Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 06:38:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lrd_23495/04_2023/7lrd_23495_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lrd_23495/04_2023/7lrd_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_23495/04_2023/7lrd_23495.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lrd_23495/04_2023/7lrd_23495.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lrd_23495/04_2023/7lrd_23495_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lrd_23495/04_2023/7lrd_23495_updated.pdb" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 7.78, per 1000 atoms: 0.54 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: 5.59 Conformation dependent library (CDL) restraints added in 2.1 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: 1.42 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: 6.01 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: 8582 16.68 - 33.35: 202 33.35 - 50.03: 30 50.03 - 66.70: 2 66.70 - 83.38: 2 Dihedral angle restraints: 8818 sinusoidal: 3638 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 8815 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: 2.590 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: 8.580 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 39.870 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.080 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.810 ------------------------------------------------------------------------------- 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 : 7.695 83.376 5466 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 % 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 *********************** 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 : 1.790 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 116 average time/residue: 0.3158 time to fit residues: 52.6072 Evaluate side-chains 72 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 68 time to evaluate : 1.646 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1411 time to fit residues: 3.3632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 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... Flipped N/Q/H residues before XYZ refinement: ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.0869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 14642 Z= 0.139 Angle : 0.422 6.784 19748 Z= 0.216 Chirality : 0.036 0.134 2164 Planarity : 0.003 0.042 2516 Dihedral : 3.587 39.560 1918 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer Outliers : 0.38 % 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: 2.75 (0.20), residues: 1742 helix: 2.80 (0.18), residues: 886 sheet: 1.96 (0.40), residues: 164 loop : 0.55 (0.22), residues: 692 *********************** 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 74 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 68 time to evaluate : 1.816 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 72 average time/residue: 0.2386 time to fit residues: 28.7244 Evaluate side-chains 68 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 62 time to evaluate : 1.840 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1379 time to fit residues: 3.8065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.2980 chunk 108 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 160 optimal weight: 2.9990 chunk 172 optimal weight: 8.9990 chunk 142 optimal weight: 10.0000 chunk 158 optimal weight: 6.9990 chunk 54 optimal weight: 10.0000 chunk 128 optimal weight: 0.0870 overall best weight: 3.2764 ------------------------------------------------------------------------------- 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: 0.7832 moved from start: 0.1942 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= 0.391 Angle : 0.552 6.940 19748 Z= 0.284 Chirality : 0.039 0.138 2164 Planarity : 0.004 0.043 2516 Dihedral : 3.974 32.747 1918 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer Outliers : 0.70 % 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: 2.64 (0.20), residues: 1742 helix: 2.73 (0.18), residues: 874 sheet: 1.96 (0.39), residues: 164 loop : 0.48 (0.22), residues: 704 *********************** 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 77 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 66 time to evaluate : 1.989 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 72 average time/residue: 0.2286 time to fit residues: 27.6094 Evaluate side-chains 68 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 62 time to evaluate : 1.637 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1411 time to fit residues: 3.7924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 0.2980 chunk 120 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 160 optimal weight: 0.6980 chunk 170 optimal weight: 3.9990 chunk 152 optimal weight: 0.0570 chunk 45 optimal weight: 0.0970 chunk 141 optimal weight: 5.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- 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: 0.7735 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 0.024 14642 Z= 0.114 Angle : 0.422 7.680 19748 Z= 0.215 Chirality : 0.036 0.134 2164 Planarity : 0.003 0.038 2516 Dihedral : 3.695 34.779 1918 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer Outliers : 0.13 % 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: 2.76 (0.20), residues: 1742 helix: 2.81 (0.18), residues: 872 sheet: 2.10 (0.40), residues: 162 loop : 0.56 (0.23), residues: 708 *********************** 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 64 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 62 time to evaluate : 1.822 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 62 average time/residue: 0.2442 time to fit residues: 25.6405 Evaluate side-chains 62 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 1.816 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 126 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 145 optimal weight: 8.9990 chunk 117 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 86 optimal weight: 8.9990 chunk 152 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- 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: 0.7901 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.052 14642 Z= 0.534 Angle : 0.639 6.667 19748 Z= 0.327 Chirality : 0.041 0.159 2164 Planarity : 0.004 0.040 2516 Dihedral : 4.194 32.515 1918 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 0.70 % 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: 2.29 (0.20), residues: 1742 helix: 2.50 (0.17), residues: 868 sheet: 1.79 (0.39), residues: 164 loop : 0.25 (0.22), residues: 710 *********************** 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 72 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 61 time to evaluate : 1.936 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 9 residues processed: 70 average time/residue: 0.2244 time to fit residues: 26.8449 Evaluate side-chains 70 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 61 time to evaluate : 1.784 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1350 time to fit residues: 4.5384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 170 optimal weight: 0.7980 chunk 141 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 164 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 820 ASN D 740 HIS D 820 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 14642 Z= 0.147 Angle : 0.434 8.754 19748 Z= 0.221 Chirality : 0.037 0.132 2164 Planarity : 0.003 0.039 2516 Dihedral : 3.768 33.186 1918 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer Outliers : 0.19 % 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: 2.67 (0.20), residues: 1742 helix: 2.86 (0.18), residues: 860 sheet: 1.82 (0.39), residues: 162 loop : 0.46 (0.23), residues: 720 *********************** 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 65 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 1.689 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 63 average time/residue: 0.2283 time to fit residues: 24.2776 Evaluate side-chains 63 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 62 time to evaluate : 1.641 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1264 time to fit residues: 2.5864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 96 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 169 optimal weight: 4.9990 chunk 106 optimal weight: 8.9990 chunk 103 optimal weight: 0.0370 chunk 78 optimal weight: 8.9990 chunk 104 optimal weight: 0.6980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 740 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 14642 Z= 0.132 Angle : 0.420 7.176 19748 Z= 0.215 Chirality : 0.036 0.133 2164 Planarity : 0.003 0.039 2516 Dihedral : 3.694 34.247 1918 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.89 % Favored : 97.99 % Rotamer Outliers : 0.13 % 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: 2.64 (0.20), residues: 1742 helix: 2.78 (0.18), residues: 870 sheet: 1.81 (0.39), residues: 162 loop : 0.48 (0.23), residues: 710 *********************** 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 64 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 62 time to evaluate : 1.871 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 64 average time/residue: 0.2417 time to fit residues: 26.4381 Evaluate side-chains 62 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 1.854 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 6.9990 chunk 101 optimal weight: 7.9990 chunk 51 optimal weight: 0.0070 chunk 33 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 133 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 overall best weight: 2.8004 ------------------------------------------------------------------------------- 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: 0.7853 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 14642 Z= 0.336 Angle : 0.521 9.867 19748 Z= 0.262 Chirality : 0.038 0.135 2164 Planarity : 0.003 0.038 2516 Dihedral : 3.918 32.976 1918 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer Outliers : 0.13 % 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: 2.54 (0.20), residues: 1742 helix: 2.71 (0.18), residues: 872 sheet: 1.75 (0.39), residues: 162 loop : 0.42 (0.23), residues: 708 *********************** 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 63 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 61 time to evaluate : 1.775 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 63 average time/residue: 0.2289 time to fit residues: 24.5981 Evaluate side-chains 61 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 1.792 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 158 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 142 optimal weight: 9.9990 chunk 149 optimal weight: 0.5980 chunk 157 optimal weight: 0.9980 chunk 103 optimal weight: 8.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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: 0.7794 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 14642 Z= 0.165 Angle : 0.442 9.430 19748 Z= 0.222 Chirality : 0.037 0.135 2164 Planarity : 0.003 0.038 2516 Dihedral : 3.698 34.059 1918 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.84 % Favored : 98.05 % Rotamer Outliers : 0.00 % 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: 2.77 (0.18), residues: 868 sheet: 1.80 (0.40), residues: 162 loop : 0.52 (0.23), residues: 712 *********************** 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 61 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 1.815 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.2436 time to fit residues: 25.4238 Evaluate side-chains 61 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 1.732 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 9.9990 chunk 102 optimal weight: 0.9980 chunk 79 optimal weight: 9.9990 chunk 116 optimal weight: 0.8980 chunk 175 optimal weight: 7.9990 chunk 161 optimal weight: 4.9990 chunk 139 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.049 14642 Z= 0.382 Angle : 0.573 13.905 19748 Z= 0.286 Chirality : 0.038 0.134 2164 Planarity : 0.004 0.039 2516 Dihedral : 4.062 33.329 1918 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer Outliers : 0.25 % 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: 2.37 (0.20), residues: 1742 helix: 2.56 (0.18), residues: 874 sheet: 1.70 (0.39), residues: 162 loop : 0.33 (0.23), residues: 706 ********************** 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 65 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 61 time to evaluate : 1.911 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 61 average time/residue: 0.2486 time to fit residues: 26.1677 Evaluate side-chains 60 residues out of total 1572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.822 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 128 optimal weight: 0.1980 chunk 20 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 139 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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 = 0.3217 r_free = 0.3217 target = 0.045033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.034280 restraints weight = 76475.320| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 3.91 r_work: 0.2652 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 14642 Z= 0.234 Angle : 0.485 9.473 19748 Z= 0.246 Chirality : 0.037 0.133 2164 Planarity : 0.003 0.052 2516 Dihedral : 3.980 33.627 1918 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 0.13 % 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: 2.44 (0.20), residues: 1742 helix: 2.69 (0.18), residues: 858 sheet: 1.77 (0.40), residues: 162 loop : 0.30 (0.23), residues: 722 =============================================================================== Job complete usr+sys time: 2153.71 seconds wall clock time: 40 minutes 50.23 seconds (2450.23 seconds total)