Starting phenix.real_space_refine on Sat Mar 16 09:58:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lrd_23495/03_2024/7lrd_23495_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lrd_23495/03_2024/7lrd_23495.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lrd_23495/03_2024/7lrd_23495.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lrd_23495/03_2024/7lrd_23495.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lrd_23495/03_2024/7lrd_23495_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lrd_23495/03_2024/7lrd_23495_updated.pdb" } resolution = 3.22 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= 0.002 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: 7 Type Number sf(0) Gaussians Mn 2 7.51 5 Zn 2 6.06 5 Mg 2 5.21 5 S 94 5.16 5 C 9190 2.51 5 N 2418 2.21 5 O 2638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 897": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 897": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 14346 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 4150 Classifications: {'peptide': 512} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 501} Chain breaks: 2 Chain: "B" Number of atoms: 2998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2998 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 18, 'TRANS': 352} Chain breaks: 2 Chain: "C" Number of atoms: 4150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 4150 Classifications: {'peptide': 512} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 501} Chain breaks: 2 Chain: "D" Number of atoms: 2998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2998 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 18, 'TRANS': 352} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 24 Unusual residues: {' MG': 1, ' MN': 1, 'X5M': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 24 Unusual residues: {' MG': 1, ' MN': 1, 'X5M': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2161 SG CYS A 277 78.349 64.701 53.901 1.00 52.28 S ATOM 2434 SG CYS A 311 79.121 63.550 50.334 1.00 41.08 S ATOM 2440 SG CYS A 312 75.876 62.456 52.045 1.00 39.93 S ATOM 9309 SG CYS C 277 40.702 28.841 53.894 1.00 53.47 S ATOM 9582 SG CYS C 311 39.931 29.993 50.327 1.00 41.62 S ATOM 9588 SG CYS C 312 43.176 31.086 52.039 1.00 40.29 S Time building chain proxies: 7.82, per 1000 atoms: 0.55 Number of scatterers: 14346 At special positions: 0 Unit cell: (120.119, 94.607, 130.749, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Mn 2 24.99 S 94 16.00 Mg 2 11.99 O 2638 8.00 N 2418 7.00 C 9190 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.64 Conformation dependent library (CDL) restraints added in 2.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" ND1 HIS A 275 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 277 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 311 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 312 " pdb=" ZN C 601 " pdb="ZN ZN C 601 " - pdb=" ND1 HIS C 275 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 277 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 311 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 312 " Number of angles added : 6 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3352 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 74 helices and 12 sheets defined 47.5% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.66 Creating SS restraints... Processing helix chain 'A' and resid 25 through 29 Processing helix chain 'A' and resid 34 through 54 Processing helix chain 'A' and resid 70 through 73 No H-bonds generated for 'chain 'A' and resid 70 through 73' Processing helix chain 'A' and resid 77 through 86 Processing helix chain 'A' and resid 90 through 93 No H-bonds generated for 'chain 'A' and resid 90 through 93' Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 174 through 185 Processing helix chain 'A' and resid 211 through 232 removed outlier: 4.448A pdb=" N LEU A 215 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLN A 216 " --> pdb=" O GLU A 212 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS A 219 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU A 220 " --> pdb=" O GLN A 216 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A 222 " --> pdb=" O ILE A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 254 through 270 Processing helix chain 'A' and resid 334 through 342 Processing helix chain 'A' and resid 393 through 402 Processing helix chain 'A' and resid 404 through 416 removed outlier: 3.594A pdb=" N GLN A 408 " --> pdb=" O GLU A 404 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N SER A 416 " --> pdb=" O GLU A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 431 No H-bonds generated for 'chain 'A' and resid 428 through 431' Processing helix chain 'A' and resid 467 through 482 Processing helix chain 'A' and resid 520 through 523 Processing helix chain 'A' and resid 527 through 540 Processing helix chain 'A' and resid 552 through 558 Processing helix chain 'B' and resid 680 through 682 No H-bonds generated for 'chain 'B' and resid 680 through 682' Processing helix chain 'B' and resid 685 through 690 removed outlier: 4.163A pdb=" N ASN B 690 " --> pdb=" O GLU B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 703 Processing helix chain 'B' and resid 710 through 722 Processing helix chain 'B' and resid 724 through 727 No H-bonds generated for 'chain 'B' and resid 724 through 727' Processing helix chain 'B' and resid 732 through 745 Processing helix chain 'B' and resid 754 through 769 Processing helix chain 'B' and resid 817 through 819 No H-bonds generated for 'chain 'B' and resid 817 through 819' Processing helix chain 'B' and resid 823 through 834 Processing helix chain 'B' and resid 845 through 850 Processing helix chain 'B' and resid 854 through 858 Processing helix chain 'B' and resid 864 through 879 Processing helix chain 'B' and resid 881 through 883 No H-bonds generated for 'chain 'B' and resid 881 through 883' Processing helix chain 'B' and resid 891 through 908 removed outlier: 3.679A pdb=" N THR B 908 " --> pdb=" O ALA B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 925 Processing helix chain 'B' and resid 935 through 955 removed outlier: 3.584A pdb=" N ILE B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N GLY B 953 " --> pdb=" O ALA B 949 " (cutoff:3.500A) Proline residue: B 954 - end of helix Processing helix chain 'B' and resid 958 through 982 Processing helix chain 'B' and resid 997 through 1007 Processing helix chain 'B' and resid 1009 through 1019 Processing helix chain 'B' and resid 1074 through 1099 Processing helix chain 'C' and resid 25 through 29 Processing helix chain 'C' and resid 34 through 54 Processing helix chain 'C' and resid 70 through 73 No H-bonds generated for 'chain 'C' and resid 70 through 73' Processing helix chain 'C' and resid 77 through 86 Processing helix chain 'C' and resid 90 through 93 No H-bonds generated for 'chain 'C' and resid 90 through 93' Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 174 through 185 Processing helix chain 'C' and resid 211 through 232 removed outlier: 4.448A pdb=" N LEU C 215 " --> pdb=" O THR C 211 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLN C 216 " --> pdb=" O GLU C 212 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS C 219 " --> pdb=" O LEU C 215 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU C 220 " --> pdb=" O GLN C 216 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU C 222 " --> pdb=" O ILE C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 254 through 270 Processing helix chain 'C' and resid 334 through 342 Processing helix chain 'C' and resid 393 through 402 Processing helix chain 'C' and resid 404 through 416 removed outlier: 3.595A pdb=" N GLN C 408 " --> pdb=" O GLU C 404 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N SER C 416 " --> pdb=" O GLU C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 431 No H-bonds generated for 'chain 'C' and resid 428 through 431' Processing helix chain 'C' and resid 467 through 482 Processing helix chain 'C' and resid 520 through 523 Processing helix chain 'C' and resid 527 through 540 Processing helix chain 'C' and resid 552 through 558 Processing helix chain 'D' and resid 680 through 682 No H-bonds generated for 'chain 'D' and resid 680 through 682' Processing helix chain 'D' and resid 685 through 690 removed outlier: 4.163A pdb=" N ASN D 690 " --> pdb=" O GLU D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 696 through 703 Processing helix chain 'D' and resid 710 through 722 Processing helix chain 'D' and resid 724 through 727 No H-bonds generated for 'chain 'D' and resid 724 through 727' Processing helix chain 'D' and resid 732 through 745 Processing helix chain 'D' and resid 754 through 769 Processing helix chain 'D' and resid 817 through 819 No H-bonds generated for 'chain 'D' and resid 817 through 819' Processing helix chain 'D' and resid 823 through 834 Processing helix chain 'D' and resid 845 through 850 Processing helix chain 'D' and resid 854 through 858 Processing helix chain 'D' and resid 864 through 879 Processing helix chain 'D' and resid 881 through 883 No H-bonds generated for 'chain 'D' and resid 881 through 883' Processing helix chain 'D' and resid 891 through 908 removed outlier: 3.679A pdb=" N THR D 908 " --> pdb=" O ALA D 904 " (cutoff:3.500A) Processing helix chain 'D' and resid 913 through 925 Processing helix chain 'D' and resid 935 through 955 removed outlier: 3.586A pdb=" N ILE D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N GLY D 953 " --> pdb=" O ALA D 949 " (cutoff:3.500A) Proline residue: D 954 - end of helix Processing helix chain 'D' and resid 958 through 982 Processing helix chain 'D' and resid 997 through 1007 Processing helix chain 'D' and resid 1009 through 1019 Processing helix chain 'D' and resid 1074 through 1099 Processing sheet with id= A, first strand: chain 'A' and resid 14 through 17 Processing sheet with id= B, first strand: chain 'A' and resid 127 through 130 Processing sheet with id= C, first strand: chain 'A' and resid 189 through 191 removed outlier: 8.097A pdb=" N LEU A 190 " --> pdb=" O PHE A 289 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N GLY A 291 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY A 300 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ASP A 294 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LEU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 322 through 325 Processing sheet with id= E, first strand: chain 'A' and resid 388 through 391 removed outlier: 7.383A pdb=" N GLY A 420 " --> pdb=" O THR A 389 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N THR A 391 " --> pdb=" O GLY A 420 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU A 422 " --> pdb=" O THR A 391 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N PHE A 458 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ASP A 443 " --> pdb=" O TYR A 456 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N TYR A 456 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU A 445 " --> pdb=" O VAL A 454 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL A 454 " --> pdb=" O LEU A 445 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR A 510 " --> pdb=" O ILE A 497 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N TYR A 499 " --> pdb=" O CYS A 508 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N CYS A 508 " --> pdb=" O TYR A 499 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 1025 through 1027 removed outlier: 3.506A pdb=" N LYS B1070 " --> pdb=" O VAL B1027 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 14 through 17 Processing sheet with id= H, first strand: chain 'C' and resid 127 through 130 Processing sheet with id= I, first strand: chain 'C' and resid 189 through 191 removed outlier: 8.096A pdb=" N LEU C 190 " --> pdb=" O PHE C 289 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLY C 291 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY C 300 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ASP C 294 " --> pdb=" O LEU C 298 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N LEU C 298 " --> pdb=" O ASP C 294 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 322 through 325 Processing sheet with id= K, first strand: chain 'C' and resid 388 through 391 removed outlier: 7.383A pdb=" N GLY C 420 " --> pdb=" O THR C 389 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N THR C 391 " --> pdb=" O GLY C 420 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU C 422 " --> pdb=" O THR C 391 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N PHE C 458 " --> pdb=" O LEU C 441 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASP C 443 " --> pdb=" O TYR C 456 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N TYR C 456 " --> pdb=" O ASP C 443 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LEU C 445 " --> pdb=" O VAL C 454 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL C 454 " --> pdb=" O LEU C 445 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR C 510 " --> pdb=" O ILE C 497 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N TYR C 499 " --> pdb=" O CYS C 508 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N CYS C 508 " --> pdb=" O TYR C 499 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 1025 through 1027 removed outlier: 3.505A pdb=" N LYS D1070 " --> pdb=" O VAL D1027 " (cutoff:3.500A) 634 hydrogen bonds defined for protein. 1848 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.42 Time building geometry restraints manager: 6.10 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: 2902 1.33 - 1.45: 3404 1.45 - 1.57: 8190 1.57 - 1.69: 0 1.69 - 1.81: 146 Bond restraints: 14642 Sorted by residual: bond pdb=" N LYS C 150 " pdb=" CA LYS C 150 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.78e+00 bond pdb=" N LYS A 150 " pdb=" CA LYS A 150 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.78e+00 bond pdb=" N PHE C 548 " pdb=" CA PHE C 548 " ideal model delta sigma weight residual 1.456 1.485 -0.028 1.23e-02 6.61e+03 5.19e+00 bond pdb=" N PHE A 548 " pdb=" CA PHE A 548 " ideal model delta sigma weight residual 1.456 1.484 -0.028 1.23e-02 6.61e+03 5.18e+00 bond pdb=" N GLU A 552 " pdb=" CA GLU A 552 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.21e-02 6.83e+03 4.33e+00 ... (remaining 14637 not shown) Histogram of bond angle deviations from ideal: 99.48 - 106.39: 348 106.39 - 113.29: 7872 113.29 - 120.20: 5186 120.20 - 127.10: 6199 127.10 - 134.01: 143 Bond angle restraints: 19748 Sorted by residual: angle pdb=" C05 X5M B2003 " pdb=" C04 X5M B2003 " pdb=" N03 X5M B2003 " ideal model delta sigma weight residual 115.49 104.72 10.77 3.00e+00 1.11e-01 1.29e+01 angle pdb=" C05 X5M D2003 " pdb=" C04 X5M D2003 " pdb=" N03 X5M D2003 " ideal model delta sigma weight residual 115.49 104.77 10.72 3.00e+00 1.11e-01 1.28e+01 angle pdb=" N ARG A 129 " pdb=" CA ARG A 129 " pdb=" C ARG A 129 " ideal model delta sigma weight residual 107.99 113.54 -5.55 1.77e+00 3.19e-01 9.82e+00 angle pdb=" N ARG C 129 " pdb=" CA ARG C 129 " pdb=" C ARG C 129 " ideal model delta sigma weight residual 107.99 113.51 -5.52 1.77e+00 3.19e-01 9.71e+00 angle pdb=" C GLN C 547 " pdb=" N PHE C 548 " pdb=" CA PHE C 548 " ideal model delta sigma weight residual 122.72 118.43 4.29 1.38e+00 5.25e-01 9.68e+00 ... (remaining 19743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.68: 8598 16.68 - 33.35: 202 33.35 - 50.03: 34 50.03 - 66.70: 2 66.70 - 83.38: 2 Dihedral angle restraints: 8838 sinusoidal: 3658 harmonic: 5180 Sorted by residual: dihedral pdb=" CB GLU C 205 " pdb=" CG GLU C 205 " pdb=" CD GLU C 205 " pdb=" OE1 GLU C 205 " ideal model delta sinusoidal sigma weight residual 0.00 -83.38 83.38 1 3.00e+01 1.11e-03 9.44e+00 dihedral pdb=" CB GLU A 205 " pdb=" CG GLU A 205 " pdb=" CD GLU A 205 " pdb=" OE1 GLU A 205 " ideal model delta sinusoidal sigma weight residual 0.00 -83.36 83.36 1 3.00e+01 1.11e-03 9.43e+00 dihedral pdb=" CA MET D 835 " pdb=" C MET D 835 " pdb=" N HIS D 836 " pdb=" CA HIS D 836 " ideal model delta harmonic sigma weight residual -180.00 -166.05 -13.95 0 5.00e+00 4.00e-02 7.79e+00 ... (remaining 8835 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1815 0.049 - 0.097: 261 0.097 - 0.146: 82 0.146 - 0.194: 2 0.194 - 0.243: 4 Chirality restraints: 2164 Sorted by residual: chirality pdb=" CB ILE C 131 " pdb=" CA ILE C 131 " pdb=" CG1 ILE C 131 " pdb=" CG2 ILE C 131 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CB ILE A 131 " pdb=" CA ILE A 131 " pdb=" CG1 ILE A 131 " pdb=" CG2 ILE A 131 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" C21 X5M D2003 " pdb=" C15 X5M D2003 " pdb=" C20 X5M D2003 " pdb=" C22 X5M D2003 " both_signs ideal model delta sigma weight residual False -2.63 -2.84 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 2161 not shown) Planarity restraints: 2516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C02 X5M B2003 " 0.057 2.00e-02 2.50e+03 1.00e-01 1.01e+02 pdb=" C04 X5M B2003 " 0.057 2.00e-02 2.50e+03 pdb=" C06 X5M B2003 " 0.060 2.00e-02 2.50e+03 pdb=" N03 X5M B2003 " -0.174 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 X5M D2003 " 0.056 2.00e-02 2.50e+03 1.00e-01 1.00e+02 pdb=" C04 X5M D2003 " 0.057 2.00e-02 2.50e+03 pdb=" C06 X5M D2003 " 0.060 2.00e-02 2.50e+03 pdb=" N03 X5M D2003 " -0.174 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C18 X5M D2003 " 0.014 2.00e-02 2.50e+03 5.87e-02 4.31e+01 pdb=" C20 X5M D2003 " 0.016 2.00e-02 2.50e+03 pdb=" N16 X5M D2003 " -0.070 2.00e-02 2.50e+03 pdb=" N17 X5M D2003 " 0.095 2.00e-02 2.50e+03 pdb=" O19 X5M D2003 " -0.055 2.00e-02 2.50e+03 ... (remaining 2513 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 40 2.42 - 3.04: 8939 3.04 - 3.66: 20369 3.66 - 4.28: 33384 4.28 - 4.90: 55786 Nonbonded interactions: 118518 Sorted by model distance: nonbonded pdb=" OD1 ASP B 950 " pdb="MN MN B2001 " model vdw 1.795 2.320 nonbonded pdb=" OD1 ASP D 950 " pdb="MN MN D2001 " model vdw 1.795 2.320 nonbonded pdb=" OD2 ASP D 837 " pdb="MN MN D2001 " model vdw 2.046 2.320 nonbonded pdb=" OD2 ASP B 837 " pdb="MN MN B2001 " model vdw 2.046 2.320 nonbonded pdb=" OD1 ASP D 837 " pdb="MG MG D2002 " model vdw 2.141 2.170 ... (remaining 118513 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.450 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: 7.920 Check model and map are aligned: 0.180 Set scattering table: 0.130 Process input model: 42.460 Find NCS groups from input model: 0.700 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: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14642 Z= 0.168 Angle : 0.479 10.767 19748 Z= 0.286 Chirality : 0.039 0.243 2164 Planarity : 0.004 0.100 2516 Dihedral : 7.755 83.376 5486 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.25 % Allowed : 1.27 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.71 (0.20), residues: 1742 helix: 2.82 (0.18), residues: 882 sheet: 1.81 (0.40), residues: 164 loop : 0.49 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 874 HIS 0.002 0.000 HIS B 869 PHE 0.012 0.001 PHE C 548 TYR 0.012 0.001 TYR B 738 ARG 0.002 0.000 ARG C 309 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 112 time to evaluate : 1.473 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 116 average time/residue: 0.3066 time to fit residues: 50.9667 Evaluate side-chains 72 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 68 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain D residue 710 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 5.9990 chunk 133 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 137 optimal weight: 0.2980 chunk 53 optimal weight: 8.9990 chunk 83 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 159 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7661 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14642 Z= 0.138 Angle : 0.418 6.395 19748 Z= 0.214 Chirality : 0.036 0.134 2164 Planarity : 0.003 0.042 2516 Dihedral : 3.953 41.028 1946 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 0.76 % Allowed : 4.13 % Favored : 95.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.80 (0.20), residues: 1742 helix: 2.85 (0.18), residues: 876 sheet: 1.97 (0.40), residues: 164 loop : 0.61 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 874 HIS 0.003 0.000 HIS C 274 PHE 0.014 0.001 PHE A 145 TYR 0.007 0.001 TYR A 390 ARG 0.004 0.000 ARG C 328 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 68 time to evaluate : 1.567 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 10 residues processed: 78 average time/residue: 0.2073 time to fit residues: 27.2410 Evaluate side-chains 72 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 62 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 812 ASP Chi-restraints excluded: chain B residue 861 ASP Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain D residue 696 ILE Chi-restraints excluded: chain D residue 710 ILE Chi-restraints excluded: chain D residue 812 ASP Chi-restraints excluded: chain D residue 861 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 133 optimal weight: 0.8980 chunk 108 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 172 optimal weight: 6.9990 chunk 142 optimal weight: 10.0000 chunk 158 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 128 optimal weight: 0.9990 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 274 HIS B 999 ASN C 274 HIS D 999 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 14642 Z= 0.366 Angle : 0.530 7.050 19748 Z= 0.271 Chirality : 0.039 0.139 2164 Planarity : 0.004 0.042 2516 Dihedral : 4.228 39.574 1946 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.95 % Allowed : 4.45 % Favored : 94.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.71 (0.20), residues: 1742 helix: 2.81 (0.18), residues: 876 sheet: 2.01 (0.39), residues: 164 loop : 0.48 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B1026 HIS 0.008 0.001 HIS B 868 PHE 0.016 0.002 PHE A 145 TYR 0.012 0.002 TYR C 529 ARG 0.004 0.000 ARG A 526 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 66 time to evaluate : 1.776 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 10 residues processed: 76 average time/residue: 0.2283 time to fit residues: 29.1616 Evaluate side-chains 72 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 62 time to evaluate : 1.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 861 ASP Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain D residue 710 ILE Chi-restraints excluded: chain D residue 715 SER Chi-restraints excluded: chain D residue 861 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 chunk 160 optimal weight: 0.5980 chunk 170 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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: 0.7759 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14642 Z= 0.160 Angle : 0.424 7.678 19748 Z= 0.217 Chirality : 0.036 0.134 2164 Planarity : 0.003 0.038 2516 Dihedral : 4.031 39.068 1946 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.83 % Allowed : 4.90 % Favored : 94.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.78 (0.20), residues: 1742 helix: 2.83 (0.18), residues: 882 sheet: 2.10 (0.40), residues: 162 loop : 0.52 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 932 HIS 0.002 0.001 HIS A 403 PHE 0.013 0.001 PHE A 145 TYR 0.007 0.001 TYR D 766 ARG 0.002 0.000 ARG C 328 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 62 time to evaluate : 1.575 Fit side-chains outliers start: 13 outliers final: 12 residues processed: 72 average time/residue: 0.2217 time to fit residues: 26.9704 Evaluate side-chains 74 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 62 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 812 ASP Chi-restraints excluded: chain B residue 861 ASP Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain D residue 710 ILE Chi-restraints excluded: chain D residue 715 SER Chi-restraints excluded: chain D residue 812 ASP Chi-restraints excluded: chain D residue 861 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 145 optimal weight: 8.9990 chunk 117 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 152 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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: 0.7896 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.044 14642 Z= 0.493 Angle : 0.610 5.862 19748 Z= 0.314 Chirality : 0.041 0.143 2164 Planarity : 0.004 0.039 2516 Dihedral : 4.506 37.741 1946 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.27 % Allowed : 4.71 % Favored : 94.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.31 (0.20), residues: 1742 helix: 2.59 (0.17), residues: 856 sheet: 1.68 (0.38), residues: 164 loop : 0.24 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 428 HIS 0.010 0.002 HIS D 868 PHE 0.020 0.002 PHE C 185 TYR 0.016 0.002 TYR A 529 ARG 0.004 0.001 ARG C 526 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 62 time to evaluate : 1.854 Fit side-chains REVERT: B 738 TYR cc_start: 0.7331 (t80) cc_final: 0.7027 (t80) REVERT: D 738 TYR cc_start: 0.7327 (t80) cc_final: 0.7024 (t80) outliers start: 20 outliers final: 14 residues processed: 78 average time/residue: 0.2083 time to fit residues: 27.4983 Evaluate side-chains 76 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 62 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 861 ASP Chi-restraints excluded: chain B residue 1073 CYS Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain D residue 710 ILE Chi-restraints excluded: chain D residue 715 SER Chi-restraints excluded: chain D residue 861 ASP Chi-restraints excluded: chain D residue 1073 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 41 optimal weight: 0.0070 chunk 170 optimal weight: 1.9990 chunk 141 optimal weight: 9.9990 chunk 78 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 56 optimal weight: 8.9990 chunk 89 optimal weight: 6.9990 chunk 164 optimal weight: 2.9990 overall best weight: 0.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 820 ASN D 820 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14642 Z= 0.146 Angle : 0.452 9.360 19748 Z= 0.227 Chirality : 0.037 0.133 2164 Planarity : 0.003 0.040 2516 Dihedral : 4.153 39.411 1946 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.78 % Favored : 98.11 % Rotamer: Outliers : 1.02 % Allowed : 4.90 % Favored : 94.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.62 (0.20), residues: 1742 helix: 2.84 (0.18), residues: 858 sheet: 1.77 (0.39), residues: 162 loop : 0.40 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 110 HIS 0.002 0.000 HIS A 403 PHE 0.014 0.001 PHE C 145 TYR 0.007 0.001 TYR C 487 ARG 0.002 0.000 ARG A 513 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 62 time to evaluate : 1.744 Fit side-chains outliers start: 16 outliers final: 10 residues processed: 74 average time/residue: 0.2183 time to fit residues: 27.2413 Evaluate side-chains 72 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 62 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 861 ASP Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain D residue 710 ILE Chi-restraints excluded: chain D residue 715 SER Chi-restraints excluded: chain D residue 861 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 143 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 169 optimal weight: 5.9990 chunk 106 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 chunk 78 optimal weight: 8.9990 chunk 104 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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: 0.7866 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 14642 Z= 0.354 Angle : 0.518 6.931 19748 Z= 0.265 Chirality : 0.038 0.134 2164 Planarity : 0.003 0.039 2516 Dihedral : 4.301 39.908 1946 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.30 % Favored : 97.65 % Rotamer: Outliers : 0.95 % Allowed : 5.22 % Favored : 93.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.51 (0.20), residues: 1742 helix: 2.78 (0.18), residues: 858 sheet: 1.68 (0.39), residues: 162 loop : 0.33 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 874 HIS 0.006 0.001 HIS B 868 PHE 0.017 0.001 PHE C 145 TYR 0.012 0.001 TYR C 529 ARG 0.003 0.000 ARG C 513 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 61 time to evaluate : 1.602 Fit side-chains outliers start: 15 outliers final: 15 residues processed: 73 average time/residue: 0.2169 time to fit residues: 26.8489 Evaluate side-chains 76 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 61 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 861 ASP Chi-restraints excluded: chain B residue 944 MET Chi-restraints excluded: chain B residue 1073 CYS Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain D residue 710 ILE Chi-restraints excluded: chain D residue 715 SER Chi-restraints excluded: chain D residue 861 ASP Chi-restraints excluded: chain D residue 1073 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 107 optimal weight: 0.0980 chunk 115 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 133 optimal weight: 0.0870 chunk 154 optimal weight: 0.0980 overall best weight: 0.3960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 740 HIS D 740 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14642 Z= 0.118 Angle : 0.442 9.551 19748 Z= 0.222 Chirality : 0.036 0.131 2164 Planarity : 0.003 0.040 2516 Dihedral : 4.080 41.653 1946 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.78 % Favored : 98.11 % Rotamer: Outliers : 0.95 % Allowed : 5.15 % Favored : 93.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.66 (0.20), residues: 1742 helix: 2.87 (0.18), residues: 858 sheet: 1.83 (0.39), residues: 162 loop : 0.42 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 337 HIS 0.002 0.000 HIS B 913 PHE 0.015 0.001 PHE C 145 TYR 0.006 0.001 TYR C 487 ARG 0.004 0.000 ARG A 513 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 62 time to evaluate : 1.743 Fit side-chains outliers start: 15 outliers final: 11 residues processed: 73 average time/residue: 0.2199 time to fit residues: 27.0186 Evaluate side-chains 73 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 62 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 861 ASP Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain D residue 710 ILE Chi-restraints excluded: chain D residue 715 SER Chi-restraints excluded: chain D residue 861 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 158 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 chunk 157 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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: 0.7831 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14642 Z= 0.255 Angle : 0.486 8.442 19748 Z= 0.244 Chirality : 0.037 0.133 2164 Planarity : 0.003 0.039 2516 Dihedral : 4.167 42.069 1946 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.18 % Favored : 97.70 % Rotamer: Outliers : 0.83 % Allowed : 5.03 % Favored : 94.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.65 (0.20), residues: 1742 helix: 2.82 (0.18), residues: 868 sheet: 1.97 (0.39), residues: 162 loop : 0.41 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 932 HIS 0.005 0.001 HIS B 868 PHE 0.018 0.001 PHE C 145 TYR 0.009 0.001 TYR C 529 ARG 0.002 0.000 ARG C 513 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 63 time to evaluate : 1.851 Fit side-chains outliers start: 13 outliers final: 13 residues processed: 75 average time/residue: 0.2273 time to fit residues: 28.3643 Evaluate side-chains 74 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 61 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 861 ASP Chi-restraints excluded: chain B residue 1073 CYS Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain D residue 710 ILE Chi-restraints excluded: chain D residue 715 SER Chi-restraints excluded: chain D residue 861 ASP Chi-restraints excluded: chain D residue 944 MET Chi-restraints excluded: chain D residue 1073 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 7.9990 chunk 102 optimal weight: 0.8980 chunk 79 optimal weight: 7.9990 chunk 116 optimal weight: 0.0370 chunk 175 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 139 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 85 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 overall best weight: 1.5262 ------------------------------------------------------------------------------- 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: 0.7813 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14642 Z= 0.200 Angle : 0.463 8.415 19748 Z= 0.231 Chirality : 0.037 0.134 2164 Planarity : 0.003 0.039 2516 Dihedral : 4.161 42.841 1946 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.95 % Favored : 97.93 % Rotamer: Outliers : 1.02 % Allowed : 5.09 % Favored : 93.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.68 (0.20), residues: 1742 helix: 2.88 (0.18), residues: 856 sheet: 2.03 (0.40), residues: 162 loop : 0.40 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 932 HIS 0.004 0.001 HIS D 868 PHE 0.008 0.001 PHE B 735 TYR 0.008 0.001 TYR C 529 ARG 0.002 0.000 ARG C 513 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3484 Ramachandran restraints generated. 1742 Oldfield, 0 Emsley, 1742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 64 time to evaluate : 1.689 Fit side-chains REVERT: A 494 MET cc_start: 0.7146 (mmm) cc_final: 0.6908 (mmm) REVERT: B 738 TYR cc_start: 0.7395 (t80) cc_final: 0.6939 (t80) REVERT: D 738 TYR cc_start: 0.7389 (t80) cc_final: 0.6935 (t80) outliers start: 16 outliers final: 14 residues processed: 76 average time/residue: 0.2144 time to fit residues: 27.6642 Evaluate side-chains 78 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 64 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 861 ASP Chi-restraints excluded: chain B residue 944 MET Chi-restraints excluded: chain B residue 1073 CYS Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain D residue 710 ILE Chi-restraints excluded: chain D residue 715 SER Chi-restraints excluded: chain D residue 861 ASP Chi-restraints excluded: chain D residue 944 MET Chi-restraints excluded: chain D residue 1073 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 139 optimal weight: 8.9990 chunk 58 optimal weight: 6.9990 chunk 143 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.043901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.033346 restraints weight = 78087.865| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 3.80 r_work: 0.2618 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 14642 Z= 0.479 Angle : 0.619 10.267 19748 Z= 0.313 Chirality : 0.040 0.136 2164 Planarity : 0.004 0.038 2516 Dihedral : 4.594 43.293 1946 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.89 % Allowed : 5.22 % Favored : 93.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.22 (0.20), residues: 1742 helix: 2.51 (0.18), residues: 856 sheet: 1.79 (0.39), residues: 162 loop : 0.17 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D1086 HIS 0.007 0.001 HIS D 868 PHE 0.015 0.002 PHE C 185 TYR 0.016 0.002 TYR C 529 ARG 0.004 0.001 ARG C 526 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2396.07 seconds wall clock time: 44 minutes 36.21 seconds (2676.21 seconds total)