Starting phenix.real_space_refine on Wed Feb 14 22:03:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ils_35545/02_2024/8ils_35545_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ils_35545/02_2024/8ils_35545.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ils_35545/02_2024/8ils_35545_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ils_35545/02_2024/8ils_35545_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ils_35545/02_2024/8ils_35545_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ils_35545/02_2024/8ils_35545.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ils_35545/02_2024/8ils_35545.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ils_35545/02_2024/8ils_35545_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ils_35545/02_2024/8ils_35545_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.102 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 73 5.16 5 C 6602 2.51 5 N 1792 2.21 5 O 1907 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 76": "OE1" <-> "OE2" Residue "A GLU 80": "OE1" <-> "OE2" Residue "A GLU 116": "OE1" <-> "OE2" Residue "A GLU 493": "OE1" <-> "OE2" Residue "A GLU 529": "OE1" <-> "OE2" Residue "A GLU 547": "OE1" <-> "OE2" Residue "A GLU 563": "OE1" <-> "OE2" Residue "A GLU 722": "OE1" <-> "OE2" Residue "A GLU 726": "OE1" <-> "OE2" Residue "A GLU 737": "OE1" <-> "OE2" Residue "A GLU 982": "OE1" <-> "OE2" Residue "B GLU 342": "OE1" <-> "OE2" Residue "B GLU 345": "OE1" <-> "OE2" Residue "B GLU 462": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10374 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7980 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 977, 7980 Classifications: {'peptide': 977} Link IDs: {'PTRANS': 47, 'TRANS': 929} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2346 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 4, 'TRANS': 271} Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 48 Unusual residues: {'7U5': 1} Classifications: {'undetermined': 1, 'water': 8} Link IDs: {None: 8} Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N BGLU A 950 " occ=0.46 ... (7 atoms not shown) pdb=" OE2BGLU A 950 " occ=0.46 residue: pdb=" N BARG A 951 " occ=0.46 ... (9 atoms not shown) pdb=" NH2BARG A 951 " occ=0.46 residue: pdb=" N BVAL A 952 " occ=0.46 ... (4 atoms not shown) pdb=" CG2BVAL A 952 " occ=0.46 residue: pdb=" N BPRO A 953 " occ=0.46 ... (5 atoms not shown) pdb=" CD BPRO A 953 " occ=0.46 residue: pdb=" N BVAL A 955 " occ=0.46 ... (5 atoms not shown) pdb=" CG2BVAL A 955 " occ=0.46 residue: pdb=" N BLEU A 956 " occ=0.50 ... (6 atoms not shown) pdb=" CD2BLEU A 956 " occ=0.50 Time building chain proxies: 5.71, per 1000 atoms: 0.55 Number of scatterers: 10374 At special positions: 0 Unit cell: (85.696, 131.456, 109.824, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 73 16.00 O 1907 8.00 N 1792 7.00 C 6602 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.05 Conformation dependent library (CDL) restraints added in 1.7 seconds 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2398 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 8 sheets defined 45.6% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.52 Creating SS restraints... Processing helix chain 'A' and resid 42 through 55 removed outlier: 3.547A pdb=" N GLU A 52 " --> pdb=" O GLU A 48 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ARG A 54 " --> pdb=" O PHE A 50 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 92 removed outlier: 3.557A pdb=" N LEU A 92 " --> pdb=" O LEU A 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 89 through 92' Processing helix chain 'A' and resid 110 through 120 removed outlier: 4.106A pdb=" N ARG A 115 " --> pdb=" O LYS A 111 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU A 116 " --> pdb=" O ILE A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 130 Processing helix chain 'A' and resid 134 through 153 removed outlier: 3.526A pdb=" N ARG A 141 " --> pdb=" O GLN A 137 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LEU A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ASN A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N VAL A 146 " --> pdb=" O ASN A 142 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS A 147 " --> pdb=" O ILE A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 166 removed outlier: 3.506A pdb=" N TYR A 165 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 184 removed outlier: 4.011A pdb=" N LYS A 184 " --> pdb=" O HIS A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 202 No H-bonds generated for 'chain 'A' and resid 200 through 202' Processing helix chain 'A' and resid 217 through 228 removed outlier: 3.569A pdb=" N LYS A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 269 No H-bonds generated for 'chain 'A' and resid 267 through 269' Processing helix chain 'A' and resid 271 through 279 Processing helix chain 'A' and resid 290 through 296 removed outlier: 3.612A pdb=" N GLN A 296 " --> pdb=" O SER A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 309 Processing helix chain 'A' and resid 327 through 329 No H-bonds generated for 'chain 'A' and resid 327 through 329' Processing helix chain 'A' and resid 393 through 395 No H-bonds generated for 'chain 'A' and resid 393 through 395' Processing helix chain 'A' and resid 489 through 495 Processing helix chain 'A' and resid 529 through 535 Processing helix chain 'A' and resid 545 through 553 removed outlier: 3.562A pdb=" N SER A 553 " --> pdb=" O ASP A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 560 No H-bonds generated for 'chain 'A' and resid 558 through 560' Processing helix chain 'A' and resid 562 through 570 Proline residue: A 566 - end of helix removed outlier: 3.970A pdb=" N LEU A 569 " --> pdb=" O PRO A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 587 removed outlier: 3.606A pdb=" N GLN A 582 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N CYS A 585 " --> pdb=" O ALA A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 598 No H-bonds generated for 'chain 'A' and resid 595 through 598' Processing helix chain 'A' and resid 609 through 622 removed outlier: 3.607A pdb=" N LYS A 621 " --> pdb=" O ARG A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 628 No H-bonds generated for 'chain 'A' and resid 625 through 628' Processing helix chain 'A' and resid 632 through 639 removed outlier: 3.680A pdb=" N GLN A 637 " --> pdb=" O ILE A 633 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU A 639 " --> pdb=" O LEU A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 657 Processing helix chain 'A' and resid 661 through 674 removed outlier: 3.504A pdb=" N PHE A 666 " --> pdb=" O ARG A 662 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLU A 674 " --> pdb=" O HIS A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 694 Processing helix chain 'A' and resid 696 through 721 removed outlier: 3.987A pdb=" N LEU A 699 " --> pdb=" O GLY A 696 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 702 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN A 703 " --> pdb=" O LYS A 700 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN A 705 " --> pdb=" O LEU A 702 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL A 706 " --> pdb=" O ASN A 703 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASN A 714 " --> pdb=" O LYS A 711 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN A 721 " --> pdb=" O ILE A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 739 Processing helix chain 'A' and resid 742 through 747 Processing helix chain 'A' and resid 766 through 768 No H-bonds generated for 'chain 'A' and resid 766 through 768' Processing helix chain 'A' and resid 788 through 790 No H-bonds generated for 'chain 'A' and resid 788 through 790' Processing helix chain 'A' and resid 808 through 827 removed outlier: 3.546A pdb=" N LEU A 812 " --> pdb=" O ARG A 808 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN A 815 " --> pdb=" O MET A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 864 Processing helix chain 'A' and resid 876 through 884 Processing helix chain 'A' and resid 888 through 911 removed outlier: 3.620A pdb=" N ASP A 891 " --> pdb=" O GLU A 888 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE A 897 " --> pdb=" O ILE A 894 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR A 898 " --> pdb=" O ASP A 895 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER A 900 " --> pdb=" O PHE A 897 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR A 904 " --> pdb=" O CYS A 901 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA A 907 " --> pdb=" O TYR A 904 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N THR A 908 " --> pdb=" O CYS A 905 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE A 910 " --> pdb=" O ALA A 907 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU A 911 " --> pdb=" O THR A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 964 removed outlier: 3.659A pdb=" N VAL A 963 " --> pdb=" O ASP A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 1008 removed outlier: 3.695A pdb=" N HIS A 994 " --> pdb=" O ALA A 990 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ASN A 996 " --> pdb=" O ARG A 992 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU A 997 " --> pdb=" O GLN A 993 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE A 998 " --> pdb=" O HIS A 994 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE A1002 " --> pdb=" O PHE A 998 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N MET A1005 " --> pdb=" O LEU A1001 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU A1006 " --> pdb=" O PHE A1002 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N GLY A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N SER A1008 " --> pdb=" O MET A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1025 removed outlier: 3.596A pdb=" N ILE A1022 " --> pdb=" O ILE A1019 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR A1025 " --> pdb=" O ILE A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1046 Processing helix chain 'B' and resid 328 through 330 No H-bonds generated for 'chain 'B' and resid 328 through 330' Processing helix chain 'B' and resid 340 through 347 Processing helix chain 'B' and resid 401 through 410 Processing helix chain 'B' and resid 434 through 436 No H-bonds generated for 'chain 'B' and resid 434 through 436' Processing helix chain 'B' and resid 442 through 504 removed outlier: 3.684A pdb=" N GLY B 446 " --> pdb=" O ILE B 442 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU B 502 " --> pdb=" O CYS B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 514 Processing helix chain 'B' and resid 518 through 586 removed outlier: 3.653A pdb=" N GLU B 547 " --> pdb=" O ARG B 543 " (cutoff:3.500A) Proline residue: B 568 - end of helix removed outlier: 3.778A pdb=" N THR B 585 " --> pdb=" O LEU B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 597 removed outlier: 3.971A pdb=" N GLU B 596 " --> pdb=" O LYS B 592 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 31 through 35 removed outlier: 3.542A pdb=" N VAL A 32 " --> pdb=" O CYS A 24 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 203 through 212 removed outlier: 8.024A pdb=" N TRP A 195 " --> pdb=" O PRO A 283 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU A 285 " --> pdb=" O TRP A 195 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N ILE A 197 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N LEU A 287 " --> pdb=" O ILE A 197 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 324 through 326 removed outlier: 6.089A pdb=" N VAL A 483 " --> pdb=" O LYS A 325 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 385 through 388 removed outlier: 3.511A pdb=" N GLU A 385 " --> pdb=" O ILE A 338 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 353 through 361 removed outlier: 3.634A pdb=" N LYS A 353 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA A 423 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N SER A 408 " --> pdb=" O PRO A 421 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 779 through 782 Processing sheet with id= G, first strand: chain 'A' and resid 854 through 856 Processing sheet with id= H, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.895A pdb=" N THR B 354 " --> pdb=" O ARG B 373 " (cutoff:3.500A) 394 hydrogen bonds defined for protein. 1050 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: 3.06 Time building geometry restraints manager: 4.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2212 1.33 - 1.45: 2311 1.45 - 1.57: 5950 1.57 - 1.69: 0 1.69 - 1.81: 114 Bond restraints: 10587 Sorted by residual: bond pdb=" C02 7U5 A1101 " pdb=" N03 7U5 A1101 " ideal model delta sigma weight residual 1.451 1.346 0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" C08 7U5 A1101 " pdb=" N07 7U5 A1101 " ideal model delta sigma weight residual 1.449 1.348 0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" C28 7U5 A1101 " pdb=" C29 7U5 A1101 " ideal model delta sigma weight residual 1.532 1.450 0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" C30 7U5 A1101 " pdb=" C31 7U5 A1101 " ideal model delta sigma weight residual 1.531 1.450 0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" CA SER A 773 " pdb=" C SER A 773 " ideal model delta sigma weight residual 1.522 1.470 0.052 1.40e-02 5.10e+03 1.37e+01 ... (remaining 10582 not shown) Histogram of bond angle deviations from ideal: 99.82 - 115.10: 6661 115.10 - 130.38: 7564 130.38 - 145.66: 53 145.66 - 160.94: 0 160.94 - 176.22: 2 Bond angle restraints: 14280 Sorted by residual: angle pdb=" N ALA A 775 " pdb=" CA ALA A 775 " pdb=" C ALA A 775 " ideal model delta sigma weight residual 110.80 121.49 -10.69 2.13e+00 2.20e-01 2.52e+01 angle pdb=" C15 7U5 A1101 " pdb=" C14 7U5 A1101 " pdb=" C16 7U5 A1101 " ideal model delta sigma weight residual 134.26 122.71 11.55 3.00e+00 1.11e-01 1.48e+01 angle pdb=" C15 7U5 A1101 " pdb=" C14 7U5 A1101 " pdb=" N13 7U5 A1101 " ideal model delta sigma weight residual 105.59 115.75 -10.16 3.00e+00 1.11e-01 1.15e+01 angle pdb=" C TRP A 383 " pdb=" N ASN A 384 " pdb=" CA ASN A 384 " ideal model delta sigma weight residual 122.05 118.05 4.00 1.48e+00 4.57e-01 7.32e+00 angle pdb=" C ALA A 775 " pdb=" N LYS A 776 " pdb=" CA LYS A 776 " ideal model delta sigma weight residual 122.83 118.84 3.99 1.54e+00 4.22e-01 6.71e+00 ... (remaining 14275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.89: 5862 20.89 - 41.77: 529 41.77 - 62.66: 46 62.66 - 83.54: 16 83.54 - 104.43: 5 Dihedral angle restraints: 6458 sinusoidal: 2763 harmonic: 3695 Sorted by residual: dihedral pdb=" CA LYS A 111 " pdb=" C LYS A 111 " pdb=" N ILE A 112 " pdb=" CA ILE A 112 " ideal model delta harmonic sigma weight residual 180.00 149.95 30.05 0 5.00e+00 4.00e-02 3.61e+01 dihedral pdb=" C02 7U5 A1101 " pdb=" C04 7U5 A1101 " pdb=" N03 7U5 A1101 " pdb=" C05 7U5 A1101 " ideal model delta sinusoidal sigma weight residual 176.98 72.55 104.43 1 3.00e+01 1.11e-03 1.33e+01 dihedral pdb=" CA SER A 158 " pdb=" C SER A 158 " pdb=" N PRO A 159 " pdb=" CA PRO A 159 " ideal model delta harmonic sigma weight residual 180.00 162.14 17.86 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 6455 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1306 0.057 - 0.114: 210 0.114 - 0.170: 20 0.170 - 0.227: 0 0.227 - 0.284: 1 Chirality restraints: 1537 Sorted by residual: chirality pdb=" CA ALA A 775 " pdb=" N ALA A 775 " pdb=" C ALA A 775 " pdb=" CB ALA A 775 " both_signs ideal model delta sigma weight residual False 2.48 2.20 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C06 7U5 A1101 " pdb=" C02 7U5 A1101 " pdb=" C22 7U5 A1101 " pdb=" N07 7U5 A1101 " both_signs ideal model delta sigma weight residual False -2.61 -2.45 -0.16 2.00e-01 2.50e+01 6.24e-01 chirality pdb=" CA ILE A 561 " pdb=" N ILE A 561 " pdb=" C ILE A 561 " pdb=" CB ILE A 561 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.65e-01 ... (remaining 1534 not shown) Planarity restraints: 1835 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C29 7U5 A1101 " -0.095 2.00e-02 2.50e+03 4.77e-02 6.81e+01 pdb=" C30 7U5 A1101 " -0.017 2.00e-02 2.50e+03 pdb=" C31 7U5 A1101 " 0.039 2.00e-02 2.50e+03 pdb=" C32 7U5 A1101 " 0.024 2.00e-02 2.50e+03 pdb=" C33 7U5 A1101 " 0.019 2.00e-02 2.50e+03 pdb=" C34 7U5 A1101 " 0.073 2.00e-02 2.50e+03 pdb=" C35 7U5 A1101 " 0.048 2.00e-02 2.50e+03 pdb=" C36 7U5 A1101 " 0.018 2.00e-02 2.50e+03 pdb=" C38 7U5 A1101 " -0.065 2.00e-02 2.50e+03 pdb=" C39 7U5 A1101 " -0.040 2.00e-02 2.50e+03 pdb=" N37 7U5 A1101 " -0.031 2.00e-02 2.50e+03 pdb=" N40 7U5 A1101 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C22 7U5 A1101 " 0.107 2.00e-02 2.50e+03 5.00e-02 5.63e+01 pdb=" C23 7U5 A1101 " -0.018 2.00e-02 2.50e+03 pdb=" C24 7U5 A1101 " -0.039 2.00e-02 2.50e+03 pdb=" C25 7U5 A1101 " -0.034 2.00e-02 2.50e+03 pdb=" C26 7U5 A1101 " -0.039 2.00e-02 2.50e+03 pdb=" C27 7U5 A1101 " -0.040 2.00e-02 2.50e+03 pdb=" C28 7U5 A1101 " -0.022 2.00e-02 2.50e+03 pdb=" C29 7U5 A1101 " 0.022 2.00e-02 2.50e+03 pdb=" C30 7U5 A1101 " 0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C08 7U5 A1101 " 0.042 2.00e-02 2.50e+03 3.01e-02 2.94e+01 pdb=" C09 7U5 A1101 " 0.028 2.00e-02 2.50e+03 pdb=" C10 7U5 A1101 " -0.005 2.00e-02 2.50e+03 pdb=" C11 7U5 A1101 " -0.050 2.00e-02 2.50e+03 pdb=" C12 7U5 A1101 " -0.028 2.00e-02 2.50e+03 pdb=" C14 7U5 A1101 " 0.012 2.00e-02 2.50e+03 pdb=" C15 7U5 A1101 " 0.067 2.00e-02 2.50e+03 pdb=" C16 7U5 A1101 " -0.010 2.00e-02 2.50e+03 pdb=" C17 7U5 A1101 " -0.014 2.00e-02 2.50e+03 pdb=" C19 7U5 A1101 " -0.019 2.00e-02 2.50e+03 pdb=" C20 7U5 A1101 " 0.006 2.00e-02 2.50e+03 pdb=" N13 7U5 A1101 " -0.004 2.00e-02 2.50e+03 pdb=" N18 7U5 A1101 " -0.024 2.00e-02 2.50e+03 ... (remaining 1832 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 83 2.57 - 3.16: 8996 3.16 - 3.74: 15248 3.74 - 4.32: 23111 4.32 - 4.90: 37754 Nonbonded interactions: 85192 Sorted by model distance: nonbonded pdb=" OD1 ASN A 428 " pdb=" NE2 GLN A 643 " model vdw 1.993 2.520 nonbonded pdb=" OE2 GLU A 642 " pdb=" O HOH A1201 " model vdw 2.027 2.440 nonbonded pdb=" O ASP A 138 " pdb=" ND2 ASN A 142 " model vdw 2.110 2.520 nonbonded pdb=" N SER B 399 " pdb=" OE2 GLU B 403 " model vdw 2.124 2.520 nonbonded pdb=" O ALA B 331 " pdb=" NZ LYS B 430 " model vdw 2.150 2.520 ... (remaining 85187 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.46 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: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.130 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 30.770 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 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 0.105 10587 Z= 0.394 Angle : 0.578 11.550 14280 Z= 0.304 Chirality : 0.042 0.284 1537 Planarity : 0.004 0.050 1835 Dihedral : 15.084 104.425 4060 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 25.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.57 % Favored : 93.34 % Rotamer: Outliers : 0.17 % Allowed : 0.52 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.20 (0.24), residues: 1239 helix: -0.26 (0.22), residues: 550 sheet: -1.56 (0.40), residues: 168 loop : -0.96 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 597 HIS 0.003 0.001 HIS A 917 PHE 0.016 0.002 PHE A 430 TYR 0.011 0.001 TYR A 432 ARG 0.003 0.000 ARG A 87 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 179 time to evaluate : 1.244 Fit side-chains revert: symmetry clash REVERT: A 286 MET cc_start: 0.7614 (ttp) cc_final: 0.7346 (ttp) REVERT: A 488 ASP cc_start: 0.7504 (p0) cc_final: 0.7054 (p0) outliers start: 2 outliers final: 0 residues processed: 181 average time/residue: 0.2547 time to fit residues: 63.2484 Evaluate side-chains 154 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 50 optimal weight: 0.0010 chunk 97 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 59 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 overall best weight: 0.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN A 384 ASN A 749 GLN A 809 GLN ** A 918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1047 HIS B 501 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10587 Z= 0.184 Angle : 0.539 6.925 14280 Z= 0.278 Chirality : 0.042 0.197 1537 Planarity : 0.004 0.057 1835 Dihedral : 5.150 67.357 1378 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.90 % Favored : 96.02 % Rotamer: Outliers : 1.04 % Allowed : 7.04 % Favored : 91.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.24), residues: 1239 helix: 0.42 (0.22), residues: 563 sheet: -1.21 (0.43), residues: 143 loop : -1.00 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 597 HIS 0.004 0.001 HIS A1047 PHE 0.020 0.002 PHE A 70 TYR 0.009 0.001 TYR A 904 ARG 0.005 0.000 ARG B 503 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 160 time to evaluate : 1.096 Fit side-chains REVERT: A 162 ARG cc_start: 0.8352 (tpp80) cc_final: 0.7518 (mtm180) REVERT: A 164 MET cc_start: 0.8854 (mmm) cc_final: 0.8600 (mmm) REVERT: A 352 ASP cc_start: 0.7429 (m-30) cc_final: 0.7084 (m-30) REVERT: A 488 ASP cc_start: 0.7727 (p0) cc_final: 0.7289 (p0) REVERT: A 532 LYS cc_start: 0.8429 (mtpt) cc_final: 0.8211 (mtmt) REVERT: A 545 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7600 (mm-30) REVERT: A 976 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7091 (mm-30) REVERT: B 525 MET cc_start: 0.8228 (mmp) cc_final: 0.8009 (mmp) outliers start: 12 outliers final: 9 residues processed: 169 average time/residue: 0.2346 time to fit residues: 55.9988 Evaluate side-chains 152 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 143 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain A residue 810 ASP Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 584 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 112 optimal weight: 10.0000 chunk 121 optimal weight: 9.9990 chunk 100 optimal weight: 9.9990 chunk 111 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN A 682 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10587 Z= 0.267 Angle : 0.533 5.698 14280 Z= 0.272 Chirality : 0.042 0.150 1537 Planarity : 0.004 0.064 1835 Dihedral : 4.947 52.949 1378 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.11 % Favored : 94.81 % Rotamer: Outliers : 1.83 % Allowed : 9.65 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.24), residues: 1239 helix: 0.60 (0.22), residues: 565 sheet: -1.41 (0.38), residues: 168 loop : -1.01 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 479 HIS 0.004 0.001 HIS A 665 PHE 0.023 0.002 PHE A 734 TYR 0.012 0.001 TYR B 470 ARG 0.004 0.000 ARG B 503 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 150 time to evaluate : 1.325 Fit side-chains revert: symmetry clash REVERT: A 162 ARG cc_start: 0.8396 (tpp80) cc_final: 0.7531 (mtm180) REVERT: A 352 ASP cc_start: 0.7491 (m-30) cc_final: 0.7087 (m-30) REVERT: A 488 ASP cc_start: 0.7640 (p0) cc_final: 0.7211 (p0) REVERT: A 545 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7817 (mm-30) REVERT: A 610 MET cc_start: 0.8001 (mmm) cc_final: 0.7722 (mmm) REVERT: B 525 MET cc_start: 0.8208 (mmp) cc_final: 0.7849 (mmp) outliers start: 21 outliers final: 17 residues processed: 163 average time/residue: 0.2481 time to fit residues: 57.0836 Evaluate side-chains 157 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 140 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 599 MET Chi-restraints excluded: chain A residue 746 ASP Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 810 ASP Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 584 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 8.9990 chunk 84 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 12 optimal weight: 0.0870 chunk 53 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 119 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN A 384 ASN A 703 ASN A 749 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10587 Z= 0.144 Angle : 0.469 7.116 14280 Z= 0.240 Chirality : 0.040 0.136 1537 Planarity : 0.004 0.065 1835 Dihedral : 4.713 58.292 1378 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.81 % Favored : 96.10 % Rotamer: Outliers : 1.91 % Allowed : 10.70 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.24), residues: 1239 helix: 0.81 (0.22), residues: 576 sheet: -1.17 (0.40), residues: 149 loop : -1.06 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 479 HIS 0.004 0.001 HIS A 59 PHE 0.022 0.001 PHE A 734 TYR 0.012 0.001 TYR B 470 ARG 0.003 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 154 time to evaluate : 1.127 Fit side-chains revert: symmetry clash REVERT: A 278 MET cc_start: 0.8206 (tpp) cc_final: 0.7993 (tpp) REVERT: A 352 ASP cc_start: 0.7420 (m-30) cc_final: 0.7058 (m-30) REVERT: A 488 ASP cc_start: 0.7613 (p0) cc_final: 0.7240 (p0) REVERT: A 532 LYS cc_start: 0.8409 (mtpt) cc_final: 0.8196 (mtmt) REVERT: B 525 MET cc_start: 0.8107 (mmp) cc_final: 0.7119 (tpp) outliers start: 22 outliers final: 18 residues processed: 169 average time/residue: 0.2377 time to fit residues: 56.0167 Evaluate side-chains 162 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 144 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 647 ASN Chi-restraints excluded: chain A residue 746 ASP Chi-restraints excluded: chain A residue 810 ASP Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 584 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 89 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN A 384 ASN A 703 ASN A 803 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 10587 Z= 0.400 Angle : 0.578 6.792 14280 Z= 0.292 Chirality : 0.044 0.153 1537 Planarity : 0.004 0.069 1835 Dihedral : 4.905 54.828 1378 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.52 % Favored : 94.40 % Rotamer: Outliers : 2.70 % Allowed : 11.22 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.24), residues: 1239 helix: 0.59 (0.22), residues: 572 sheet: -1.19 (0.40), residues: 149 loop : -1.16 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 479 HIS 0.005 0.001 HIS A 665 PHE 0.021 0.002 PHE A 734 TYR 0.014 0.001 TYR B 470 ARG 0.004 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 147 time to evaluate : 1.316 Fit side-chains REVERT: A 30 MET cc_start: 0.6168 (mmp) cc_final: 0.5789 (mmm) REVERT: A 162 ARG cc_start: 0.8501 (tpp80) cc_final: 0.7632 (mtm180) REVERT: A 278 MET cc_start: 0.8250 (tpp) cc_final: 0.7979 (tpp) REVERT: A 347 ASN cc_start: 0.7388 (t0) cc_final: 0.6994 (t0) REVERT: A 352 ASP cc_start: 0.7472 (m-30) cc_final: 0.7001 (m-30) REVERT: A 476 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7101 (tm-30) REVERT: A 488 ASP cc_start: 0.7654 (p0) cc_final: 0.7257 (p0) REVERT: B 525 MET cc_start: 0.8091 (mmp) cc_final: 0.7097 (tpp) outliers start: 31 outliers final: 23 residues processed: 166 average time/residue: 0.2421 time to fit residues: 56.2932 Evaluate side-chains 163 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 139 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 647 ASN Chi-restraints excluded: chain A residue 746 ASP Chi-restraints excluded: chain A residue 810 ASP Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 584 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 119 optimal weight: 9.9990 chunk 99 optimal weight: 0.4980 chunk 55 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN A 384 ASN A 703 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10587 Z= 0.201 Angle : 0.492 6.497 14280 Z= 0.250 Chirality : 0.041 0.137 1537 Planarity : 0.004 0.065 1835 Dihedral : 4.777 58.908 1378 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.55 % Favored : 95.37 % Rotamer: Outliers : 2.17 % Allowed : 12.61 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.24), residues: 1239 helix: 0.75 (0.22), residues: 572 sheet: -1.15 (0.39), residues: 149 loop : -1.11 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 479 HIS 0.003 0.001 HIS A 665 PHE 0.017 0.001 PHE A 734 TYR 0.013 0.001 TYR B 470 ARG 0.002 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 150 time to evaluate : 1.163 Fit side-chains REVERT: A 83 PHE cc_start: 0.7818 (m-80) cc_final: 0.7375 (m-80) REVERT: A 162 ARG cc_start: 0.8498 (tpp80) cc_final: 0.7653 (mtm180) REVERT: A 278 MET cc_start: 0.8222 (tpp) cc_final: 0.7999 (tpp) REVERT: A 347 ASN cc_start: 0.7468 (t0) cc_final: 0.7005 (t0) REVERT: A 352 ASP cc_start: 0.7456 (m-30) cc_final: 0.7038 (m-30) REVERT: A 469 GLU cc_start: 0.6746 (OUTLIER) cc_final: 0.5954 (tm-30) REVERT: A 476 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7110 (tm-30) REVERT: A 488 ASP cc_start: 0.7604 (p0) cc_final: 0.7181 (p0) REVERT: B 525 MET cc_start: 0.7982 (mmp) cc_final: 0.7021 (tpp) REVERT: B 584 LEU cc_start: 0.6599 (OUTLIER) cc_final: 0.6391 (tt) outliers start: 25 outliers final: 20 residues processed: 167 average time/residue: 0.2385 time to fit residues: 55.4870 Evaluate side-chains 171 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 148 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 647 ASN Chi-restraints excluded: chain A residue 810 ASP Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 1031 THR Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 584 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 20.0000 chunk 13 optimal weight: 2.9990 chunk 68 optimal weight: 0.4980 chunk 87 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 100 optimal weight: 9.9990 chunk 66 optimal weight: 0.8980 chunk 119 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN A 384 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 10587 Z= 0.161 Angle : 0.481 8.861 14280 Z= 0.244 Chirality : 0.040 0.158 1537 Planarity : 0.004 0.064 1835 Dihedral : 4.663 59.895 1378 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.03 % Favored : 94.89 % Rotamer: Outliers : 2.17 % Allowed : 13.22 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.24), residues: 1239 helix: 0.85 (0.22), residues: 578 sheet: -1.22 (0.39), residues: 155 loop : -1.11 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 479 HIS 0.003 0.000 HIS A 665 PHE 0.014 0.001 PHE A 734 TYR 0.013 0.001 TYR B 470 ARG 0.005 0.000 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 154 time to evaluate : 1.127 Fit side-chains REVERT: A 83 PHE cc_start: 0.7827 (m-80) cc_final: 0.7267 (m-80) REVERT: A 162 ARG cc_start: 0.8450 (tpp80) cc_final: 0.7598 (mtm180) REVERT: A 278 MET cc_start: 0.8216 (tpp) cc_final: 0.8015 (tpp) REVERT: A 352 ASP cc_start: 0.7456 (m-30) cc_final: 0.7025 (m-30) REVERT: A 476 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7106 (tm-30) REVERT: A 488 ASP cc_start: 0.7583 (p0) cc_final: 0.7160 (p0) REVERT: B 525 MET cc_start: 0.7954 (mmp) cc_final: 0.7439 (mmp) outliers start: 25 outliers final: 21 residues processed: 171 average time/residue: 0.2491 time to fit residues: 59.1864 Evaluate side-chains 168 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 146 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 647 ASN Chi-restraints excluded: chain A residue 810 ASP Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 1031 THR Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 570 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 108 optimal weight: 20.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN A 296 GLN A 384 ASN A 981 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10587 Z= 0.276 Angle : 0.530 6.710 14280 Z= 0.266 Chirality : 0.042 0.152 1537 Planarity : 0.004 0.066 1835 Dihedral : 4.752 57.583 1378 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.52 % Favored : 94.40 % Rotamer: Outliers : 2.09 % Allowed : 14.09 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.24), residues: 1239 helix: 0.76 (0.22), residues: 572 sheet: -1.16 (0.38), residues: 156 loop : -1.11 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 479 HIS 0.004 0.001 HIS A 665 PHE 0.034 0.002 PHE A 734 TYR 0.014 0.001 TYR B 470 ARG 0.003 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 145 time to evaluate : 1.259 Fit side-chains REVERT: A 83 PHE cc_start: 0.7813 (m-80) cc_final: 0.7183 (m-80) REVERT: A 162 ARG cc_start: 0.8475 (tpp80) cc_final: 0.7637 (mtm180) REVERT: A 278 MET cc_start: 0.8244 (tpp) cc_final: 0.8004 (tpp) REVERT: A 352 ASP cc_start: 0.7468 (m-30) cc_final: 0.7028 (m-30) REVERT: A 476 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7092 (tm-30) REVERT: A 488 ASP cc_start: 0.7594 (p0) cc_final: 0.7199 (p0) REVERT: B 525 MET cc_start: 0.7884 (mmp) cc_final: 0.7430 (mmp) outliers start: 24 outliers final: 20 residues processed: 162 average time/residue: 0.2494 time to fit residues: 57.1351 Evaluate side-chains 166 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 145 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 647 ASN Chi-restraints excluded: chain A residue 810 ASP Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 1031 THR Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 570 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 chunk 67 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 34 optimal weight: 0.0070 chunk 100 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 chunk 73 optimal weight: 0.1980 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN A 296 GLN A 384 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10587 Z= 0.217 Angle : 0.505 7.504 14280 Z= 0.255 Chirality : 0.041 0.146 1537 Planarity : 0.004 0.066 1835 Dihedral : 4.737 58.801 1378 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.79 % Favored : 95.13 % Rotamer: Outliers : 2.43 % Allowed : 13.48 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.24), residues: 1239 helix: 0.80 (0.22), residues: 573 sheet: -1.11 (0.39), residues: 153 loop : -1.07 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 479 HIS 0.004 0.001 HIS A 665 PHE 0.022 0.002 PHE A 734 TYR 0.019 0.001 TYR B 368 ARG 0.003 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 143 time to evaluate : 1.216 Fit side-chains REVERT: A 83 PHE cc_start: 0.7824 (m-80) cc_final: 0.7181 (m-80) REVERT: A 130 MET cc_start: 0.7838 (mmm) cc_final: 0.7625 (mmm) REVERT: A 162 ARG cc_start: 0.8479 (tpp80) cc_final: 0.7640 (mtm180) REVERT: A 278 MET cc_start: 0.8234 (tpp) cc_final: 0.8027 (tpp) REVERT: A 352 ASP cc_start: 0.7464 (m-30) cc_final: 0.6981 (m-30) REVERT: A 476 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7113 (tm-30) REVERT: A 488 ASP cc_start: 0.7588 (p0) cc_final: 0.7192 (p0) REVERT: A 723 LYS cc_start: 0.6635 (OUTLIER) cc_final: 0.6434 (pttp) REVERT: A 734 PHE cc_start: 0.8504 (t80) cc_final: 0.8215 (t80) REVERT: B 525 MET cc_start: 0.7833 (mmp) cc_final: 0.7382 (mmp) REVERT: B 584 LEU cc_start: 0.6702 (OUTLIER) cc_final: 0.6453 (tt) outliers start: 28 outliers final: 22 residues processed: 163 average time/residue: 0.2391 time to fit residues: 54.4049 Evaluate side-chains 165 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 140 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 647 ASN Chi-restraints excluded: chain A residue 723 LYS Chi-restraints excluded: chain A residue 737 GLU Chi-restraints excluded: chain A residue 810 ASP Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 1031 THR Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 584 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 55 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 123 optimal weight: 30.0000 chunk 113 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN A 296 GLN A 384 ASN ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 10587 Z= 0.298 Angle : 0.536 7.413 14280 Z= 0.270 Chirality : 0.043 0.143 1537 Planarity : 0.004 0.068 1835 Dihedral : 4.811 57.968 1378 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.35 % Allowed : 13.57 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.24), residues: 1239 helix: 0.69 (0.22), residues: 573 sheet: -1.09 (0.39), residues: 156 loop : -1.15 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 479 HIS 0.005 0.001 HIS A 665 PHE 0.021 0.002 PHE A 734 TYR 0.018 0.001 TYR B 368 ARG 0.003 0.000 ARG A 765 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 143 time to evaluate : 1.283 Fit side-chains REVERT: A 83 PHE cc_start: 0.7816 (m-80) cc_final: 0.7145 (m-80) REVERT: A 162 ARG cc_start: 0.8513 (tpp80) cc_final: 0.7673 (mtm180) REVERT: A 278 MET cc_start: 0.8250 (tpp) cc_final: 0.8034 (tpp) REVERT: A 352 ASP cc_start: 0.7477 (m-30) cc_final: 0.6980 (m-30) REVERT: A 476 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7089 (tm-30) REVERT: A 488 ASP cc_start: 0.7619 (p0) cc_final: 0.7219 (p0) REVERT: A 723 LYS cc_start: 0.6691 (OUTLIER) cc_final: 0.6474 (pttp) REVERT: A 734 PHE cc_start: 0.8481 (t80) cc_final: 0.8154 (t80) REVERT: B 525 MET cc_start: 0.7837 (mmp) cc_final: 0.7359 (mmp) outliers start: 27 outliers final: 23 residues processed: 162 average time/residue: 0.2401 time to fit residues: 54.6138 Evaluate side-chains 167 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 142 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 647 ASN Chi-restraints excluded: chain A residue 723 LYS Chi-restraints excluded: chain A residue 737 GLU Chi-restraints excluded: chain A residue 810 ASP Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 1031 THR Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 584 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 chunk 101 optimal weight: 8.9990 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN A 296 GLN A 384 ASN ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.172963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.112611 restraints weight = 11619.215| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.38 r_work: 0.2887 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2773 r_free = 0.2773 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2773 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10587 Z= 0.306 Angle : 0.542 7.337 14280 Z= 0.273 Chirality : 0.043 0.142 1537 Planarity : 0.004 0.067 1835 Dihedral : 4.835 57.848 1378 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.35 % Allowed : 13.65 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.24), residues: 1239 helix: 0.66 (0.22), residues: 572 sheet: -1.09 (0.39), residues: 156 loop : -1.16 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 479 HIS 0.005 0.001 HIS A 665 PHE 0.022 0.002 PHE A 734 TYR 0.017 0.001 TYR B 368 ARG 0.003 0.000 ARG A 765 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2520.23 seconds wall clock time: 46 minutes 32.47 seconds (2792.47 seconds total)