Starting phenix.real_space_refine on Tue Sep 24 10:37:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w7v_32349/09_2024/7w7v_32349.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w7v_32349/09_2024/7w7v_32349.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w7v_32349/09_2024/7w7v_32349.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w7v_32349/09_2024/7w7v_32349.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w7v_32349/09_2024/7w7v_32349.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w7v_32349/09_2024/7w7v_32349.cif" } resolution = 3.0 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mg 1 5.21 5 S 58 5.16 5 Be 1 3.05 5 C 4984 2.51 5 N 1305 2.21 5 O 1471 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 7823 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1012, 7818 Classifications: {'peptide': 1012} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 45, 'TRANS': 966} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 5 Unusual residues: {' MG': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.74, per 1000 atoms: 0.61 Number of scatterers: 7823 At special positions: 0 Unit cell: (88.395, 98.355, 141.93, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 58 16.00 Mg 1 11.99 F 3 9.00 O 1471 8.00 N 1305 7.00 C 4984 6.00 Be 1 4.00 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 - 3.00 Amino acid : True - 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.06 Conformation dependent library (CDL) restraints added in 1.0 seconds 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1896 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 6 sheets defined 54.6% alpha, 14.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 Processing helix chain 'A' and resid 8 through 17 removed outlier: 3.623A pdb=" N PHE A 16 " --> pdb=" O VAL A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 37 Processing helix chain 'A' and resid 48 through 56 Processing helix chain 'A' and resid 59 through 79 Processing helix chain 'A' and resid 84 through 87 removed outlier: 3.854A pdb=" N ALA A 87 " --> pdb=" O THR A 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 84 through 87' Processing helix chain 'A' and resid 88 through 117 removed outlier: 3.935A pdb=" N PHE A 92 " --> pdb=" O PHE A 88 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ILE A 94 " --> pdb=" O GLU A 90 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 95 " --> pdb=" O PRO A 91 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A 96 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ILE A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ALA A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU A 109 " --> pdb=" O GLY A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 120 No H-bonds generated for 'chain 'A' and resid 118 through 120' Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'A' and resid 226 through 229 Processing helix chain 'A' and resid 230 through 242 Processing helix chain 'A' and resid 247 through 276 Processing helix chain 'A' and resid 277 through 281 removed outlier: 4.009A pdb=" N ASN A 280 " --> pdb=" O GLY A 277 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASP A 281 " --> pdb=" O HIS A 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 277 through 281' Processing helix chain 'A' and resid 291 through 307 Processing helix chain 'A' and resid 310 through 329 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 403 through 406 removed outlier: 3.656A pdb=" N GLN A 406 " --> pdb=" O ASN A 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 403 through 406' Processing helix chain 'A' and resid 407 through 421 removed outlier: 3.942A pdb=" N ASN A 421 " --> pdb=" O CYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 452 Processing helix chain 'A' and resid 463 through 468 removed outlier: 4.059A pdb=" N ALA A 468 " --> pdb=" O LYS A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 478 removed outlier: 3.534A pdb=" N SER A 473 " --> pdb=" O ASN A 469 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL A 474 " --> pdb=" O ALA A 470 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 523 Processing helix chain 'A' and resid 537 through 554 removed outlier: 3.710A pdb=" N LYS A 541 " --> pdb=" O THR A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 586 removed outlier: 4.090A pdb=" N ILE A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS A 585 " --> pdb=" O ALA A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 616 removed outlier: 3.609A pdb=" N SER A 609 " --> pdb=" O GLU A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 639 Processing helix chain 'A' and resid 654 through 660 Processing helix chain 'A' and resid 661 through 672 removed outlier: 3.916A pdb=" N ASP A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 692 Processing helix chain 'A' and resid 703 through 705 No H-bonds generated for 'chain 'A' and resid 703 through 705' Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 723 through 730 Processing helix chain 'A' and resid 740 through 781 Processing helix chain 'A' and resid 787 through 807 removed outlier: 4.331A pdb=" N ASP A 799 " --> pdb=" O ASN A 795 " (cutoff:3.500A) Proline residue: A 802 - end of helix Processing helix chain 'A' and resid 829 through 857 Processing helix chain 'A' and resid 887 through 891 Processing helix chain 'A' and resid 892 through 913 removed outlier: 4.546A pdb=" N MET A 896 " --> pdb=" O SER A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 928 Processing helix chain 'A' and resid 929 through 948 removed outlier: 3.575A pdb=" N VAL A 933 " --> pdb=" O ASN A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 956 Processing helix chain 'A' and resid 962 through 974 Processing helix chain 'A' and resid 974 through 990 removed outlier: 3.861A pdb=" N LEU A 978 " --> pdb=" O LEU A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1031 removed outlier: 3.589A pdb=" N LEU A1021 " --> pdb=" O PRO A1017 " (cutoff:3.500A) Proline residue: A1024 - end of helix removed outlier: 4.690A pdb=" N TRP A1028 " --> pdb=" O PRO A1024 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER A1031 " --> pdb=" O ILE A1027 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 134 through 141 removed outlier: 6.159A pdb=" N SER A 136 " --> pdb=" O ARG A 131 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ARG A 131 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LYS A 128 " --> pdb=" O GLU A 152 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE A 150 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N VAL A 222 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N LEU A 165 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL A 224 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N ILE A 163 " --> pdb=" O VAL A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 189 removed outlier: 4.594A pdb=" N LEU A 173 " --> pdb=" O LYS A 189 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN A 213 " --> pdb=" O ASP A 176 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 331 through 333 removed outlier: 6.387A pdb=" N GLY A 716 " --> pdb=" O MET A 732 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N LEU A 734 " --> pdb=" O GLY A 716 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ALA A 718 " --> pdb=" O LEU A 734 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N THR A 697 " --> pdb=" O ILE A 715 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ILE A 717 " --> pdb=" O THR A 697 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N MET A 699 " --> pdb=" O ILE A 717 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N MET A 719 " --> pdb=" O MET A 699 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N GLY A 701 " --> pdb=" O MET A 719 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL A 347 " --> pdb=" O ALA A 698 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N THR A 700 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N CYS A 349 " --> pdb=" O THR A 700 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N PHE A 675 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N MET A 622 " --> pdb=" O PHE A 675 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 395 through 396 removed outlier: 7.470A pdb=" N THR A 376 " --> pdb=" O VAL A 372 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N VAL A 372 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N SER A 378 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N CYS A 364 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N VAL A 363 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU A 599 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS A 595 " --> pdb=" O PHE A 367 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU A 369 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N VAL A 593 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 14.347A pdb=" N ARG A 371 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 16.417A pdb=" N THR A 591 " --> pdb=" O ARG A 371 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N PHE A 592 " --> pdb=" O THR A 565 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N THR A 565 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET A 598 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N SER A 493 " --> pdb=" O PHE A 487 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N PHE A 487 " --> pdb=" O SER A 493 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N THR A 499 " --> pdb=" O LYS A 481 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LYS A 481 " --> pdb=" O THR A 499 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 395 through 396 removed outlier: 7.470A pdb=" N THR A 376 " --> pdb=" O VAL A 372 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N VAL A 372 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N SER A 378 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N CYS A 364 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N VAL A 363 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU A 599 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS A 595 " --> pdb=" O PHE A 367 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU A 369 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N VAL A 593 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 14.347A pdb=" N ARG A 371 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 16.417A pdb=" N THR A 591 " --> pdb=" O ARG A 371 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N HIS A 526 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 8.738A pdb=" N GLY A 594 " --> pdb=" O HIS A 526 " (cutoff:3.500A) removed outlier: 9.554A pdb=" N ARG A 528 " --> pdb=" O GLY A 594 " (cutoff:3.500A) removed outlier: 13.134A pdb=" N VAL A 596 " --> pdb=" O ARG A 528 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 425 through 428 428 hydrogen bonds defined for protein. 1239 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: 2.57 Time building geometry restraints manager: 2.38 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: 2554 1.34 - 1.46: 1500 1.46 - 1.58: 3824 1.58 - 1.70: 0 1.70 - 1.82: 90 Bond restraints: 7968 Sorted by residual: bond pdb=" F2 BEF A2001 " pdb="BE BEF A2001 " ideal model delta sigma weight residual 1.476 1.560 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" F3 BEF A2001 " pdb="BE BEF A2001 " ideal model delta sigma weight residual 1.476 1.546 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" F1 BEF A2001 " pdb="BE BEF A2001 " ideal model delta sigma weight residual 1.476 1.534 -0.058 2.00e-02 2.50e+03 8.32e+00 bond pdb=" C MET A1023 " pdb=" N PRO A1024 " ideal model delta sigma weight residual 1.337 1.351 -0.014 9.80e-03 1.04e+04 2.18e+00 bond pdb=" CB GLU A 748 " pdb=" CG GLU A 748 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 9.79e-01 ... (remaining 7963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 10745 2.73 - 5.46: 63 5.46 - 8.20: 3 8.20 - 10.93: 1 10.93 - 13.66: 1 Bond angle restraints: 10813 Sorted by residual: angle pdb=" F2 BEF A2001 " pdb="BE BEF A2001 " pdb=" F3 BEF A2001 " ideal model delta sigma weight residual 119.96 106.30 13.66 3.00e+00 1.11e-01 2.07e+01 angle pdb=" F1 BEF A2001 " pdb="BE BEF A2001 " pdb=" F3 BEF A2001 " ideal model delta sigma weight residual 120.12 109.90 10.22 3.00e+00 1.11e-01 1.16e+01 angle pdb=" N GLY A 291 " pdb=" CA GLY A 291 " pdb=" C GLY A 291 " ideal model delta sigma weight residual 115.66 110.50 5.16 1.56e+00 4.11e-01 1.09e+01 angle pdb=" F1 BEF A2001 " pdb="BE BEF A2001 " pdb=" F2 BEF A2001 " ideal model delta sigma weight residual 119.91 112.04 7.87 3.00e+00 1.11e-01 6.88e+00 angle pdb=" C GLN A 758 " pdb=" N PHE A 759 " pdb=" CA PHE A 759 " ideal model delta sigma weight residual 121.14 116.57 4.57 1.75e+00 3.27e-01 6.81e+00 ... (remaining 10808 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 4388 17.45 - 34.91: 365 34.91 - 52.36: 54 52.36 - 69.81: 8 69.81 - 87.27: 10 Dihedral angle restraints: 4825 sinusoidal: 1901 harmonic: 2924 Sorted by residual: dihedral pdb=" CA MET A 536 " pdb=" C MET A 536 " pdb=" N THR A 537 " pdb=" CA THR A 537 " ideal model delta harmonic sigma weight residual 180.00 161.40 18.60 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CB GLU A 439 " pdb=" CG GLU A 439 " pdb=" CD GLU A 439 " pdb=" OE1 GLU A 439 " ideal model delta sinusoidal sigma weight residual 0.00 86.67 -86.67 1 3.00e+01 1.11e-03 1.00e+01 dihedral pdb=" CA GLU A 950 " pdb=" C GLU A 950 " pdb=" N PRO A 951 " pdb=" CA PRO A 951 " ideal model delta harmonic sigma weight residual -180.00 -164.86 -15.14 0 5.00e+00 4.00e-02 9.16e+00 ... (remaining 4822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 862 0.036 - 0.072: 288 0.072 - 0.109: 95 0.109 - 0.145: 22 0.145 - 0.181: 2 Chirality restraints: 1269 Sorted by residual: chirality pdb=" CA PHE A 759 " pdb=" N PHE A 759 " pdb=" C PHE A 759 " pdb=" CB PHE A 759 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.21e-01 chirality pdb=" CA GLU A 90 " pdb=" N GLU A 90 " pdb=" C GLU A 90 " pdb=" CB GLU A 90 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.29e-01 chirality pdb=" CA LEU A 974 " pdb=" N LEU A 974 " pdb=" C LEU A 974 " pdb=" CB LEU A 974 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.27e-01 ... (remaining 1266 not shown) Planarity restraints: 1378 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 534 " -0.065 5.00e-02 4.00e+02 9.88e-02 1.56e+01 pdb=" N PRO A 535 " 0.171 5.00e-02 4.00e+02 pdb=" CA PRO A 535 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 535 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 796 " 0.009 2.00e-02 2.50e+03 1.71e-02 2.94e+00 pdb=" C LEU A 796 " -0.030 2.00e-02 2.50e+03 pdb=" O LEU A 796 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL A 797 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 759 " -0.011 2.00e-02 2.50e+03 1.04e-02 1.90e+00 pdb=" CG PHE A 759 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE A 759 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 759 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 759 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 759 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 759 " -0.004 2.00e-02 2.50e+03 ... (remaining 1375 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 69 2.59 - 3.17: 6785 3.17 - 3.74: 12824 3.74 - 4.32: 16942 4.32 - 4.90: 27900 Nonbonded interactions: 64520 Sorted by model distance: nonbonded pdb=" OD2 ASP A 351 " pdb=" F3 BEF A2001 " model vdw 2.010 2.990 nonbonded pdb=" OD2 ASP A 351 " pdb="MG MG A2002 " model vdw 2.064 2.170 nonbonded pdb=" O THR A 353 " pdb="MG MG A2002 " model vdw 2.064 2.170 nonbonded pdb=" OD1 ASP A 702 " pdb="MG MG A2002 " model vdw 2.076 2.170 nonbonded pdb=" OE2 GLU A 373 " pdb=" OG1 THR A 376 " model vdw 2.130 3.040 ... (remaining 64515 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: 0.260 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.100 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 7968 Z= 0.171 Angle : 0.555 13.660 10813 Z= 0.299 Chirality : 0.041 0.181 1269 Planarity : 0.004 0.099 1378 Dihedral : 13.316 87.266 2929 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: 0.63 (0.27), residues: 1006 helix: 1.34 (0.24), residues: 483 sheet: -0.15 (0.51), residues: 97 loop : -0.44 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 831 HIS 0.009 0.001 HIS A 278 PHE 0.024 0.001 PHE A 759 TYR 0.007 0.001 TYR A 842 ARG 0.004 0.000 ARG A 666 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 0.998 Fit side-chains revert: symmetry clash REVERT: A 8 THR cc_start: 0.7687 (p) cc_final: 0.7479 (t) REVERT: A 207 MET cc_start: 0.8443 (mmm) cc_final: 0.7943 (mmm) REVERT: A 218 LYS cc_start: 0.8225 (ttmt) cc_final: 0.7872 (ttmt) REVERT: A 238 GLU cc_start: 0.6968 (tt0) cc_final: 0.6700 (tt0) REVERT: A 259 GLN cc_start: 0.5474 (mt0) cc_final: 0.5268 (mt0) REVERT: A 361 MET cc_start: 0.8148 (tpp) cc_final: 0.7754 (tpp) REVERT: A 437 VAL cc_start: 0.6945 (m) cc_final: 0.6724 (t) REVERT: A 452 MET cc_start: 0.8382 (ptt) cc_final: 0.8095 (ptt) REVERT: A 466 GLU cc_start: 0.6981 (pm20) cc_final: 0.6280 (tp30) REVERT: A 487 PHE cc_start: 0.6587 (t80) cc_final: 0.6231 (t80) REVERT: A 508 MET cc_start: 0.5266 (tmm) cc_final: 0.3693 (tpp) REVERT: A 536 MET cc_start: 0.3243 (mmp) cc_final: 0.2114 (tpp) REVERT: A 670 LEU cc_start: 0.7702 (mm) cc_final: 0.7441 (mt) REVERT: A 699 MET cc_start: 0.8088 (tpt) cc_final: 0.5974 (tpt) REVERT: A 824 LYS cc_start: 0.7183 (mmtt) cc_final: 0.6570 (mmpt) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 1.1973 time to fit residues: 209.3351 Evaluate side-chains 112 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.0980 chunk 76 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN A 380 ASN A 428 ASN A 477 GLN A 918 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7968 Z= 0.197 Angle : 0.552 10.712 10813 Z= 0.288 Chirality : 0.043 0.172 1269 Planarity : 0.005 0.076 1378 Dihedral : 3.981 19.857 1070 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.55 % Allowed : 10.88 % Favored : 86.57 % 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: 0.59 (0.27), residues: 1006 helix: 1.23 (0.24), residues: 504 sheet: -0.53 (0.51), residues: 93 loop : -0.34 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 927 HIS 0.006 0.001 HIS A 405 PHE 0.030 0.001 PHE A 367 TYR 0.013 0.001 TYR A 497 ARG 0.005 0.001 ARG A 324 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 121 time to evaluate : 0.836 Fit side-chains REVERT: A 33 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7106 (tptp) REVERT: A 157 ASP cc_start: 0.7475 (OUTLIER) cc_final: 0.6779 (m-30) REVERT: A 218 LYS cc_start: 0.8269 (ttmt) cc_final: 0.7959 (ttmt) REVERT: A 238 GLU cc_start: 0.6935 (tt0) cc_final: 0.6640 (tt0) REVERT: A 259 GLN cc_start: 0.5907 (mt0) cc_final: 0.5517 (mt0) REVERT: A 361 MET cc_start: 0.8105 (tpp) cc_final: 0.7694 (tpp) REVERT: A 413 LEU cc_start: 0.7892 (tp) cc_final: 0.7443 (tt) REVERT: A 437 VAL cc_start: 0.6937 (m) cc_final: 0.6736 (t) REVERT: A 439 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6616 (tm-30) REVERT: A 466 GLU cc_start: 0.7215 (pm20) cc_final: 0.6458 (tp30) REVERT: A 487 PHE cc_start: 0.6606 (t80) cc_final: 0.6234 (t80) REVERT: A 508 MET cc_start: 0.5338 (tmm) cc_final: 0.3622 (tpp) REVERT: A 536 MET cc_start: 0.3616 (mmp) cc_final: 0.2690 (tpp) REVERT: A 575 MET cc_start: 0.3779 (mmp) cc_final: 0.3126 (mmt) REVERT: A 670 LEU cc_start: 0.7800 (mm) cc_final: 0.7344 (mt) REVERT: A 699 MET cc_start: 0.8126 (tpt) cc_final: 0.5749 (tpt) REVERT: A 731 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6694 (mt-10) REVERT: A 756 MET cc_start: 0.7308 (OUTLIER) cc_final: 0.6919 (mmt) REVERT: A 824 LYS cc_start: 0.7249 (mmtt) cc_final: 0.6640 (mmpt) REVERT: A 1023 MET cc_start: 0.3161 (tmt) cc_final: 0.2447 (ptt) outliers start: 22 outliers final: 9 residues processed: 137 average time/residue: 1.0949 time to fit residues: 159.9696 Evaluate side-chains 117 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 103 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 669 CYS Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 916 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 6.9990 chunk 28 optimal weight: 0.0070 chunk 76 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 81 optimal weight: 0.0970 chunk 31 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 ASN A 477 GLN A 918 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7968 Z= 0.194 Angle : 0.512 6.499 10813 Z= 0.271 Chirality : 0.042 0.172 1269 Planarity : 0.005 0.064 1378 Dihedral : 3.982 20.429 1070 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.47 % Allowed : 13.43 % Favored : 83.10 % 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: 0.67 (0.26), residues: 1006 helix: 1.44 (0.24), residues: 490 sheet: -0.78 (0.50), residues: 93 loop : -0.38 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 927 HIS 0.003 0.001 HIS A 566 PHE 0.026 0.001 PHE A 759 TYR 0.010 0.001 TYR A 497 ARG 0.003 0.000 ARG A 324 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 118 time to evaluate : 0.794 Fit side-chains REVERT: A 33 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7191 (tptp) REVERT: A 157 ASP cc_start: 0.7489 (OUTLIER) cc_final: 0.6809 (m-30) REVERT: A 179 ILE cc_start: 0.7727 (mp) cc_final: 0.7341 (mp) REVERT: A 218 LYS cc_start: 0.8254 (ttmt) cc_final: 0.8024 (ttmt) REVERT: A 228 VAL cc_start: 0.8202 (t) cc_final: 0.7997 (m) REVERT: A 238 GLU cc_start: 0.6878 (tt0) cc_final: 0.6639 (tt0) REVERT: A 250 GLN cc_start: 0.7302 (mt0) cc_final: 0.7082 (mt0) REVERT: A 259 GLN cc_start: 0.5924 (mt0) cc_final: 0.5592 (mt0) REVERT: A 413 LEU cc_start: 0.7848 (tp) cc_final: 0.7374 (tt) REVERT: A 466 GLU cc_start: 0.7314 (pm20) cc_final: 0.6450 (tp30) REVERT: A 487 PHE cc_start: 0.6638 (t80) cc_final: 0.6223 (t80) REVERT: A 508 MET cc_start: 0.5203 (tmm) cc_final: 0.3326 (tpp) REVERT: A 536 MET cc_start: 0.3640 (mmp) cc_final: 0.2910 (tpt) REVERT: A 559 ARG cc_start: 0.7800 (mtp85) cc_final: 0.7433 (mtm110) REVERT: A 575 MET cc_start: 0.3450 (mmp) cc_final: 0.2447 (ppp) REVERT: A 731 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6715 (mt-10) REVERT: A 824 LYS cc_start: 0.7207 (mmtt) cc_final: 0.6626 (mmpt) REVERT: A 1023 MET cc_start: 0.3317 (tmt) cc_final: 0.2492 (ptt) outliers start: 30 outliers final: 14 residues processed: 140 average time/residue: 1.0867 time to fit residues: 162.1660 Evaluate side-chains 125 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 108 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 110 ARG Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 595 CYS Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 916 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 GLN A 918 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 7968 Z= 0.422 Angle : 0.656 7.294 10813 Z= 0.348 Chirality : 0.049 0.196 1269 Planarity : 0.006 0.061 1378 Dihedral : 4.600 24.639 1070 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.51 % Allowed : 15.16 % Favored : 80.32 % 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: -0.01 (0.26), residues: 1006 helix: 0.73 (0.23), residues: 491 sheet: -0.71 (0.50), residues: 95 loop : -0.61 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 927 HIS 0.005 0.001 HIS A 943 PHE 0.035 0.003 PHE A 367 TYR 0.016 0.002 TYR A 762 ARG 0.006 0.001 ARG A 750 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 117 time to evaluate : 0.909 Fit side-chains revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7258 (tptp) REVERT: A 157 ASP cc_start: 0.7518 (OUTLIER) cc_final: 0.6744 (m-30) REVERT: A 179 ILE cc_start: 0.7731 (mp) cc_final: 0.7397 (mp) REVERT: A 202 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.7381 (mt0) REVERT: A 218 LYS cc_start: 0.8261 (ttmt) cc_final: 0.7950 (ttmt) REVERT: A 238 GLU cc_start: 0.6963 (tt0) cc_final: 0.6722 (tt0) REVERT: A 259 GLN cc_start: 0.6076 (mt0) cc_final: 0.5702 (mt0) REVERT: A 381 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7795 (mm-30) REVERT: A 384 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8061 (mp) REVERT: A 413 LEU cc_start: 0.7952 (tp) cc_final: 0.7483 (tt) REVERT: A 466 GLU cc_start: 0.7576 (pm20) cc_final: 0.6656 (tp30) REVERT: A 508 MET cc_start: 0.5468 (tmm) cc_final: 0.3426 (tpp) REVERT: A 536 MET cc_start: 0.3963 (mmp) cc_final: 0.3293 (tpt) REVERT: A 559 ARG cc_start: 0.7860 (mtp85) cc_final: 0.7421 (mtm110) REVERT: A 575 MET cc_start: 0.3224 (mmp) cc_final: 0.2846 (mmt) REVERT: A 644 ASP cc_start: 0.7288 (p0) cc_final: 0.7057 (p0) REVERT: A 731 GLU cc_start: 0.6940 (OUTLIER) cc_final: 0.6555 (mp0) REVERT: A 814 ASP cc_start: 0.6920 (OUTLIER) cc_final: 0.6718 (t70) REVERT: A 824 LYS cc_start: 0.7255 (mmtt) cc_final: 0.6628 (mmpt) REVERT: A 1023 MET cc_start: 0.3799 (tmt) cc_final: 0.2824 (ptt) outliers start: 39 outliers final: 22 residues processed: 146 average time/residue: 1.1697 time to fit residues: 181.4637 Evaluate side-chains 133 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 105 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 202 GLN Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 595 CYS Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 814 ASP Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 916 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 chunk 83 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 87 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 ASN ** A 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 918 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7968 Z= 0.222 Angle : 0.535 6.519 10813 Z= 0.283 Chirality : 0.043 0.171 1269 Planarity : 0.005 0.056 1378 Dihedral : 4.270 22.109 1070 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.51 % Allowed : 16.55 % Favored : 78.94 % 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: 0.19 (0.26), residues: 1006 helix: 0.99 (0.23), residues: 498 sheet: -1.11 (0.49), residues: 88 loop : -0.56 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 927 HIS 0.004 0.001 HIS A 405 PHE 0.026 0.002 PHE A 759 TYR 0.010 0.001 TYR A 762 ARG 0.003 0.000 ARG A 750 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 118 time to evaluate : 0.915 Fit side-chains REVERT: A 33 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7230 (tptp) REVERT: A 88 PHE cc_start: 0.5891 (m-80) cc_final: 0.5556 (m-80) REVERT: A 126 MET cc_start: 0.7125 (tpp) cc_final: 0.6918 (tpp) REVERT: A 179 ILE cc_start: 0.7609 (mp) cc_final: 0.7381 (mp) REVERT: A 218 LYS cc_start: 0.8188 (ttmt) cc_final: 0.7938 (ttmt) REVERT: A 238 GLU cc_start: 0.6833 (tt0) cc_final: 0.6573 (tt0) REVERT: A 259 GLN cc_start: 0.6186 (mt0) cc_final: 0.5867 (mt0) REVERT: A 381 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7648 (mm-30) REVERT: A 384 ILE cc_start: 0.8345 (mm) cc_final: 0.8035 (mm) REVERT: A 413 LEU cc_start: 0.7905 (tp) cc_final: 0.7442 (tt) REVERT: A 435 GLU cc_start: 0.7142 (mp0) cc_final: 0.6484 (mp0) REVERT: A 439 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.7104 (tm-30) REVERT: A 466 GLU cc_start: 0.7481 (pm20) cc_final: 0.6593 (tp30) REVERT: A 487 PHE cc_start: 0.6672 (t80) cc_final: 0.6429 (t80) REVERT: A 508 MET cc_start: 0.5395 (tmm) cc_final: 0.3389 (tpp) REVERT: A 536 MET cc_start: 0.3693 (mmp) cc_final: 0.3102 (tpt) REVERT: A 559 ARG cc_start: 0.7826 (mtp85) cc_final: 0.7459 (mtm110) REVERT: A 575 MET cc_start: 0.3064 (mmp) cc_final: 0.2807 (mmt) REVERT: A 644 ASP cc_start: 0.7261 (p0) cc_final: 0.7032 (p0) REVERT: A 702 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.6478 (p0) REVERT: A 731 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.6186 (mt-10) REVERT: A 824 LYS cc_start: 0.7303 (mmtt) cc_final: 0.6712 (mmpt) REVERT: A 1023 MET cc_start: 0.3631 (tmt) cc_final: 0.2708 (ptt) outliers start: 39 outliers final: 19 residues processed: 147 average time/residue: 1.1738 time to fit residues: 183.5868 Evaluate side-chains 137 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 114 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 110 ARG Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 595 CYS Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 669 CYS Chi-restraints excluded: chain A residue 702 ASP Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 916 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 0.0020 chunk 19 optimal weight: 0.0470 chunk 57 optimal weight: 20.0000 chunk 24 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 94 optimal weight: 0.0370 overall best weight: 0.3364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 GLN A 380 ASN A 918 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7968 Z= 0.146 Angle : 0.492 6.847 10813 Z= 0.261 Chirality : 0.041 0.164 1269 Planarity : 0.004 0.051 1378 Dihedral : 3.959 18.217 1070 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.12 % Allowed : 18.29 % Favored : 78.59 % 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: 0.74 (0.27), residues: 1006 helix: 1.63 (0.24), residues: 488 sheet: -0.94 (0.50), residues: 90 loop : -0.47 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 854 HIS 0.003 0.001 HIS A 405 PHE 0.029 0.001 PHE A 759 TYR 0.011 0.001 TYR A 990 ARG 0.003 0.000 ARG A 324 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 123 time to evaluate : 0.843 Fit side-chains REVERT: A 33 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7184 (tptp) REVERT: A 218 LYS cc_start: 0.8138 (ttmt) cc_final: 0.7893 (ttmt) REVERT: A 238 GLU cc_start: 0.6748 (tt0) cc_final: 0.6478 (tt0) REVERT: A 259 GLN cc_start: 0.5962 (mt0) cc_final: 0.5616 (mt0) REVERT: A 413 LEU cc_start: 0.7958 (tp) cc_final: 0.7443 (tt) REVERT: A 435 GLU cc_start: 0.6947 (mp0) cc_final: 0.6508 (mp0) REVERT: A 466 GLU cc_start: 0.7425 (pm20) cc_final: 0.6514 (tp30) REVERT: A 487 PHE cc_start: 0.6678 (t80) cc_final: 0.6419 (t80) REVERT: A 508 MET cc_start: 0.4778 (tmm) cc_final: 0.3477 (tpp) REVERT: A 536 MET cc_start: 0.3471 (mmp) cc_final: 0.2978 (tpt) REVERT: A 559 ARG cc_start: 0.7779 (mtp85) cc_final: 0.7464 (mtm110) REVERT: A 575 MET cc_start: 0.3308 (mmp) cc_final: 0.2827 (mmt) REVERT: A 598 MET cc_start: 0.8205 (ptp) cc_final: 0.7281 (ptp) REVERT: A 731 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6371 (mt-10) REVERT: A 824 LYS cc_start: 0.7210 (mmtt) cc_final: 0.6645 (mmpt) REVERT: A 916 SER cc_start: 0.8624 (OUTLIER) cc_final: 0.8075 (m) REVERT: A 1023 MET cc_start: 0.3369 (tmt) cc_final: 0.2473 (ptt) REVERT: A 1039 MET cc_start: 0.3267 (mmm) cc_final: 0.2845 (mmm) outliers start: 27 outliers final: 10 residues processed: 144 average time/residue: 1.0924 time to fit residues: 167.5798 Evaluate side-chains 130 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 117 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 110 ARG Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 669 CYS Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 916 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 643 GLN A 918 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7968 Z= 0.191 Angle : 0.522 6.545 10813 Z= 0.274 Chirality : 0.043 0.174 1269 Planarity : 0.004 0.049 1378 Dihedral : 4.032 20.661 1070 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.36 % Allowed : 18.63 % Favored : 78.01 % 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 (0.27), residues: 1006 helix: 1.47 (0.24), residues: 494 sheet: -0.85 (0.50), residues: 89 loop : -0.44 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 927 HIS 0.004 0.001 HIS A 405 PHE 0.029 0.001 PHE A 759 TYR 0.009 0.001 TYR A 762 ARG 0.007 0.000 ARG A 334 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 117 time to evaluate : 1.043 Fit side-chains REVERT: A 33 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7194 (tptp) REVERT: A 113 GLU cc_start: 0.7323 (mm-30) cc_final: 0.7012 (mm-30) REVERT: A 218 LYS cc_start: 0.8166 (ttmt) cc_final: 0.7904 (ttmt) REVERT: A 238 GLU cc_start: 0.6823 (tt0) cc_final: 0.6513 (tt0) REVERT: A 259 GLN cc_start: 0.6170 (mt0) cc_final: 0.5846 (mt0) REVERT: A 334 ARG cc_start: 0.8214 (ttm-80) cc_final: 0.7995 (ttm-80) REVERT: A 413 LEU cc_start: 0.7972 (tp) cc_final: 0.7461 (tt) REVERT: A 435 GLU cc_start: 0.7133 (mp0) cc_final: 0.6618 (mp0) REVERT: A 466 GLU cc_start: 0.7408 (pm20) cc_final: 0.6554 (tp30) REVERT: A 508 MET cc_start: 0.4837 (tmm) cc_final: 0.3468 (tpp) REVERT: A 559 ARG cc_start: 0.7799 (mtp85) cc_final: 0.7497 (mtm110) REVERT: A 575 MET cc_start: 0.3444 (mmp) cc_final: 0.2923 (mmt) REVERT: A 598 MET cc_start: 0.8262 (ptp) cc_final: 0.7381 (ptp) REVERT: A 702 ASP cc_start: 0.7522 (OUTLIER) cc_final: 0.6407 (p0) REVERT: A 731 GLU cc_start: 0.6800 (OUTLIER) cc_final: 0.6198 (mt-10) REVERT: A 824 LYS cc_start: 0.7293 (mmtt) cc_final: 0.6694 (mmpt) REVERT: A 974 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7428 (mm) REVERT: A 1023 MET cc_start: 0.3462 (tmt) cc_final: 0.2542 (ptt) REVERT: A 1039 MET cc_start: 0.3326 (mmm) cc_final: 0.2928 (mmm) outliers start: 29 outliers final: 16 residues processed: 139 average time/residue: 1.1622 time to fit residues: 171.4179 Evaluate side-chains 133 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 113 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 110 ARG Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 702 ASP Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 974 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 18 optimal weight: 0.1980 chunk 61 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 88 optimal weight: 0.0970 chunk 93 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 643 GLN A 918 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7968 Z= 0.182 Angle : 0.525 11.006 10813 Z= 0.273 Chirality : 0.042 0.172 1269 Planarity : 0.004 0.048 1378 Dihedral : 3.992 20.020 1070 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.78 % Allowed : 19.33 % Favored : 77.89 % 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: 0.71 (0.27), residues: 1006 helix: 1.51 (0.24), residues: 494 sheet: -0.84 (0.50), residues: 90 loop : -0.42 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 927 HIS 0.003 0.001 HIS A 405 PHE 0.029 0.001 PHE A 759 TYR 0.009 0.001 TYR A 990 ARG 0.006 0.000 ARG A 334 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 115 time to evaluate : 0.875 Fit side-chains REVERT: A 33 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7198 (tptp) REVERT: A 113 GLU cc_start: 0.7327 (mm-30) cc_final: 0.6961 (mm-30) REVERT: A 126 MET cc_start: 0.7026 (OUTLIER) cc_final: 0.6692 (tpp) REVERT: A 149 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.8082 (t0) REVERT: A 218 LYS cc_start: 0.8165 (ttmt) cc_final: 0.7906 (ttmt) REVERT: A 238 GLU cc_start: 0.6816 (tt0) cc_final: 0.6515 (tt0) REVERT: A 259 GLN cc_start: 0.6204 (mt0) cc_final: 0.5891 (mt0) REVERT: A 334 ARG cc_start: 0.8233 (ttm-80) cc_final: 0.7941 (ttm-80) REVERT: A 413 LEU cc_start: 0.7958 (tp) cc_final: 0.7461 (tt) REVERT: A 435 GLU cc_start: 0.7121 (mp0) cc_final: 0.6580 (mp0) REVERT: A 466 GLU cc_start: 0.7366 (pm20) cc_final: 0.6540 (tp30) REVERT: A 508 MET cc_start: 0.4838 (tmm) cc_final: 0.3471 (tpp) REVERT: A 559 ARG cc_start: 0.7800 (mtp85) cc_final: 0.7497 (mtm110) REVERT: A 575 MET cc_start: 0.3509 (mmp) cc_final: 0.3043 (mmt) REVERT: A 598 MET cc_start: 0.8247 (ptp) cc_final: 0.7403 (ptp) REVERT: A 731 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.6426 (mt-10) REVERT: A 756 MET cc_start: 0.7118 (mtp) cc_final: 0.6914 (mtm) REVERT: A 824 LYS cc_start: 0.7204 (mmtt) cc_final: 0.6648 (mmpt) REVERT: A 974 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7415 (mm) REVERT: A 1023 MET cc_start: 0.3742 (tmt) cc_final: 0.2855 (ptt) REVERT: A 1039 MET cc_start: 0.3322 (mmm) cc_final: 0.2906 (mmm) outliers start: 24 outliers final: 18 residues processed: 133 average time/residue: 1.1338 time to fit residues: 160.7227 Evaluate side-chains 137 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 114 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 110 ARG Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 702 ASP Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 974 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 54 optimal weight: 0.0870 chunk 39 optimal weight: 1.9990 chunk 71 optimal weight: 0.4980 chunk 27 optimal weight: 0.7980 chunk 81 optimal weight: 0.0020 chunk 85 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 overall best weight: 0.4566 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 643 GLN A 918 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7968 Z= 0.147 Angle : 0.501 7.400 10813 Z= 0.261 Chirality : 0.041 0.168 1269 Planarity : 0.004 0.046 1378 Dihedral : 3.861 18.235 1070 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.89 % Allowed : 19.44 % Favored : 77.66 % 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: 0.87 (0.27), residues: 1006 helix: 1.70 (0.24), residues: 493 sheet: -0.83 (0.49), residues: 90 loop : -0.38 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 927 HIS 0.003 0.000 HIS A 405 PHE 0.028 0.001 PHE A 759 TYR 0.007 0.001 TYR A 836 ARG 0.006 0.000 ARG A 334 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 119 time to evaluate : 0.863 Fit side-chains REVERT: A 33 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7135 (tptp) REVERT: A 113 GLU cc_start: 0.7315 (mm-30) cc_final: 0.7015 (mm-30) REVERT: A 126 MET cc_start: 0.7079 (OUTLIER) cc_final: 0.6760 (tpp) REVERT: A 218 LYS cc_start: 0.8129 (ttmt) cc_final: 0.7887 (ttmt) REVERT: A 238 GLU cc_start: 0.6837 (tt0) cc_final: 0.6548 (tt0) REVERT: A 259 GLN cc_start: 0.6146 (mt0) cc_final: 0.5827 (mt0) REVERT: A 413 LEU cc_start: 0.7937 (tp) cc_final: 0.7451 (tt) REVERT: A 435 GLU cc_start: 0.7080 (mp0) cc_final: 0.6537 (mp0) REVERT: A 466 GLU cc_start: 0.7364 (pm20) cc_final: 0.6474 (tp30) REVERT: A 487 PHE cc_start: 0.6674 (t80) cc_final: 0.6236 (t80) REVERT: A 559 ARG cc_start: 0.7780 (mtp85) cc_final: 0.7476 (mtm110) REVERT: A 575 MET cc_start: 0.3538 (mmp) cc_final: 0.3077 (mmt) REVERT: A 598 MET cc_start: 0.8176 (ptp) cc_final: 0.7391 (ptp) REVERT: A 702 ASP cc_start: 0.7410 (OUTLIER) cc_final: 0.6283 (p0) REVERT: A 731 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.6380 (mt-10) REVERT: A 824 LYS cc_start: 0.7198 (mmtt) cc_final: 0.6648 (mmpt) REVERT: A 916 SER cc_start: 0.8515 (OUTLIER) cc_final: 0.8076 (m) REVERT: A 970 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7229 (mp) REVERT: A 974 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7352 (mm) REVERT: A 1023 MET cc_start: 0.3625 (tmt) cc_final: 0.2797 (ptt) outliers start: 25 outliers final: 16 residues processed: 138 average time/residue: 1.0246 time to fit residues: 151.1095 Evaluate side-chains 139 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 116 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 110 ARG Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 669 CYS Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 702 ASP Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain A residue 974 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 100 optimal weight: 0.0000 chunk 92 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 8 optimal weight: 0.0270 chunk 61 optimal weight: 0.2980 chunk 49 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 overall best weight: 0.4442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 671 ASN A 918 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7968 Z= 0.151 Angle : 0.507 7.979 10813 Z= 0.263 Chirality : 0.041 0.167 1269 Planarity : 0.004 0.046 1378 Dihedral : 3.825 18.309 1070 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.78 % Allowed : 19.91 % Favored : 77.31 % 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 (0.27), residues: 1006 helix: 1.70 (0.24), residues: 496 sheet: -0.78 (0.49), residues: 90 loop : -0.37 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 927 HIS 0.002 0.000 HIS A 405 PHE 0.029 0.001 PHE A 759 TYR 0.011 0.001 TYR A 990 ARG 0.003 0.000 ARG A 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 118 time to evaluate : 0.886 Fit side-chains REVERT: A 33 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7210 (tptp) REVERT: A 126 MET cc_start: 0.7105 (OUTLIER) cc_final: 0.6817 (tpp) REVERT: A 218 LYS cc_start: 0.8127 (ttmt) cc_final: 0.7889 (ttmt) REVERT: A 238 GLU cc_start: 0.6773 (tt0) cc_final: 0.6461 (tt0) REVERT: A 259 GLN cc_start: 0.6173 (mt0) cc_final: 0.5838 (mt0) REVERT: A 413 LEU cc_start: 0.7903 (tp) cc_final: 0.7445 (tt) REVERT: A 435 GLU cc_start: 0.7080 (mp0) cc_final: 0.6555 (mp0) REVERT: A 466 GLU cc_start: 0.7376 (pm20) cc_final: 0.6505 (tp30) REVERT: A 487 PHE cc_start: 0.6734 (t80) cc_final: 0.6274 (t80) REVERT: A 493 SER cc_start: 0.8235 (OUTLIER) cc_final: 0.7872 (p) REVERT: A 559 ARG cc_start: 0.7778 (mtp85) cc_final: 0.7477 (mtm110) REVERT: A 575 MET cc_start: 0.3377 (mmp) cc_final: 0.2918 (mmt) REVERT: A 598 MET cc_start: 0.8181 (ptp) cc_final: 0.7418 (ptp) REVERT: A 731 GLU cc_start: 0.6955 (OUTLIER) cc_final: 0.6420 (mt-10) REVERT: A 824 LYS cc_start: 0.7203 (mmtt) cc_final: 0.6647 (mmpt) REVERT: A 916 SER cc_start: 0.8506 (OUTLIER) cc_final: 0.8080 (m) REVERT: A 970 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7103 (mp) REVERT: A 974 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7206 (mm) REVERT: A 1023 MET cc_start: 0.3537 (tmt) cc_final: 0.2713 (ptt) outliers start: 24 outliers final: 13 residues processed: 135 average time/residue: 1.1379 time to fit residues: 163.4227 Evaluate side-chains 136 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 116 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 110 ARG Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 669 CYS Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain A residue 974 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 0.3980 chunk 11 optimal weight: 5.9990 chunk 22 optimal weight: 0.1980 chunk 80 optimal weight: 0.6980 chunk 33 optimal weight: 0.0770 chunk 82 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 918 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.200015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.155010 restraints weight = 8240.226| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 1.65 r_work: 0.3623 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7968 Z= 0.147 Angle : 0.499 7.804 10813 Z= 0.259 Chirality : 0.041 0.169 1269 Planarity : 0.004 0.045 1378 Dihedral : 3.798 18.364 1070 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.66 % Allowed : 20.25 % Favored : 77.08 % 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: 0.93 (0.27), residues: 1006 helix: 1.76 (0.24), residues: 495 sheet: -0.76 (0.49), residues: 90 loop : -0.39 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 927 HIS 0.002 0.000 HIS A 405 PHE 0.030 0.001 PHE A 759 TYR 0.007 0.001 TYR A 762 ARG 0.006 0.000 ARG A 324 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3314.75 seconds wall clock time: 58 minutes 26.95 seconds (3506.95 seconds total)