Starting phenix.real_space_refine on Wed Feb 14 20:49:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ilv_35547/02_2024/8ilv_35547_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ilv_35547/02_2024/8ilv_35547.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ilv_35547/02_2024/8ilv_35547_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ilv_35547/02_2024/8ilv_35547_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ilv_35547/02_2024/8ilv_35547_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ilv_35547/02_2024/8ilv_35547.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ilv_35547/02_2024/8ilv_35547.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ilv_35547/02_2024/8ilv_35547_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ilv_35547/02_2024/8ilv_35547_updated.pdb" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.098 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 69 5.16 5 C 6508 2.51 5 N 1763 2.21 5 O 1878 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 81": "OE1" <-> "OE2" Residue "A GLU 223": "OE1" <-> "OE2" Residue "A GLU 263": "OE1" <-> "OE2" Residue "A GLU 453": "OE1" <-> "OE2" Residue "A GLU 970": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10218 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 971, 7933 Classifications: {'peptide': 971} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 47, 'TRANS': 923} Chain breaks: 6 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "B" Number of atoms: 2241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2241 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 260} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {'L2V': 1} Classifications: {'undetermined': 1, 'water': 4} Link IDs: {None: 4} Time building chain proxies: 5.57, per 1000 atoms: 0.55 Number of scatterers: 10218 At special positions: 0 Unit cell: (85.68, 117.81, 121.023, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 69 16.00 O 1878 8.00 N 1763 7.00 C 6508 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: 3.98 Conformation dependent library (CDL) restraints added in 1.8 seconds 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2370 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 9 sheets defined 45.3% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.50 Creating SS restraints... Processing helix chain 'A' and resid 42 through 55 removed outlier: 3.555A pdb=" N LYS A 51 " --> pdb=" O HIS A 47 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LYS A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 65 through 67 No H-bonds generated for 'chain 'A' and resid 65 through 67' Processing helix chain 'A' and resid 90 through 92 No H-bonds generated for 'chain 'A' and resid 90 through 92' Processing helix chain 'A' and resid 108 through 121 removed outlier: 3.586A pdb=" N ILE A 112 " --> pdb=" O ARG A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 129 Processing helix chain 'A' and resid 134 through 156 removed outlier: 3.511A pdb=" N PHE A 139 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ASN A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N VAL A 146 " --> pdb=" O ASN A 142 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS A 147 " --> pdb=" O ILE A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 166 removed outlier: 3.675A pdb=" N TYR A 165 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL A 166 " --> pdb=" O ARG A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 184 removed outlier: 3.930A pdb=" N LYS A 184 " --> pdb=" O HIS A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 217 through 228 Processing helix chain 'A' and resid 267 through 269 No H-bonds generated for 'chain 'A' and resid 267 through 269' Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 290 through 296 removed outlier: 3.707A pdb=" N GLN A 296 " --> pdb=" O SER A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 309 No H-bonds generated for 'chain 'A' and resid 306 through 309' Processing helix chain 'A' and resid 327 through 329 No H-bonds generated for 'chain 'A' and resid 327 through 329' Processing helix chain 'A' and resid 393 through 395 No H-bonds generated for 'chain 'A' and resid 393 through 395' Processing helix chain 'A' and resid 489 through 495 Processing helix chain 'A' and resid 527 through 535 Processing helix chain 'A' and resid 545 through 553 Processing helix chain 'A' and resid 562 through 571 Proline residue: A 566 - end of helix removed outlier: 3.887A pdb=" N LEU A 569 " --> pdb=" O PRO A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 589 removed outlier: 3.727A pdb=" N CYS A 585 " --> pdb=" O ALA A 581 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU A 586 " --> pdb=" O GLN A 582 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP A 589 " --> pdb=" O CYS A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 598 No H-bonds generated for 'chain 'A' and resid 595 through 598' Processing helix chain 'A' and resid 600 through 602 No H-bonds generated for 'chain 'A' and resid 600 through 602' Processing helix chain 'A' and resid 609 through 622 removed outlier: 3.781A pdb=" N LYS A 621 " --> pdb=" O ARG A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 630 Processing helix chain 'A' and resid 632 through 639 removed outlier: 3.654A pdb=" N LEU A 639 " --> pdb=" O LEU A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 657 removed outlier: 4.112A pdb=" N LYS A 655 " --> pdb=" O ARG A 651 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS A 656 " --> pdb=" O PHE A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 675 removed outlier: 3.670A pdb=" N PHE A 666 " --> pdb=" O ARG A 662 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU A 674 " --> pdb=" O HIS A 670 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N MET A 675 " --> pdb=" O LEU A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 695 Processing helix chain 'A' and resid 697 through 720 removed outlier: 3.831A pdb=" N LEU A 702 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN A 703 " --> pdb=" O LYS A 700 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN A 705 " --> pdb=" O LEU A 702 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL A 706 " --> pdb=" O ASN A 703 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU A 707 " --> pdb=" O ARG A 704 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS A 711 " --> pdb=" O ALA A 708 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU A 712 " --> pdb=" O MET A 709 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN A 714 " --> pdb=" O LYS A 711 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ILE A 718 " --> pdb=" O LEU A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 740 removed outlier: 3.532A pdb=" N GLU A 737 " --> pdb=" O LYS A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 747 removed outlier: 3.524A pdb=" N ALA A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 827 Processing helix chain 'A' and resid 857 through 860 No H-bonds generated for 'chain 'A' and resid 857 through 860' Processing helix chain 'A' and resid 876 through 885 Processing helix chain 'A' and resid 888 through 911 removed outlier: 4.334A pdb=" N ILE A 894 " --> pdb=" O ASP A 891 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 896 " --> pdb=" O ALA A 893 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG A 899 " --> pdb=" O LEU A 896 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N SER A 900 " --> pdb=" O PHE A 897 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA A 902 " --> pdb=" O ARG A 899 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS A 905 " --> pdb=" O ALA A 902 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL A 906 " --> pdb=" O GLY A 903 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ALA A 907 " --> pdb=" O TYR A 904 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR A 908 " --> pdb=" O CYS A 905 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 911 " --> pdb=" O THR A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 964 removed outlier: 3.823A pdb=" N ILE A 962 " --> pdb=" O GLN A 958 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL A 963 " --> pdb=" O ASP A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 993 Processing helix chain 'A' and resid 995 through 1002 Processing helix chain 'A' and resid 1019 through 1025 removed outlier: 3.548A pdb=" N ARG A1023 " --> pdb=" O ALA A1020 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR A1025 " --> pdb=" O ILE A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1047 removed outlier: 3.573A pdb=" N LEU A1036 " --> pdb=" O GLU A1032 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU A1037 " --> pdb=" O GLN A1033 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ALA A1046 " --> pdb=" O GLN A1042 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 330 No H-bonds generated for 'chain 'B' and resid 328 through 330' Processing helix chain 'B' and resid 340 through 344 Processing helix chain 'B' and resid 401 through 409 Processing helix chain 'B' and resid 431 through 436 Processing helix chain 'B' and resid 442 through 509 removed outlier: 3.539A pdb=" N GLY B 446 " --> pdb=" O ILE B 442 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS B 447 " --> pdb=" O GLU B 443 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS B 450 " --> pdb=" O GLY B 446 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS B 506 " --> pdb=" O GLU B 502 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N GLU B 507 " --> pdb=" O ARG B 503 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N TYR B 508 " --> pdb=" O TYR B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 584 Proline residue: B 568 - end of helix Processing helix chain 'B' and resid 591 through 597 Processing sheet with id= A, first strand: chain 'A' and resid 20 through 25 removed outlier: 4.287A pdb=" N ILE A 20 " --> pdb=" O CYS A 36 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 69 through 71 Processing sheet with id= C, first strand: chain 'A' and resid 189 through 194 Processing sheet with id= D, first strand: chain 'A' and resid 324 through 326 removed outlier: 6.070A pdb=" N VAL A 483 " --> pdb=" O LYS A 325 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 385 through 388 removed outlier: 3.729A pdb=" N GLU A 385 " --> pdb=" O ILE A 338 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 353 through 356 removed outlier: 3.770A pdb=" N GLY A 425 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA A 423 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N SER A 408 " --> pdb=" O PRO A 421 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 779 through 781 Processing sheet with id= H, first strand: chain 'A' and resid 921 through 923 Processing sheet with id= I, first strand: chain 'B' and resid 355 through 358 removed outlier: 3.602A pdb=" N ASN B 377 " --> pdb=" O LYS B 374 " (cutoff:3.500A) 368 hydrogen bonds defined for protein. 987 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: 2.85 Time building geometry restraints manager: 4.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3341 1.34 - 1.46: 1476 1.46 - 1.57: 5508 1.57 - 1.69: 0 1.69 - 1.81: 106 Bond restraints: 10431 Sorted by residual: bond pdb=" C27 L2V A1101 " pdb=" N26 L2V A1101 " ideal model delta sigma weight residual 1.484 1.340 0.144 2.00e-02 2.50e+03 5.17e+01 bond pdb=" C21 L2V A1101 " pdb=" N23 L2V A1101 " ideal model delta sigma weight residual 1.462 1.347 0.115 2.00e-02 2.50e+03 3.28e+01 bond pdb=" C12 L2V A1101 " pdb=" C13 L2V A1101 " ideal model delta sigma weight residual 1.538 1.459 0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" C09 L2V A1101 " pdb=" C11 L2V A1101 " ideal model delta sigma weight residual 1.536 1.460 0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" C27 L2V A1101 " pdb=" C29 L2V A1101 " ideal model delta sigma weight residual 1.559 1.498 0.061 2.00e-02 2.50e+03 9.26e+00 ... (remaining 10426 not shown) Histogram of bond angle deviations from ideal: 99.33 - 115.27: 6585 115.27 - 131.22: 7457 131.22 - 147.17: 31 147.17 - 163.11: 0 163.11 - 179.06: 2 Bond angle restraints: 14075 Sorted by residual: angle pdb=" N ALA A 775 " pdb=" CA ALA A 775 " pdb=" C ALA A 775 " ideal model delta sigma weight residual 111.40 124.69 -13.29 1.22e+00 6.72e-01 1.19e+02 angle pdb=" C ALA A 775 " pdb=" CA ALA A 775 " pdb=" CB ALA A 775 " ideal model delta sigma weight residual 110.79 101.07 9.72 1.68e+00 3.54e-01 3.35e+01 angle pdb=" N ASN B 324 " pdb=" CA ASN B 324 " pdb=" C ASN B 324 " ideal model delta sigma weight residual 113.38 106.89 6.49 1.23e+00 6.61e-01 2.79e+01 angle pdb=" N LYS A 776 " pdb=" CA LYS A 776 " pdb=" CB LYS A 776 " ideal model delta sigma weight residual 110.49 117.33 -6.84 1.69e+00 3.50e-01 1.64e+01 angle pdb=" C ARG A 777 " pdb=" N PRO A 778 " pdb=" CA PRO A 778 " ideal model delta sigma weight residual 119.84 115.30 4.54 1.25e+00 6.40e-01 1.32e+01 ... (remaining 14070 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.13: 5326 18.13 - 36.27: 761 36.27 - 54.40: 214 54.40 - 72.54: 43 72.54 - 90.67: 14 Dihedral angle restraints: 6358 sinusoidal: 2710 harmonic: 3648 Sorted by residual: dihedral pdb=" CA LYS B 438 " pdb=" C LYS B 438 " pdb=" N GLU B 439 " pdb=" CA GLU B 439 " ideal model delta harmonic sigma weight residual 180.00 163.00 17.00 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA ASP A 725 " pdb=" CB ASP A 725 " pdb=" CG ASP A 725 " pdb=" OD1 ASP A 725 " ideal model delta sinusoidal sigma weight residual -30.00 -88.45 58.45 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CA LEU A 834 " pdb=" C LEU A 834 " pdb=" N PRO A 835 " pdb=" CA PRO A 835 " ideal model delta harmonic sigma weight residual 180.00 163.55 16.45 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 6355 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1182 0.043 - 0.086: 252 0.086 - 0.129: 81 0.129 - 0.173: 4 0.173 - 0.216: 2 Chirality restraints: 1521 Sorted by residual: chirality pdb=" CA ALA A 775 " pdb=" N ALA A 775 " pdb=" C ALA A 775 " pdb=" CB ALA A 775 " both_signs ideal model delta sigma weight residual False 2.48 2.27 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA ASP B 394 " pdb=" N ASP B 394 " pdb=" C ASP B 394 " pdb=" CB ASP B 394 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CB ILE A 543 " pdb=" CA ILE A 543 " pdb=" CG1 ILE A 543 " pdb=" CG2 ILE A 543 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.89e-01 ... (remaining 1518 not shown) Planarity restraints: 1806 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C20 L2V A1101 " -0.074 2.00e-02 2.50e+03 6.28e-02 4.93e+01 pdb=" C27 L2V A1101 " 0.032 2.00e-02 2.50e+03 pdb=" C29 L2V A1101 " -0.060 2.00e-02 2.50e+03 pdb=" N26 L2V A1101 " 0.097 2.00e-02 2.50e+03 pdb=" O28 L2V A1101 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 L2V A1101 " -0.036 2.00e-02 2.50e+03 3.95e-02 3.51e+01 pdb=" C12 L2V A1101 " -0.005 2.00e-02 2.50e+03 pdb=" C13 L2V A1101 " 0.029 2.00e-02 2.50e+03 pdb=" C14 L2V A1101 " 0.072 2.00e-02 2.50e+03 pdb=" C15 L2V A1101 " 0.039 2.00e-02 2.50e+03 pdb=" C16 L2V A1101 " 0.004 2.00e-02 2.50e+03 pdb=" C17 L2V A1101 " -0.019 2.00e-02 2.50e+03 pdb=" C18 L2V A1101 " -0.014 2.00e-02 2.50e+03 pdb=" C19 L2V A1101 " -0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C27 L2V A1101 " 0.033 2.00e-02 2.50e+03 2.87e-02 2.69e+01 pdb=" C29 L2V A1101 " 0.023 2.00e-02 2.50e+03 pdb=" C30 L2V A1101 " 0.012 2.00e-02 2.50e+03 pdb=" C31 L2V A1101 " 0.003 2.00e-02 2.50e+03 pdb=" C32 L2V A1101 " -0.027 2.00e-02 2.50e+03 pdb=" C33 L2V A1101 " -0.031 2.00e-02 2.50e+03 pdb=" C34 L2V A1101 " -0.021 2.00e-02 2.50e+03 pdb=" C36 L2V A1101 " 0.003 2.00e-02 2.50e+03 pdb=" C37 L2V A1101 " 0.071 2.00e-02 2.50e+03 pdb=" C38 L2V A1101 " -0.012 2.00e-02 2.50e+03 pdb=" C40 L2V A1101 " 0.002 2.00e-02 2.50e+03 pdb=" N35 L2V A1101 " -0.027 2.00e-02 2.50e+03 pdb=" N39 L2V A1101 " -0.031 2.00e-02 2.50e+03 ... (remaining 1803 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 106 2.64 - 3.20: 9101 3.20 - 3.77: 15201 3.77 - 4.33: 21129 4.33 - 4.90: 35232 Nonbonded interactions: 80769 Sorted by model distance: nonbonded pdb=" O VAL B 436 " pdb=" NZ LYS B 438 " model vdw 2.073 2.520 nonbonded pdb=" OG SER A 173 " pdb=" OD2 ASP A 626 " model vdw 2.197 2.440 nonbonded pdb=" O LEU A 367 " pdb=" ND2 ASN A 575 " model vdw 2.199 2.520 nonbonded pdb=" OG SER A 199 " pdb=" OD1 ASN A 201 " model vdw 2.204 2.440 nonbonded pdb=" OD2 ASP A 603 " pdb=" OG SER A1003 " model vdw 2.234 2.440 ... (remaining 80764 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.060 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 30.030 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 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 : 0.004 0.144 10431 Z= 0.276 Angle : 0.539 13.295 14075 Z= 0.286 Chirality : 0.040 0.216 1521 Planarity : 0.004 0.068 1806 Dihedral : 18.358 90.671 3988 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.26 % Allowed : 27.98 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.24), residues: 1218 helix: -0.32 (0.21), residues: 555 sheet: -0.68 (0.50), residues: 121 loop : -0.51 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 479 HIS 0.002 0.000 HIS A 665 PHE 0.016 0.001 PHE A 794 TYR 0.010 0.001 TYR A 392 ARG 0.003 0.000 ARG A 740 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 135 time to evaluate : 1.235 Fit side-chains REVERT: A 489 MET cc_start: 0.7663 (tpt) cc_final: 0.7405 (mmt) outliers start: 3 outliers final: 0 residues processed: 136 average time/residue: 0.2791 time to fit residues: 52.5067 Evaluate side-chains 129 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.5980 chunk 93 optimal weight: 3.9990 chunk 51 optimal weight: 0.3980 chunk 31 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 822 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.0666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10431 Z= 0.250 Angle : 0.510 5.670 14075 Z= 0.261 Chirality : 0.040 0.169 1521 Planarity : 0.004 0.057 1806 Dihedral : 4.811 59.851 1357 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.18 % Allowed : 26.65 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.24), residues: 1218 helix: 0.50 (0.22), residues: 558 sheet: -0.63 (0.48), residues: 131 loop : -0.51 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 669 HIS 0.004 0.001 HIS A 665 PHE 0.012 0.001 PHE A 930 TYR 0.016 0.001 TYR B 556 ARG 0.003 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 128 time to evaluate : 1.059 Fit side-chains REVERT: A 115 ARG cc_start: 0.7420 (ttt90) cc_final: 0.7000 (ttp-110) REVERT: A 138 ASP cc_start: 0.7870 (m-30) cc_final: 0.7538 (m-30) REVERT: A 226 ARG cc_start: 0.6999 (OUTLIER) cc_final: 0.5172 (ttm110) REVERT: A 262 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8432 (pp) REVERT: A 469 GLU cc_start: 0.6290 (OUTLIER) cc_final: 0.5430 (pt0) REVERT: A 570 LEU cc_start: 0.8359 (mt) cc_final: 0.8122 (mp) REVERT: B 574 ARG cc_start: 0.6928 (OUTLIER) cc_final: 0.6336 (tpt-90) outliers start: 36 outliers final: 21 residues processed: 156 average time/residue: 0.2490 time to fit residues: 54.1771 Evaluate side-chains 142 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 117 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 796 ASN Chi-restraints excluded: chain A residue 811 MET Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 574 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 120 optimal weight: 0.5980 chunk 99 optimal weight: 0.9980 chunk 110 optimal weight: 7.9990 chunk 38 optimal weight: 0.2980 chunk 89 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.7607 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10431 Z= 0.172 Angle : 0.462 5.627 14075 Z= 0.233 Chirality : 0.039 0.141 1521 Planarity : 0.003 0.052 1806 Dihedral : 4.669 59.983 1357 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.71 % Allowed : 26.65 % Favored : 69.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.24), residues: 1218 helix: 0.88 (0.23), residues: 560 sheet: -0.56 (0.47), residues: 131 loop : -0.46 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 669 HIS 0.005 0.000 HIS A 665 PHE 0.011 0.001 PHE A 794 TYR 0.013 0.001 TYR B 556 ARG 0.002 0.000 ARG A 740 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 137 time to evaluate : 1.192 Fit side-chains REVERT: A 28 ASN cc_start: 0.8620 (p0) cc_final: 0.8266 (p0) REVERT: A 115 ARG cc_start: 0.7425 (ttt90) cc_final: 0.7044 (ttp-110) REVERT: A 138 ASP cc_start: 0.7893 (m-30) cc_final: 0.7512 (m-30) REVERT: A 570 LEU cc_start: 0.8245 (mt) cc_final: 0.8020 (mp) REVERT: A 600 GLU cc_start: 0.7289 (tt0) cc_final: 0.6989 (tt0) REVERT: A 654 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7940 (mp) REVERT: A 1040 MET cc_start: 0.7522 (mtm) cc_final: 0.7209 (mtt) REVERT: B 574 ARG cc_start: 0.6924 (OUTLIER) cc_final: 0.6219 (tpt-90) outliers start: 42 outliers final: 20 residues processed: 171 average time/residue: 0.2354 time to fit residues: 56.4827 Evaluate side-chains 151 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 129 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 769 CYS Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 796 ASN Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 574 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 8.9990 chunk 84 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 112 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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: 0.7621 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10431 Z= 0.210 Angle : 0.480 7.648 14075 Z= 0.240 Chirality : 0.040 0.157 1521 Planarity : 0.003 0.053 1806 Dihedral : 4.679 59.563 1357 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.80 % Allowed : 27.18 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.24), residues: 1218 helix: 0.95 (0.23), residues: 562 sheet: -0.56 (0.47), residues: 125 loop : -0.59 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 880 HIS 0.005 0.001 HIS A 665 PHE 0.011 0.001 PHE A 930 TYR 0.015 0.001 TYR B 556 ARG 0.004 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 136 time to evaluate : 1.173 Fit side-chains REVERT: A 76 GLU cc_start: 0.6787 (pm20) cc_final: 0.6485 (pm20) REVERT: A 115 ARG cc_start: 0.7406 (ttt90) cc_final: 0.7030 (ttp-110) REVERT: A 138 ASP cc_start: 0.7912 (m-30) cc_final: 0.7493 (m-30) REVERT: A 226 ARG cc_start: 0.7069 (OUTLIER) cc_final: 0.5183 (ttm110) REVERT: A 469 GLU cc_start: 0.6428 (OUTLIER) cc_final: 0.5604 (pt0) REVERT: A 570 LEU cc_start: 0.8268 (mt) cc_final: 0.8052 (mp) REVERT: A 600 GLU cc_start: 0.7223 (tt0) cc_final: 0.6916 (tt0) REVERT: A 628 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8462 (tt) REVERT: A 654 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7942 (mp) REVERT: A 921 ILE cc_start: 0.9181 (OUTLIER) cc_final: 0.8953 (mm) REVERT: A 982 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.6776 (mp0) REVERT: A 1040 MET cc_start: 0.7469 (mtm) cc_final: 0.7205 (mtt) REVERT: B 574 ARG cc_start: 0.7031 (OUTLIER) cc_final: 0.6302 (tpt-90) outliers start: 43 outliers final: 26 residues processed: 171 average time/residue: 0.2254 time to fit residues: 54.9200 Evaluate side-chains 160 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 127 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 769 CYS Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 796 ASN Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 921 ILE Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 982 GLU Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 574 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 88 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 60 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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: 0.7613 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10431 Z= 0.191 Angle : 0.470 6.564 14075 Z= 0.237 Chirality : 0.039 0.150 1521 Planarity : 0.003 0.050 1806 Dihedral : 4.650 59.712 1357 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.15 % Allowed : 27.18 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.24), residues: 1218 helix: 0.99 (0.23), residues: 568 sheet: -0.52 (0.47), residues: 125 loop : -0.61 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 880 HIS 0.005 0.001 HIS A 665 PHE 0.010 0.001 PHE A 930 TYR 0.020 0.001 TYR A 182 ARG 0.002 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 140 time to evaluate : 1.101 Fit side-chains REVERT: A 138 ASP cc_start: 0.7881 (m-30) cc_final: 0.7419 (m-30) REVERT: A 226 ARG cc_start: 0.7029 (OUTLIER) cc_final: 0.5183 (ttm110) REVERT: A 469 GLU cc_start: 0.6569 (OUTLIER) cc_final: 0.5808 (pt0) REVERT: A 570 LEU cc_start: 0.8308 (mt) cc_final: 0.8079 (mp) REVERT: A 600 GLU cc_start: 0.7179 (tt0) cc_final: 0.6874 (tt0) REVERT: A 628 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8421 (tt) REVERT: A 654 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7942 (mp) REVERT: A 798 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7098 (mm-30) REVERT: A 921 ILE cc_start: 0.9184 (OUTLIER) cc_final: 0.8973 (mm) REVERT: A 982 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.6815 (mp0) REVERT: A 1040 MET cc_start: 0.7486 (mtm) cc_final: 0.7265 (mtt) REVERT: B 372 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8229 (tp) REVERT: B 574 ARG cc_start: 0.7015 (OUTLIER) cc_final: 0.6203 (tpt-90) outliers start: 47 outliers final: 29 residues processed: 182 average time/residue: 0.2177 time to fit residues: 56.1316 Evaluate side-chains 163 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 125 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 769 CYS Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 796 ASN Chi-restraints excluded: chain A residue 798 GLU Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 917 HIS Chi-restraints excluded: chain A residue 921 ILE Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 982 GLU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 574 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 69 optimal weight: 0.1980 chunk 29 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 0.3980 chunk 114 optimal weight: 1.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- 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: 0.7599 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10431 Z= 0.167 Angle : 0.461 5.865 14075 Z= 0.234 Chirality : 0.039 0.145 1521 Planarity : 0.003 0.048 1806 Dihedral : 4.580 58.861 1357 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.24 % Allowed : 27.10 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.25), residues: 1218 helix: 1.13 (0.23), residues: 564 sheet: -0.49 (0.47), residues: 125 loop : -0.50 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 880 HIS 0.006 0.001 HIS A 665 PHE 0.011 0.001 PHE A 794 TYR 0.021 0.001 TYR A 182 ARG 0.001 0.000 ARG A 740 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 134 time to evaluate : 1.238 Fit side-chains revert: symmetry clash REVERT: A 115 ARG cc_start: 0.7340 (ttt180) cc_final: 0.7000 (ttp-110) REVERT: A 138 ASP cc_start: 0.7876 (m-30) cc_final: 0.7364 (m-30) REVERT: A 148 LYS cc_start: 0.7548 (tppt) cc_final: 0.7285 (tptp) REVERT: A 201 ASN cc_start: 0.4047 (OUTLIER) cc_final: 0.2493 (t0) REVERT: A 226 ARG cc_start: 0.7010 (OUTLIER) cc_final: 0.5130 (ttm110) REVERT: A 469 GLU cc_start: 0.6551 (OUTLIER) cc_final: 0.5822 (pt0) REVERT: A 570 LEU cc_start: 0.8330 (mt) cc_final: 0.8093 (mp) REVERT: A 600 GLU cc_start: 0.7196 (tt0) cc_final: 0.6926 (tt0) REVERT: A 628 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8366 (tt) REVERT: A 654 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7937 (mp) REVERT: A 982 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.6836 (mp0) REVERT: A 1040 MET cc_start: 0.7576 (mtm) cc_final: 0.7311 (mtt) REVERT: B 499 GLN cc_start: 0.6719 (mp10) cc_final: 0.6399 (mp10) REVERT: B 574 ARG cc_start: 0.7074 (OUTLIER) cc_final: 0.6251 (tpt-90) outliers start: 48 outliers final: 34 residues processed: 177 average time/residue: 0.2270 time to fit residues: 56.8574 Evaluate side-chains 174 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 133 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 769 CYS Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 796 ASN Chi-restraints excluded: chain A residue 798 GLU Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 917 HIS Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 982 GLU Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 574 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 118 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 54 optimal weight: 0.0980 chunk 73 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10431 Z= 0.217 Angle : 0.482 5.318 14075 Z= 0.243 Chirality : 0.040 0.146 1521 Planarity : 0.003 0.048 1806 Dihedral : 4.643 59.436 1357 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.68 % Allowed : 26.65 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.24), residues: 1218 helix: 1.09 (0.23), residues: 562 sheet: -0.54 (0.47), residues: 125 loop : -0.57 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 880 HIS 0.004 0.001 HIS A 665 PHE 0.011 0.001 PHE A 930 TYR 0.016 0.001 TYR B 556 ARG 0.003 0.000 ARG A 740 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 136 time to evaluate : 1.172 Fit side-chains revert: symmetry clash REVERT: A 138 ASP cc_start: 0.7911 (m-30) cc_final: 0.7442 (m-30) REVERT: A 201 ASN cc_start: 0.4133 (OUTLIER) cc_final: 0.2585 (t0) REVERT: A 221 ILE cc_start: 0.6866 (OUTLIER) cc_final: 0.5758 (mt) REVERT: A 226 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.5158 (ttm110) REVERT: A 469 GLU cc_start: 0.6541 (OUTLIER) cc_final: 0.5962 (tt0) REVERT: A 570 LEU cc_start: 0.8370 (mt) cc_final: 0.8130 (mp) REVERT: A 600 GLU cc_start: 0.7186 (tt0) cc_final: 0.6879 (tt0) REVERT: A 628 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8445 (tt) REVERT: A 641 TYR cc_start: 0.8484 (m-10) cc_final: 0.7974 (m-10) REVERT: A 982 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.6856 (mp0) REVERT: B 499 GLN cc_start: 0.6640 (mp10) cc_final: 0.6319 (mp10) REVERT: B 574 ARG cc_start: 0.7117 (OUTLIER) cc_final: 0.6305 (tpt-90) outliers start: 53 outliers final: 36 residues processed: 184 average time/residue: 0.2207 time to fit residues: 57.7415 Evaluate side-chains 172 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 129 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 769 CYS Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 796 ASN Chi-restraints excluded: chain A residue 798 GLU Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 917 HIS Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 982 GLU Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 574 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 80 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 93 optimal weight: 5.9990 chunk 107 optimal weight: 0.3980 chunk 113 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10431 Z= 0.177 Angle : 0.476 5.741 14075 Z= 0.240 Chirality : 0.039 0.141 1521 Planarity : 0.003 0.047 1806 Dihedral : 4.575 58.960 1357 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 4.15 % Allowed : 27.36 % Favored : 68.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.25), residues: 1218 helix: 1.15 (0.23), residues: 566 sheet: -0.50 (0.47), residues: 125 loop : -0.50 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 880 HIS 0.005 0.000 HIS A 665 PHE 0.012 0.001 PHE A 794 TYR 0.020 0.001 TYR A 182 ARG 0.003 0.000 ARG A 740 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 135 time to evaluate : 1.275 Fit side-chains revert: symmetry clash REVERT: A 115 ARG cc_start: 0.7404 (ttt180) cc_final: 0.7007 (ttp-110) REVERT: A 138 ASP cc_start: 0.7912 (m-30) cc_final: 0.7416 (m-30) REVERT: A 201 ASN cc_start: 0.4185 (OUTLIER) cc_final: 0.2643 (t0) REVERT: A 221 ILE cc_start: 0.6860 (OUTLIER) cc_final: 0.5722 (mt) REVERT: A 226 ARG cc_start: 0.7012 (OUTLIER) cc_final: 0.5157 (ttm110) REVERT: A 469 GLU cc_start: 0.6528 (OUTLIER) cc_final: 0.5967 (tt0) REVERT: A 570 LEU cc_start: 0.8347 (mt) cc_final: 0.8109 (mp) REVERT: A 600 GLU cc_start: 0.7143 (tt0) cc_final: 0.6856 (tt0) REVERT: A 628 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8397 (tt) REVERT: A 982 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.6841 (mp0) REVERT: B 333 TRP cc_start: 0.8151 (OUTLIER) cc_final: 0.7925 (p-90) REVERT: B 499 GLN cc_start: 0.6679 (mp10) cc_final: 0.6357 (mp10) REVERT: B 574 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.6403 (tpt-90) outliers start: 47 outliers final: 35 residues processed: 178 average time/residue: 0.2192 time to fit residues: 55.6942 Evaluate side-chains 172 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 129 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 769 CYS Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 796 ASN Chi-restraints excluded: chain A residue 798 GLU Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 917 HIS Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 982 GLU Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain B residue 333 TRP Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 574 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.0030 chunk 110 optimal weight: 7.9990 chunk 113 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10431 Z= 0.187 Angle : 0.477 5.182 14075 Z= 0.241 Chirality : 0.039 0.142 1521 Planarity : 0.003 0.047 1806 Dihedral : 4.576 58.762 1357 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.97 % Allowed : 27.45 % Favored : 68.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.25), residues: 1218 helix: 1.15 (0.23), residues: 566 sheet: -0.54 (0.47), residues: 125 loop : -0.50 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 880 HIS 0.005 0.001 HIS A 665 PHE 0.011 0.001 PHE A 794 TYR 0.014 0.001 TYR B 556 ARG 0.003 0.000 ARG A 740 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 131 time to evaluate : 1.184 Fit side-chains revert: symmetry clash REVERT: A 115 ARG cc_start: 0.7400 (ttt180) cc_final: 0.7008 (ttp-110) REVERT: A 138 ASP cc_start: 0.7933 (m-30) cc_final: 0.7425 (m-30) REVERT: A 201 ASN cc_start: 0.4046 (OUTLIER) cc_final: 0.2461 (t0) REVERT: A 221 ILE cc_start: 0.6860 (OUTLIER) cc_final: 0.5717 (mt) REVERT: A 226 ARG cc_start: 0.7037 (OUTLIER) cc_final: 0.5203 (ttm110) REVERT: A 469 GLU cc_start: 0.6525 (OUTLIER) cc_final: 0.5964 (tt0) REVERT: A 570 LEU cc_start: 0.8358 (mt) cc_final: 0.8123 (mp) REVERT: A 600 GLU cc_start: 0.7185 (tt0) cc_final: 0.6877 (tt0) REVERT: A 628 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8400 (tt) REVERT: A 982 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.6848 (mp0) REVERT: B 333 TRP cc_start: 0.8160 (OUTLIER) cc_final: 0.7939 (p-90) REVERT: B 438 LYS cc_start: 0.6414 (mmtm) cc_final: 0.5853 (mtpt) REVERT: B 499 GLN cc_start: 0.6765 (mp10) cc_final: 0.6436 (mp10) REVERT: B 574 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.6313 (tpt-90) outliers start: 45 outliers final: 37 residues processed: 172 average time/residue: 0.2178 time to fit residues: 53.5758 Evaluate side-chains 174 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 129 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 769 CYS Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 796 ASN Chi-restraints excluded: chain A residue 798 GLU Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 917 HIS Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 982 GLU Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain B residue 333 TRP Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 574 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 0.0050 chunk 55 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 122 optimal weight: 9.9990 chunk 112 optimal weight: 0.9990 chunk 97 optimal weight: 8.9990 chunk 10 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10431 Z= 0.179 Angle : 0.478 5.103 14075 Z= 0.242 Chirality : 0.039 0.141 1521 Planarity : 0.003 0.047 1806 Dihedral : 4.555 58.317 1357 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.24 % Allowed : 27.27 % Favored : 68.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.25), residues: 1218 helix: 1.17 (0.23), residues: 567 sheet: -0.59 (0.45), residues: 134 loop : -0.54 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 479 HIS 0.005 0.001 HIS A 665 PHE 0.011 0.001 PHE A 794 TYR 0.014 0.001 TYR B 556 ARG 0.003 0.000 ARG A 740 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 132 time to evaluate : 1.217 Fit side-chains revert: symmetry clash REVERT: A 138 ASP cc_start: 0.7928 (m-30) cc_final: 0.7415 (m-30) REVERT: A 201 ASN cc_start: 0.4023 (OUTLIER) cc_final: 0.2467 (t0) REVERT: A 226 ARG cc_start: 0.7034 (OUTLIER) cc_final: 0.5213 (ttm110) REVERT: A 469 GLU cc_start: 0.6511 (OUTLIER) cc_final: 0.6040 (tt0) REVERT: A 570 LEU cc_start: 0.8353 (mt) cc_final: 0.8118 (mp) REVERT: A 600 GLU cc_start: 0.7223 (tt0) cc_final: 0.6941 (tt0) REVERT: A 628 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8395 (tt) REVERT: A 982 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.6889 (mp0) REVERT: B 333 TRP cc_start: 0.8146 (OUTLIER) cc_final: 0.7895 (p-90) REVERT: B 499 GLN cc_start: 0.6663 (mp10) cc_final: 0.6328 (mp10) REVERT: B 574 ARG cc_start: 0.7126 (OUTLIER) cc_final: 0.6299 (tpt-90) outliers start: 48 outliers final: 38 residues processed: 176 average time/residue: 0.2369 time to fit residues: 59.5900 Evaluate side-chains 174 residues out of total 1137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 129 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 769 CYS Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 796 ASN Chi-restraints excluded: chain A residue 798 GLU Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 917 HIS Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 982 GLU Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain B residue 333 TRP Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 574 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 0.0270 chunk 97 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 overall best weight: 0.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.201927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.161939 restraints weight = 11773.660| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 2.22 r_work: 0.3768 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10431 Z= 0.189 Angle : 0.493 10.726 14075 Z= 0.247 Chirality : 0.039 0.141 1521 Planarity : 0.003 0.047 1806 Dihedral : 4.554 58.159 1357 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.15 % Allowed : 27.63 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.25), residues: 1218 helix: 1.14 (0.23), residues: 567 sheet: -0.61 (0.45), residues: 134 loop : -0.55 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 479 HIS 0.005 0.001 HIS A 665 PHE 0.011 0.001 PHE A 794 TYR 0.014 0.001 TYR B 556 ARG 0.003 0.000 ARG A 740 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2261.59 seconds wall clock time: 41 minutes 53.41 seconds (2513.41 seconds total)