final: 0.7790 (m-80) REVERT: B 800 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7555 (tt0) outliers start: 18 outliers final: 13 residues processed: 68 average time/residue: 0.6117 time to fit residues: 60.9825 Evaluate side-chains 72 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 55 time to evaluate : 1.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 645 ARG Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 645 ARG Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 800 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 150 optimal weight: 0.9980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 13242 Z= 0.235 Angle : 0.432 5.057 17896 Z= 0.235 Chirality : 0.038 0.126 1974 Planarity : 0.003 0.033 2214 Dihedral : 10.749 89.407 2110 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.90 % Favored : 95.97 % Rotamer: Outliers : 1.29 % Allowed : 6.14 % Favored : 92.58 % 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: 1.77 (0.21), residues: 1564 helix: 2.51 (0.18), residues: 830 sheet: 0.57 (0.46), residues: 130 loop : -0.62 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 933 HIS 0.003 0.001 HIS B 679 PHE 0.013 0.001 PHE A 984 TYR 0.009 0.001 TYR B 684 ARG 0.002 0.000 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 72 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 55 time to evaluate : 2.201 Fit side-chains REVERT: A 699 TYR cc_start: 0.8480 (OUTLIER) cc_final: 0.7768 (m-80) REVERT: A 800 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7525 (tt0) REVERT: B 699 TYR cc_start: 0.8477 (OUTLIER) cc_final: 0.7774 (m-80) REVERT: B 800 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7545 (tt0) outliers start: 17 outliers final: 13 residues processed: 67 average time/residue: 0.6096 time to fit residues: 59.1079 Evaluate side-chains 72 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 55 time to evaluate : 1.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 645 ARG Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 645 ARG Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 800 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 91 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 157 optimal weight: 4.9990 chunk 144 optimal weight: 9.9990 chunk 125 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13242 Z= 0.256 Angle : 0.437 5.064 17896 Z= 0.237 Chirality : 0.038 0.125 1974 Planarity : 0.003 0.032 2214 Dihedral : 10.678 88.984 2110 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.54 % Favored : 95.33 % Rotamer: Outliers : 1.29 % Allowed : 6.14 % Favored : 92.58 % 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: 1.75 (0.21), residues: 1564 helix: 2.50 (0.18), residues: 830 sheet: 0.52 (0.46), residues: 130 loop : -0.63 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 933 HIS 0.003 0.001 HIS B 679 PHE 0.013 0.001 PHE B 984 TYR 0.008 0.001 TYR B 684 ARG 0.003 0.000 ARG B 366 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue LYS 501 is missing expected H atoms. Skipping. Residue SER 671 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 737 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue LEU 875 is missing expected H atoms. Skipping. Residue THR 880 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue VAL 915 is missing expected H atoms. Skipping. Residue THR 916 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 72 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 55 time to evaluate : 2.130 Fit side-chains REVERT: A 699 TYR cc_start: 0.8487 (OUTLIER) cc_final: 0.7775 (m-80) REVERT: B 699 TYR cc_start: 0.8482 (OUTLIER) cc_final: 0.7779 (m-80) REVERT: B 800 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7542 (tt0) outliers start: 17 outliers final: 14 residues processed: 67 average time/residue: 0.6341 time to fit residues: 62.1356 Evaluate side-chains 72 residues out of total 1384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 55 time to evaluate : 2.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 645 ARG Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 645 ARG Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 800 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 38 optimal weight: 5.9990 chunk 115 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 125 optimal weight: 0.0980 chunk 52 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 110 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 521 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 = 0.3663 r_free = 0.3663 target = 0.122218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.084772 restraints weight = 53288.002| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.46 r_work: 0.2966 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13242 Z= 0.219 Angle : 0.422 5.001 17896 Z= 0.228 Chirality : 0.037 0.125 1974 Planarity : 0.003 0.032 2214 Dihedral : 10.483 89.331 2110 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.77 % Favored : 96.10 % Rotamer: Outliers : 1.36 % Allowed : 6.06 % Favored : 92.58 % 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: 1.84 (0.21), residues: 1564 helix: 2.57 (0.18), residues: 830 sheet: 0.57 (0.46), residues: 130 loop : -0.60 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 933 HIS 0.003 0.001 HIS B 679 PHE 0.012 0.001 PHE A 984 TYR 0.009 0.001 TYR B 684 ARG 0.002 0.000 ARG A 366 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4284.04 seconds wall clock time: 80 minutes 50.85 seconds (4850.85 seconds total)