Starting phenix.real_space_refine on Sun Dec 10 03:51:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8om9_16971/12_2023/8om9_16971_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8om9_16971/12_2023/8om9_16971.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8om9_16971/12_2023/8om9_16971.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8om9_16971/12_2023/8om9_16971.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8om9_16971/12_2023/8om9_16971_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8om9_16971/12_2023/8om9_16971_updated.pdb" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 48 5.49 5 Mg 2 5.21 5 S 62 5.16 5 C 8317 2.51 5 N 2286 2.21 5 O 2599 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 364": "OE1" <-> "OE2" Residue "A GLU 464": "OE1" <-> "OE2" Residue "A GLU 572": "OE1" <-> "OE2" Residue "A GLU 590": "OE1" <-> "OE2" Residue "B GLU 373": "OE1" <-> "OE2" Residue "B GLU 806": "OE1" <-> "OE2" Residue "B GLU 976": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 13314 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 5783 Classifications: {'peptide': 732} Link IDs: {'PTRANS': 22, 'TRANS': 709} Chain breaks: 7 Chain: "B" Number of atoms: 6566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 6566 Classifications: {'peptide': 816} Link IDs: {'PTRANS': 25, 'TRANS': 790} Chain breaks: 6 Chain: "C" Number of atoms: 499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 499 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain breaks: 1 Chain: "D" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 410 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.80, per 1000 atoms: 0.59 Number of scatterers: 13314 At special positions: 0 Unit cell: (95.0768, 170.041, 134.387, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 62 16.00 P 48 15.00 Mg 2 11.99 O 2599 8.00 N 2286 7.00 C 8317 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: 6.05 Conformation dependent library (CDL) restraints added in 2.3 seconds 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2948 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 61 helices and 12 sheets defined 49.4% alpha, 8.4% beta 19 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 6.81 Creating SS restraints... Processing helix chain 'A' and resid 185 through 194 Processing helix chain 'A' and resid 209 through 220 removed outlier: 3.641A pdb=" N GLN A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 232 No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 237 through 241 Processing helix chain 'A' and resid 259 through 262 Processing helix chain 'A' and resid 264 through 277 removed outlier: 3.593A pdb=" N SER A 269 " --> pdb=" O VAL A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 298 No H-bonds generated for 'chain 'A' and resid 296 through 298' Processing helix chain 'A' and resid 304 through 309 Processing helix chain 'A' and resid 326 through 330 Processing helix chain 'A' and resid 336 through 347 Processing helix chain 'A' and resid 353 through 368 Processing helix chain 'A' and resid 370 through 378 Processing helix chain 'A' and resid 387 through 395 Processing helix chain 'A' and resid 401 through 412 Processing helix chain 'A' and resid 414 through 423 Processing helix chain 'A' and resid 432 through 435 Processing helix chain 'A' and resid 437 through 455 removed outlier: 4.704A pdb=" N LYS A 449 " --> pdb=" O SER A 445 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N PHE A 450 " --> pdb=" O ASP A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 465 removed outlier: 4.120A pdb=" N ASN A 465 " --> pdb=" O ASP A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 502 Processing helix chain 'A' and resid 527 through 535 removed outlier: 4.683A pdb=" N ARG A 534 " --> pdb=" O GLU A 530 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ASN A 535 " --> pdb=" O LYS A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 614 removed outlier: 3.780A pdb=" N ASN A 566 " --> pdb=" O GLU A 562 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY A 587 " --> pdb=" O ASN A 583 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N TYR A 588 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N GLU A 590 " --> pdb=" O SER A 586 " (cutoff:3.500A) Proline residue: A 591 - end of helix Processing helix chain 'A' and resid 640 through 643 No H-bonds generated for 'chain 'A' and resid 640 through 643' Processing helix chain 'A' and resid 675 through 689 Processing helix chain 'A' and resid 724 through 738 Processing helix chain 'A' and resid 756 through 772 Processing helix chain 'A' and resid 786 through 793 Processing helix chain 'A' and resid 829 through 832 Processing helix chain 'A' and resid 838 through 851 Processing helix chain 'A' and resid 877 through 893 Processing helix chain 'A' and resid 901 through 918 removed outlier: 3.881A pdb=" N THR A 905 " --> pdb=" O GLU A 901 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE A 906 " --> pdb=" O GLU A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 926 Processing helix chain 'B' and resid 231 through 242 removed outlier: 3.907A pdb=" N GLN B 242 " --> pdb=" O GLU B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 270 removed outlier: 4.148A pdb=" N LEU B 270 " --> pdb=" O ALA B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 299 Processing helix chain 'B' and resid 412 through 421 Processing helix chain 'B' and resid 434 through 441 Processing helix chain 'B' and resid 469 through 474 Processing helix chain 'B' and resid 497 through 513 removed outlier: 3.606A pdb=" N PHE B 513 " --> pdb=" O TYR B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 519 No H-bonds generated for 'chain 'B' and resid 517 through 519' Processing helix chain 'B' and resid 522 through 524 No H-bonds generated for 'chain 'B' and resid 522 through 524' Processing helix chain 'B' and resid 539 through 544 Processing helix chain 'B' and resid 560 through 564 Processing helix chain 'B' and resid 570 through 581 Processing helix chain 'B' and resid 587 through 602 Processing helix chain 'B' and resid 609 through 615 Processing helix chain 'B' and resid 621 through 629 Processing helix chain 'B' and resid 635 through 662 Proline residue: B 657 - end of helix Processing helix chain 'B' and resid 668 through 687 Proline residue: B 676 - end of helix Proline residue: B 681 - end of helix removed outlier: 4.823A pdb=" N HIS B 684 " --> pdb=" O SER B 680 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS B 687 " --> pdb=" O GLU B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 695 Processing helix chain 'B' and resid 710 through 736 Processing helix chain 'B' and resid 758 through 761 No H-bonds generated for 'chain 'B' and resid 758 through 761' Processing helix chain 'B' and resid 783 through 842 removed outlier: 3.574A pdb=" N GLU B 816 " --> pdb=" O GLU B 812 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N HIS B 817 " --> pdb=" O LYS B 813 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N HIS B 819 " --> pdb=" O SER B 815 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N SER B 820 " --> pdb=" O GLU B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 870 Processing helix chain 'B' and resid 902 through 917 Processing helix chain 'B' and resid 952 through 963 Processing helix chain 'B' and resid 983 through 999 Processing helix chain 'B' and resid 1012 through 1021 removed outlier: 3.775A pdb=" N LEU B1017 " --> pdb=" O PRO B1013 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLU B1018 " --> pdb=" O VAL B1014 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N LYS B1019 " --> pdb=" O CYS B1015 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN B1020 " --> pdb=" O GLU B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1068 through 1075 Processing helix chain 'B' and resid 1080 through 1111 Processing helix chain 'B' and resid 1116 through 1122 Processing sheet with id= A, first strand: chain 'A' and resid 147 through 149 removed outlier: 6.977A pdb=" N GLU A 198 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU A 223 " --> pdb=" O CYS A 199 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N LEU A 201 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR A 225 " --> pdb=" O LEU A 201 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 173 through 175 Processing sheet with id= C, first strand: chain 'A' and resid 512 through 516 Processing sheet with id= D, first strand: chain 'A' and resid 623 through 625 Processing sheet with id= E, first strand: chain 'A' and resid 778 through 781 removed outlier: 4.593A pdb=" N GLN A 816 " --> pdb=" O THR A 803 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 708 through 711 removed outlier: 6.163A pdb=" N LEU A 744 " --> pdb=" O LEU A 709 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ARG A 711 " --> pdb=" O LEU A 744 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ILE A 746 " --> pdb=" O ARG A 711 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 246 through 250 removed outlier: 6.580A pdb=" N LYS B 303 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N CYS B 249 " --> pdb=" O LYS B 303 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLY B 305 " --> pdb=" O CYS B 249 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 255 through 259 Processing sheet with id= I, first strand: chain 'B' and resid 368 through 371 removed outlier: 6.875A pdb=" N GLU B 425 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N ILE B 371 " --> pdb=" O GLU B 425 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU B 427 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ARG B 454 " --> pdb=" O LEU B 426 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N LEU B 428 " --> pdb=" O ARG B 454 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLU B 456 " --> pdb=" O LEU B 428 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 386 through 392 Processing sheet with id= K, first strand: chain 'B' and resid 882 through 884 removed outlier: 3.643A pdb=" N VAL B 858 " --> pdb=" O THR B 928 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU B 926 " --> pdb=" O LYS B 860 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 1059 through 1061 removed outlier: 6.519A pdb=" N VAL B 891 " --> pdb=" O GLY B1026 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N TYR B1028 " --> pdb=" O VAL B 891 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ILE B 893 " --> pdb=" O TYR B1028 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N MET B1030 " --> pdb=" O ILE B 893 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N THR B 895 " --> pdb=" O MET B1030 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N THR B1005 " --> pdb=" O MET B 892 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ILE B 894 " --> pdb=" O THR B1005 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N PHE B1007 " --> pdb=" O ILE B 894 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLY B 934 " --> pdb=" O LEU B 971 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ILE B 973 " --> pdb=" O GLY B 934 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N PHE B 936 " --> pdb=" O ILE B 973 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ASP B 975 " --> pdb=" O PHE B 936 " (cutoff:3.500A) 547 hydrogen bonds defined for protein. 1563 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 47 hydrogen bonds 94 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 5.00 Time building geometry restraints manager: 6.45 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: 2681 1.33 - 1.46: 4196 1.46 - 1.58: 6562 1.58 - 1.71: 91 1.71 - 1.83: 99 Bond restraints: 13629 Sorted by residual: bond pdb=" C LEU A 414 " pdb=" N PRO A 415 " ideal model delta sigma weight residual 1.331 1.385 -0.054 7.90e-03 1.60e+04 4.64e+01 bond pdb=" C4 ADP A2000 " pdb=" C5 ADP A2000 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" C4 ADP B2000 " pdb=" C5 ADP B2000 " ideal model delta sigma weight residual 1.490 1.384 0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" N PRO A 415 " pdb=" CA PRO A 415 " ideal model delta sigma weight residual 1.470 1.417 0.053 1.01e-02 9.80e+03 2.77e+01 bond pdb=" N PRO A 415 " pdb=" CD PRO A 415 " ideal model delta sigma weight residual 1.473 1.536 -0.063 1.40e-02 5.10e+03 2.03e+01 ... (remaining 13624 not shown) Histogram of bond angle deviations from ideal: 67.52 - 82.19: 3 82.19 - 96.86: 1 96.86 - 111.53: 5423 111.53 - 126.20: 12902 126.20 - 140.87: 249 Bond angle restraints: 18578 Sorted by residual: angle pdb=" C PRO A 415 " pdb=" CA PRO A 415 " pdb=" CB PRO A 415 " ideal model delta sigma weight residual 110.00 140.87 -30.87 1.12e+00 7.97e-01 7.60e+02 angle pdb=" N PRO A 415 " pdb=" CA PRO A 415 " pdb=" CB PRO A 415 " ideal model delta sigma weight residual 102.17 75.57 26.60 1.05e+00 9.07e-01 6.42e+02 angle pdb=" N PRO A 415 " pdb=" CD PRO A 415 " pdb=" CG PRO A 415 " ideal model delta sigma weight residual 103.20 74.69 28.51 1.50e+00 4.44e-01 3.61e+02 angle pdb=" CB PRO A 415 " pdb=" CG PRO A 415 " pdb=" CD PRO A 415 " ideal model delta sigma weight residual 106.10 67.52 38.58 3.20e+00 9.77e-02 1.45e+02 angle pdb=" C LEU A 414 " pdb=" N PRO A 415 " pdb=" CA PRO A 415 " ideal model delta sigma weight residual 121.00 109.91 11.09 1.16e+00 7.43e-01 9.14e+01 ... (remaining 18573 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.71: 7694 33.71 - 67.43: 476 67.43 - 101.14: 15 101.14 - 134.85: 2 134.85 - 168.56: 1 Dihedral angle restraints: 8188 sinusoidal: 3661 harmonic: 4527 Sorted by residual: dihedral pdb=" N PRO A 415 " pdb=" C PRO A 415 " pdb=" CA PRO A 415 " pdb=" CB PRO A 415 " ideal model delta harmonic sigma weight residual 115.10 86.80 28.30 0 2.50e+00 1.60e-01 1.28e+02 dihedral pdb=" C PRO A 415 " pdb=" N PRO A 415 " pdb=" CA PRO A 415 " pdb=" CB PRO A 415 " ideal model delta harmonic sigma weight residual -120.70 -139.41 18.71 0 2.50e+00 1.60e-01 5.60e+01 dihedral pdb=" O1B ADP B2000 " pdb=" O3A ADP B2000 " pdb=" PB ADP B2000 " pdb=" PA ADP B2000 " ideal model delta sinusoidal sigma weight residual 300.00 131.43 168.56 1 2.00e+01 2.50e-03 4.75e+01 ... (remaining 8185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 1966 0.146 - 0.293: 162 0.293 - 0.439: 4 0.439 - 0.585: 0 0.585 - 0.731: 1 Chirality restraints: 2133 Sorted by residual: chirality pdb=" CA PRO A 415 " pdb=" N PRO A 415 " pdb=" C PRO A 415 " pdb=" CB PRO A 415 " both_signs ideal model delta sigma weight residual False 2.72 1.99 0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" CA LEU A 414 " pdb=" N LEU A 414 " pdb=" C LEU A 414 " pdb=" CB LEU A 414 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.61e+00 chirality pdb=" C3' DG C 36 " pdb=" C4' DG C 36 " pdb=" O3' DG C 36 " pdb=" C2' DG C 36 " both_signs ideal model delta sigma weight residual False -2.66 -2.30 -0.36 2.00e-01 2.50e+01 3.20e+00 ... (remaining 2130 not shown) Planarity restraints: 2201 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 415 " -0.020 2.00e-02 2.50e+03 4.09e-02 1.67e+01 pdb=" C PRO A 415 " 0.071 2.00e-02 2.50e+03 pdb=" O PRO A 415 " -0.026 2.00e-02 2.50e+03 pdb=" N ASN A 416 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 414 " -0.039 5.00e-02 4.00e+02 5.73e-02 5.25e+00 pdb=" N PRO A 415 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 415 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 415 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' ADP B2000 " -0.029 2.00e-02 2.50e+03 1.30e-02 4.62e+00 pdb=" C2 ADP B2000 " 0.012 2.00e-02 2.50e+03 pdb=" C4 ADP B2000 " 0.006 2.00e-02 2.50e+03 pdb=" C5 ADP B2000 " -0.004 2.00e-02 2.50e+03 pdb=" C6 ADP B2000 " -0.006 2.00e-02 2.50e+03 pdb=" C8 ADP B2000 " 0.015 2.00e-02 2.50e+03 pdb=" N1 ADP B2000 " -0.003 2.00e-02 2.50e+03 pdb=" N3 ADP B2000 " -0.001 2.00e-02 2.50e+03 pdb=" N6 ADP B2000 " -0.008 2.00e-02 2.50e+03 pdb=" N7 ADP B2000 " -0.003 2.00e-02 2.50e+03 pdb=" N9 ADP B2000 " 0.022 2.00e-02 2.50e+03 ... (remaining 2198 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 191 2.60 - 3.18: 11994 3.18 - 3.75: 23270 3.75 - 4.33: 31826 4.33 - 4.90: 48478 Nonbonded interactions: 115759 Sorted by model distance: nonbonded pdb=" O3B ADP A2000 " pdb="MG MG A2001 " model vdw 2.025 2.170 nonbonded pdb=" OH TYR A 757 " pdb=" CD1 ILE B1097 " model vdw 2.056 3.460 nonbonded pdb=" O2B ADP B2000 " pdb="MG MG B2001 " model vdw 2.073 2.170 nonbonded pdb=" OG SER B 903 " pdb=" OD2 ASP B 975 " model vdw 2.079 2.440 nonbonded pdb=" O HIS A 785 " pdb=" OG1 THR A 788 " model vdw 2.118 2.440 ... (remaining 115754 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: 1.660 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: 0.020 Extract box with map and model: 7.230 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 44.230 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 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 : 0.008 0.188 13629 Z= 0.493 Angle : 1.286 38.579 18578 Z= 0.843 Chirality : 0.088 0.731 2133 Planarity : 0.005 0.057 2201 Dihedral : 18.878 168.563 5240 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 25.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.76 % Allowed : 22.53 % Favored : 74.71 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.21), residues: 1518 helix: 0.15 (0.18), residues: 766 sheet: -2.38 (0.36), residues: 172 loop : -1.92 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.005 TRP A 764 HIS 0.011 0.003 HIS A 829 PHE 0.027 0.004 PHE B 784 TYR 0.027 0.004 TYR B1021 ARG 0.013 0.002 ARG B 593 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 271 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 16 residues processed: 298 average time/residue: 0.2947 time to fit residues: 122.1079 Evaluate side-chains 273 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 257 time to evaluate : 1.390 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1192 time to fit residues: 5.6025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 0.7980 chunk 119 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 75 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 846 GLN B 550 ASN ** B 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 729 HIS ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 898 ASN ** B 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1098 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 13629 Z= 0.240 Angle : 0.627 6.701 18578 Z= 0.327 Chirality : 0.041 0.159 2133 Planarity : 0.004 0.047 2201 Dihedral : 17.833 174.666 2147 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 20.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 4.00 % Allowed : 22.46 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.22), residues: 1518 helix: 0.47 (0.19), residues: 774 sheet: -2.24 (0.36), residues: 181 loop : -1.78 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 764 HIS 0.008 0.001 HIS B 984 PHE 0.022 0.002 PHE A 468 TYR 0.018 0.002 TYR B 846 ARG 0.006 0.001 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 264 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 27 residues processed: 298 average time/residue: 0.2976 time to fit residues: 123.1919 Evaluate side-chains 278 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 251 time to evaluate : 1.432 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.1329 time to fit residues: 8.5715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 119 optimal weight: 0.4980 chunk 97 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 143 optimal weight: 0.5980 chunk 155 optimal weight: 7.9990 chunk 128 optimal weight: 0.9990 chunk 142 optimal weight: 0.6980 chunk 49 optimal weight: 0.4980 chunk 115 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 402 GLN ** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 792 ASN A 816 GLN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 898 ASN ** B 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 13629 Z= 0.224 Angle : 0.600 6.905 18578 Z= 0.313 Chirality : 0.041 0.168 2133 Planarity : 0.004 0.054 2201 Dihedral : 17.793 169.343 2147 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 20.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.76 % Allowed : 23.26 % Favored : 73.98 % 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: -0.86 (0.22), residues: 1518 helix: 0.61 (0.19), residues: 767 sheet: -2.12 (0.36), residues: 186 loop : -1.58 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 764 HIS 0.019 0.001 HIS B 729 PHE 0.016 0.002 PHE A 468 TYR 0.016 0.001 TYR B1011 ARG 0.008 0.001 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 266 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 16 residues processed: 291 average time/residue: 0.2969 time to fit residues: 120.0974 Evaluate side-chains 276 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 260 time to evaluate : 1.473 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1288 time to fit residues: 5.9098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 96 optimal weight: 0.3980 chunk 144 optimal weight: 0.1980 chunk 152 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 136 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 402 GLN ** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13629 Z= 0.200 Angle : 0.588 10.326 18578 Z= 0.306 Chirality : 0.041 0.243 2133 Planarity : 0.004 0.055 2201 Dihedral : 17.668 159.705 2147 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 18.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.98 % Allowed : 23.98 % Favored : 73.04 % 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: -0.77 (0.22), residues: 1518 helix: 0.69 (0.19), residues: 764 sheet: -1.97 (0.38), residues: 178 loop : -1.60 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 764 HIS 0.011 0.001 HIS B 729 PHE 0.017 0.002 PHE A 836 TYR 0.016 0.001 TYR B1011 ARG 0.009 0.001 ARG B 796 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 259 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 16 residues processed: 284 average time/residue: 0.2970 time to fit residues: 117.6490 Evaluate side-chains 266 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 250 time to evaluate : 1.387 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1575 time to fit residues: 6.2100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 113 optimal weight: 0.3980 chunk 63 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 105 optimal weight: 0.0570 chunk 0 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 137 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 ASN ** B 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13629 Z= 0.256 Angle : 0.637 9.529 18578 Z= 0.332 Chirality : 0.042 0.172 2133 Planarity : 0.005 0.054 2201 Dihedral : 17.607 154.505 2147 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 20.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.83 % Allowed : 25.07 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.22), residues: 1518 helix: 0.62 (0.19), residues: 757 sheet: -1.85 (0.39), residues: 172 loop : -1.56 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 764 HIS 0.020 0.001 HIS B 729 PHE 0.022 0.002 PHE B 784 TYR 0.024 0.002 TYR B1011 ARG 0.009 0.001 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 265 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 19 residues processed: 286 average time/residue: 0.2888 time to fit residues: 115.0307 Evaluate side-chains 270 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 251 time to evaluate : 1.310 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1849 time to fit residues: 7.4122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 0.9980 chunk 137 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 37 optimal weight: 0.0050 chunk 152 optimal weight: 0.7980 chunk 126 optimal weight: 0.0570 chunk 70 optimal weight: 3.9990 chunk 12 optimal weight: 0.0770 chunk 50 optimal weight: 0.1980 chunk 80 optimal weight: 3.9990 overall best weight: 0.1870 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 GLN ** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 ASN A 662 GLN ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 HIS ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 984 HIS ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13629 Z= 0.181 Angle : 0.615 9.259 18578 Z= 0.320 Chirality : 0.040 0.150 2133 Planarity : 0.004 0.055 2201 Dihedral : 17.490 143.772 2147 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.35 % Favored : 95.59 % Rotamer: Outliers : 1.96 % Allowed : 25.87 % Favored : 72.17 % 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: -0.60 (0.22), residues: 1518 helix: 0.78 (0.19), residues: 766 sheet: -1.77 (0.37), residues: 189 loop : -1.47 (0.28), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 764 HIS 0.020 0.001 HIS B 729 PHE 0.024 0.001 PHE B 784 TYR 0.017 0.001 TYR B 685 ARG 0.008 0.000 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 253 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 12 residues processed: 269 average time/residue: 0.3392 time to fit residues: 127.5626 Evaluate side-chains 253 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 241 time to evaluate : 1.486 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1357 time to fit residues: 5.1570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 0.2980 chunk 17 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 111 optimal weight: 0.5980 chunk 86 optimal weight: 0.2980 chunk 128 optimal weight: 0.5980 chunk 85 optimal weight: 0.8980 chunk 152 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 984 HIS ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 13629 Z= 0.209 Angle : 0.631 9.228 18578 Z= 0.326 Chirality : 0.041 0.166 2133 Planarity : 0.004 0.054 2201 Dihedral : 17.475 140.247 2147 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 20.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.07 % Favored : 94.86 % Rotamer: Outliers : 1.67 % Allowed : 27.11 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.22), residues: 1518 helix: 0.74 (0.19), residues: 766 sheet: -1.71 (0.38), residues: 189 loop : -1.56 (0.27), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 764 HIS 0.009 0.001 HIS A 829 PHE 0.022 0.001 PHE A 836 TYR 0.018 0.001 TYR B1011 ARG 0.012 0.001 ARG B 796 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 249 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 8 residues processed: 266 average time/residue: 0.2971 time to fit residues: 110.1489 Evaluate side-chains 246 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 238 time to evaluate : 1.279 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1455 time to fit residues: 4.1286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 94 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13629 Z= 0.265 Angle : 0.665 9.327 18578 Z= 0.345 Chirality : 0.042 0.231 2133 Planarity : 0.005 0.053 2201 Dihedral : 17.525 142.369 2147 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 21.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.73 % Favored : 94.20 % Rotamer: Outliers : 1.67 % Allowed : 27.40 % Favored : 70.93 % 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: -0.85 (0.22), residues: 1518 helix: 0.58 (0.19), residues: 770 sheet: -1.80 (0.37), residues: 182 loop : -1.68 (0.27), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 764 HIS 0.013 0.001 HIS B 729 PHE 0.025 0.002 PHE A 760 TYR 0.025 0.002 TYR B1011 ARG 0.013 0.001 ARG B 796 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 241 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 13 residues processed: 251 average time/residue: 0.3110 time to fit residues: 108.8706 Evaluate side-chains 251 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 238 time to evaluate : 1.440 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1620 time to fit residues: 5.8562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 0.0980 chunk 133 optimal weight: 0.8980 chunk 141 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 128 optimal weight: 0.9980 chunk 134 optimal weight: 0.5980 chunk 93 optimal weight: 0.0980 chunk 150 optimal weight: 0.9980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13629 Z= 0.208 Angle : 0.662 18.709 18578 Z= 0.337 Chirality : 0.041 0.172 2133 Planarity : 0.005 0.054 2201 Dihedral : 17.441 143.575 2147 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 18.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.20 % Favored : 94.73 % Rotamer: Outliers : 0.94 % Allowed : 27.98 % Favored : 71.08 % 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: -0.73 (0.22), residues: 1518 helix: 0.71 (0.19), residues: 765 sheet: -1.91 (0.37), residues: 182 loop : -1.58 (0.27), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP B 768 HIS 0.008 0.001 HIS A 829 PHE 0.022 0.002 PHE A 836 TYR 0.018 0.001 TYR A 678 ARG 0.011 0.001 ARG B 669 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 235 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 241 average time/residue: 0.3030 time to fit residues: 101.6886 Evaluate side-chains 238 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 233 time to evaluate : 1.452 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1550 time to fit residues: 3.5458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 91 optimal weight: 5.9990 chunk 71 optimal weight: 8.9990 chunk 104 optimal weight: 0.7980 chunk 157 optimal weight: 5.9990 chunk 144 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 96 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 GLN ** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 984 HIS ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13629 Z= 0.287 Angle : 0.705 18.043 18578 Z= 0.362 Chirality : 0.043 0.174 2133 Planarity : 0.005 0.056 2201 Dihedral : 17.498 143.437 2147 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 21.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.99 % Favored : 93.94 % Rotamer: Outliers : 0.73 % Allowed : 27.91 % Favored : 71.37 % 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: -0.90 (0.22), residues: 1518 helix: 0.51 (0.19), residues: 763 sheet: -1.84 (0.38), residues: 175 loop : -1.62 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 768 HIS 0.008 0.001 HIS A 785 PHE 0.037 0.002 PHE A 760 TYR 0.041 0.002 TYR A 678 ARG 0.009 0.001 ARG B 669 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 244 time to evaluate : 1.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 249 average time/residue: 0.3003 time to fit residues: 104.0696 Evaluate side-chains 245 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 242 time to evaluate : 1.395 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1447 time to fit residues: 2.7842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 38 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 125 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 128 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 110 optimal weight: 0.0370 chunk 7 optimal weight: 0.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 ASN A 653 ASN ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 750 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.203437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.165581 restraints weight = 20766.851| |-----------------------------------------------------------------------------| r_work (start): 0.4198 rms_B_bonded: 3.04 r_work: 0.4046 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6492 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13629 Z= 0.232 Angle : 0.701 17.577 18578 Z= 0.356 Chirality : 0.042 0.266 2133 Planarity : 0.005 0.054 2201 Dihedral : 17.444 143.056 2147 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 21.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.53 % Favored : 94.40 % Rotamer: Outliers : 0.44 % Allowed : 29.29 % Favored : 70.28 % 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: -0.91 (0.22), residues: 1518 helix: 0.50 (0.19), residues: 769 sheet: -1.92 (0.37), residues: 181 loop : -1.61 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 764 HIS 0.008 0.001 HIS B 984 PHE 0.034 0.002 PHE A 760 TYR 0.018 0.002 TYR B1011 ARG 0.011 0.001 ARG B 796 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3618.12 seconds wall clock time: 66 minutes 28.60 seconds (3988.60 seconds total)