Starting phenix.real_space_refine on Wed Feb 14 21:33:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f1e_28796/02_2024/8f1e_28796_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f1e_28796/02_2024/8f1e_28796.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f1e_28796/02_2024/8f1e_28796.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f1e_28796/02_2024/8f1e_28796.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f1e_28796/02_2024/8f1e_28796_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f1e_28796/02_2024/8f1e_28796_updated.pdb" } resolution = 3.28 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= 0.002 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 163 atoms to isotropic. 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 3 5.49 5 Mg 1 5.21 5 S 39 5.16 5 C 6509 2.51 5 N 1681 2.21 5 O 1941 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 74": "OE1" <-> "OE2" Residue "A GLU 161": "OE1" <-> "OE2" Residue "A GLU 183": "OE1" <-> "OE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A GLU 347": "OE1" <-> "OE2" Residue "A ASP 496": "OD1" <-> "OD2" Residue "A TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 660": "OD1" <-> "OD2" Residue "A GLU 673": "OE1" <-> "OE2" Residue "A PHE 887": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 108": "OE1" <-> "OE2" Residue "C TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 36": "OE1" <-> "OE2" Residue "D GLU 38": "OE1" <-> "OE2" Residue "D PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 79": "OD1" <-> "OD2" Residue "D GLU 115": "OE1" <-> "OE2" Residue "D GLU 130": "OE1" <-> "OE2" Residue "D TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10174 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 934, 7442 Classifications: {'peptide': 934} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 907} Chain breaks: 1 Chain: "B" Number of atoms: 629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 629 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "C" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 677 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "D" Number of atoms: 1426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1426 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'peptide': 171, 'undetermined': 2} Link IDs: {'PTRANS': 6, 'TRANS': 164, None: 2} Not linked: pdbres="VAL D 179 " pdbres=" MG D 201 " Not linked: pdbres=" MG D 201 " pdbres="GTP D 202 " Time building chain proxies: 5.74, per 1000 atoms: 0.56 Number of scatterers: 10174 At special positions: 0 Unit cell: (97.94, 109.56, 117.03, 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 39 16.00 P 3 15.00 Mg 1 11.99 O 1941 8.00 N 1681 7.00 C 6509 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.85 Conformation dependent library (CDL) restraints added in 1.9 seconds 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2462 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 60 helices and 1 sheets defined 67.4% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.97 Creating SS restraints... Processing helix chain 'A' and resid 3 through 10 removed outlier: 3.525A pdb=" N GLY A 9 " --> pdb=" O GLU A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 30 Processing helix chain 'A' and resid 33 through 45 Processing helix chain 'A' and resid 51 through 68 removed outlier: 3.535A pdb=" N LYS A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR A 66 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET A 67 " --> pdb=" O LYS A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 97 Processing helix chain 'A' and resid 105 through 120 Processing helix chain 'A' and resid 128 through 141 removed outlier: 3.751A pdb=" N THR A 132 " --> pdb=" O PRO A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 156 Processing helix chain 'A' and resid 160 through 163 No H-bonds generated for 'chain 'A' and resid 160 through 163' Processing helix chain 'A' and resid 168 through 181 Processing helix chain 'A' and resid 187 through 206 removed outlier: 3.541A pdb=" N ALA A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET A 204 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 235 removed outlier: 3.649A pdb=" N THR A 235 " --> pdb=" O GLY A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 262 Processing helix chain 'A' and resid 271 through 297 removed outlier: 4.119A pdb=" N MET A 280 " --> pdb=" O GLN A 276 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN A 292 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA A 293 " --> pdb=" O THR A 289 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ASN A 294 " --> pdb=" O HIS A 290 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N THR A 297 " --> pdb=" O ALA A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 320 removed outlier: 3.532A pdb=" N GLU A 305 " --> pdb=" O GLU A 301 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR A 313 " --> pdb=" O ASP A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 341 removed outlier: 3.529A pdb=" N ASN A 332 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS A 333 " --> pdb=" O GLU A 329 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 340 " --> pdb=" O THR A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 354 Processing helix chain 'A' and resid 356 through 364 Processing helix chain 'A' and resid 372 through 381 Processing helix chain 'A' and resid 385 through 402 removed outlier: 4.275A pdb=" N LEU A 390 " --> pdb=" O PRO A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 420 removed outlier: 4.572A pdb=" N GLU A 410 " --> pdb=" O TYR A 406 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N SER A 411 " --> pdb=" O SER A 407 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 412 " --> pdb=" O THR A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.732A pdb=" N LEU A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 469 Proline residue: A 464 - end of helix Processing helix chain 'A' and resid 477 through 494 Processing helix chain 'A' and resid 498 through 514 removed outlier: 3.604A pdb=" N PHE A 514 " --> pdb=" O TYR A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 521 Processing helix chain 'A' and resid 523 through 543 removed outlier: 3.916A pdb=" N SER A 542 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ASP A 543 " --> pdb=" O GLN A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 562 removed outlier: 3.973A pdb=" N GLY A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 587 Processing helix chain 'A' and resid 592 through 608 removed outlier: 4.492A pdb=" N ASN A 608 " --> pdb=" O LYS A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 633 Proline residue: A 623 - end of helix removed outlier: 3.592A pdb=" N VAL A 628 " --> pdb=" O SER A 624 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A 629 " --> pdb=" O PHE A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 655 removed outlier: 3.673A pdb=" N VAL A 652 " --> pdb=" O GLU A 648 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE A 653 " --> pdb=" O PHE A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 679 removed outlier: 4.771A pdb=" N GLU A 673 " --> pdb=" O GLN A 669 " (cutoff:3.500A) Proline residue: A 674 - end of helix Processing helix chain 'A' and resid 685 through 700 removed outlier: 3.661A pdb=" N GLU A 693 " --> pdb=" O GLN A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 722 Proline residue: A 709 - end of helix removed outlier: 5.193A pdb=" N MET A 712 " --> pdb=" O GLU A 708 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ASP A 713 " --> pdb=" O PRO A 709 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS A 716 " --> pdb=" O MET A 712 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A 717 " --> pdb=" O ASP A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 730 No H-bonds generated for 'chain 'A' and resid 728 through 730' Processing helix chain 'A' and resid 732 through 744 Proline residue: A 736 - end of helix Processing helix chain 'A' and resid 750 through 766 removed outlier: 4.398A pdb=" N GLY A 754 " --> pdb=" O GLN A 750 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ARG A 755 " --> pdb=" O PRO A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 786 Processing helix chain 'A' and resid 788 through 797 Processing helix chain 'A' and resid 805 through 819 removed outlier: 4.251A pdb=" N GLU A 818 " --> pdb=" O ILE A 814 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N VAL A 819 " --> pdb=" O GLU A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 839 Processing helix chain 'A' and resid 842 through 846 Processing helix chain 'A' and resid 879 through 893 Processing helix chain 'A' and resid 965 through 979 removed outlier: 3.649A pdb=" N LYS A 979 " --> pdb=" O GLU A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 990 Processing helix chain 'A' and resid 993 through 1002 removed outlier: 3.503A pdb=" N ALA A1002 " --> pdb=" O VAL A 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 38 removed outlier: 3.780A pdb=" N GLY B 38 " --> pdb=" O LEU B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 73 removed outlier: 4.693A pdb=" N VAL B 50 " --> pdb=" O SER B 46 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU B 66 " --> pdb=" O GLU B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 90 Processing helix chain 'B' and resid 92 through 98 Processing helix chain 'C' and resid 42 through 51 Processing helix chain 'C' and resid 59 through 87 Processing helix chain 'C' and resid 94 through 104 Processing helix chain 'C' and resid 108 through 125 Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 78 through 81 Processing helix chain 'D' and resid 97 through 113 Proline residue: D 104 - end of helix Processing helix chain 'D' and resid 139 through 143 removed outlier: 3.923A pdb=" N LYS D 143 " --> pdb=" O THR D 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 139 through 143' Processing helix chain 'D' and resid 161 through 171 Processing sheet with id= A, first strand: chain 'D' and resid 147 through 150 removed outlier: 3.920A pdb=" N GLN D 147 " --> pdb=" O ILE D 119 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LYS D 62 " --> pdb=" O PHE D 13 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N LEU D 15 " --> pdb=" O LYS D 62 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ASP D 64 " --> pdb=" O LEU D 15 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LEU D 17 " --> pdb=" O ASP D 64 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TRP D 66 " --> pdb=" O LEU D 17 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE D 61 " --> pdb=" O PHE D 54 " (cutoff:3.500A) 574 hydrogen bonds defined for protein. 1695 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: 3.11 Time building geometry restraints manager: 4.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3294 1.34 - 1.46: 2199 1.46 - 1.58: 4792 1.58 - 1.70: 5 1.70 - 1.82: 58 Bond restraints: 10348 Sorted by residual: bond pdb=" N ILE C 104 " pdb=" CA ILE C 104 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.77e+00 bond pdb=" N VAL B 55 " pdb=" CA VAL B 55 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.17e-02 7.31e+03 7.77e+00 bond pdb=" N VAL C 69 " pdb=" CA VAL C 69 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.21e-02 6.83e+03 7.46e+00 bond pdb=" N VAL A 831 " pdb=" CA VAL A 831 " ideal model delta sigma weight residual 1.461 1.492 -0.032 1.19e-02 7.06e+03 7.05e+00 bond pdb=" N VAL C 101 " pdb=" CA VAL C 101 " ideal model delta sigma weight residual 1.461 1.492 -0.031 1.19e-02 7.06e+03 6.75e+00 ... (remaining 10343 not shown) Histogram of bond angle deviations from ideal: 97.02 - 104.41: 107 104.41 - 111.80: 5106 111.80 - 119.19: 3569 119.19 - 126.57: 5144 126.57 - 133.96: 96 Bond angle restraints: 14022 Sorted by residual: angle pdb=" N LYS B 75 " pdb=" CA LYS B 75 " pdb=" C LYS B 75 " ideal model delta sigma weight residual 113.23 108.37 4.86 1.22e+00 6.72e-01 1.59e+01 angle pdb=" N ASN B 74 " pdb=" CA ASN B 74 " pdb=" C ASN B 74 " ideal model delta sigma weight residual 113.01 108.44 4.57 1.20e+00 6.94e-01 1.45e+01 angle pdb=" N ASN C 66 " pdb=" CA ASN C 66 " pdb=" C ASN C 66 " ideal model delta sigma weight residual 111.11 106.56 4.55 1.20e+00 6.94e-01 1.44e+01 angle pdb=" PB GTP D 202 " pdb=" O3B GTP D 202 " pdb=" PG GTP D 202 " ideal model delta sigma weight residual 120.50 131.74 -11.24 3.00e+00 1.11e-01 1.40e+01 angle pdb=" CB MET A 866 " pdb=" CG MET A 866 " pdb=" SD MET A 866 " ideal model delta sigma weight residual 112.70 123.88 -11.18 3.00e+00 1.11e-01 1.39e+01 ... (remaining 14017 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.46: 5849 27.46 - 54.91: 421 54.91 - 82.37: 28 82.37 - 109.83: 7 109.83 - 137.28: 3 Dihedral angle restraints: 6308 sinusoidal: 2537 harmonic: 3771 Sorted by residual: dihedral pdb=" C8 GTP D 202 " pdb=" C1' GTP D 202 " pdb=" N9 GTP D 202 " pdb=" O4' GTP D 202 " ideal model delta sinusoidal sigma weight residual 104.59 -32.69 137.28 1 2.00e+01 2.50e-03 4.16e+01 dihedral pdb=" O3A GTP D 202 " pdb=" O3B GTP D 202 " pdb=" PB GTP D 202 " pdb=" PG GTP D 202 " ideal model delta sinusoidal sigma weight residual 303.79 174.97 128.82 1 2.00e+01 2.50e-03 3.90e+01 dihedral pdb=" O2G GTP D 202 " pdb=" O3B GTP D 202 " pdb=" PG GTP D 202 " pdb=" PB GTP D 202 " ideal model delta sinusoidal sigma weight residual 177.30 -61.76 -120.94 1 2.00e+01 2.50e-03 3.63e+01 ... (remaining 6305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1266 0.043 - 0.087: 294 0.087 - 0.130: 87 0.130 - 0.174: 10 0.174 - 0.217: 3 Chirality restraints: 1660 Sorted by residual: chirality pdb=" C3' GTP D 202 " pdb=" C2' GTP D 202 " pdb=" C4' GTP D 202 " pdb=" O3' GTP D 202 " both_signs ideal model delta sigma weight residual False -2.47 -2.69 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CB THR C 122 " pdb=" CA THR C 122 " pdb=" OG1 THR C 122 " pdb=" CG2 THR C 122 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.24e-01 chirality pdb=" CA ILE C 72 " pdb=" N ILE C 72 " pdb=" C ILE C 72 " pdb=" CB ILE C 72 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.16e-01 ... (remaining 1657 not shown) Planarity restraints: 1769 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 75 " -0.008 2.00e-02 2.50e+03 1.65e-02 2.71e+00 pdb=" C ARG C 75 " 0.028 2.00e-02 2.50e+03 pdb=" O ARG C 75 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE C 76 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 123 " 0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO A 124 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 124 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 124 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 80 " -0.025 5.00e-02 4.00e+02 3.81e-02 2.33e+00 pdb=" N PRO B 81 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 81 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 81 " -0.021 5.00e-02 4.00e+02 ... (remaining 1766 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 67 2.46 - 3.07: 7299 3.07 - 3.68: 16296 3.68 - 4.29: 23046 4.29 - 4.90: 36401 Nonbonded interactions: 83109 Sorted by model distance: nonbonded pdb="MG MG D 201 " pdb=" O3B GTP D 202 " model vdw 1.853 2.170 nonbonded pdb="MG MG D 201 " pdb=" O2A GTP D 202 " model vdw 2.011 2.170 nonbonded pdb=" OG1 THR D 44 " pdb="MG MG D 201 " model vdw 2.162 2.170 nonbonded pdb=" O GLU A 975 " pdb=" OG SER A 978 " model vdw 2.285 2.440 nonbonded pdb=" OH TYR A 254 " pdb=" OD2 ASP A 284 " model vdw 2.294 2.440 ... (remaining 83104 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: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 7.270 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 29.170 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 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 0.047 10348 Z= 0.212 Angle : 0.668 11.237 14022 Z= 0.387 Chirality : 0.042 0.217 1660 Planarity : 0.003 0.039 1769 Dihedral : 17.516 137.281 3846 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.17 % Allowed : 30.37 % Favored : 69.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.76 (0.23), residues: 1263 helix: 1.74 (0.17), residues: 872 sheet: 1.64 (0.85), residues: 37 loop : -0.24 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 106 HIS 0.002 0.000 HIS B 83 PHE 0.010 0.001 PHE A 578 TYR 0.023 0.001 TYR A 513 ARG 0.008 0.000 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 70 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 GLU cc_start: 0.8929 (pt0) cc_final: 0.8508 (pt0) REVERT: C 62 MET cc_start: 0.7388 (pmm) cc_final: 0.7116 (pmm) REVERT: C 65 LEU cc_start: 0.9086 (mm) cc_final: 0.8819 (tp) REVERT: C 71 ASP cc_start: 0.9307 (t0) cc_final: 0.9033 (m-30) REVERT: C 96 GLU cc_start: 0.8986 (mp0) cc_final: 0.8572 (mp0) REVERT: D 55 TYR cc_start: 0.8771 (m-80) cc_final: 0.8428 (m-80) outliers start: 2 outliers final: 1 residues processed: 72 average time/residue: 0.2600 time to fit residues: 26.5976 Evaluate side-chains 50 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 49 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 753 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 20.0000 chunk 95 optimal weight: 0.0170 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 98 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 overall best weight: 1.0024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 627 ASN A 829 ASN A 835 ASN C 70 ASN D 147 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10348 Z= 0.173 Angle : 0.527 10.749 14022 Z= 0.268 Chirality : 0.039 0.168 1660 Planarity : 0.003 0.038 1769 Dihedral : 6.868 125.976 1374 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.26 % Allowed : 29.77 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.86 (0.23), residues: 1263 helix: 1.82 (0.17), residues: 892 sheet: 1.51 (1.00), residues: 30 loop : -0.31 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 66 HIS 0.004 0.001 HIS B 83 PHE 0.039 0.001 PHE A 887 TYR 0.014 0.001 TYR D 148 ARG 0.005 0.000 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 58 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 MET cc_start: 0.9261 (mmm) cc_final: 0.8916 (mmt) REVERT: B 57 GLU cc_start: 0.9022 (pt0) cc_final: 0.8557 (pt0) REVERT: B 65 GLU cc_start: 0.9371 (tt0) cc_final: 0.9127 (tm-30) REVERT: C 62 MET cc_start: 0.7297 (pmm) cc_final: 0.6919 (pmm) REVERT: C 96 GLU cc_start: 0.8974 (mp0) cc_final: 0.8597 (mp0) REVERT: C 102 ARG cc_start: 0.8381 (mmm160) cc_final: 0.8087 (mmm160) outliers start: 26 outliers final: 17 residues processed: 82 average time/residue: 0.2596 time to fit residues: 31.6480 Evaluate side-chains 68 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 51 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASN Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 91 MET Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 133 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 0.4980 chunk 35 optimal weight: 0.1980 chunk 95 optimal weight: 20.0000 chunk 77 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 102 optimal weight: 30.0000 chunk 113 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 91 optimal weight: 5.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 GLN ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10348 Z= 0.142 Angle : 0.481 10.451 14022 Z= 0.244 Chirality : 0.037 0.138 1660 Planarity : 0.003 0.038 1769 Dihedral : 5.870 117.078 1372 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.52 % Allowed : 29.33 % Favored : 68.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.23), residues: 1263 helix: 1.91 (0.17), residues: 894 sheet: 1.52 (0.91), residues: 37 loop : -0.21 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 66 HIS 0.002 0.000 HIS A 207 PHE 0.029 0.001 PHE A 887 TYR 0.011 0.001 TYR A 511 ARG 0.004 0.000 ARG A 705 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 55 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 MET cc_start: 0.9269 (mmm) cc_final: 0.8922 (mmt) REVERT: A 191 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8896 (mp) REVERT: B 57 GLU cc_start: 0.9035 (pt0) cc_final: 0.8532 (pt0) REVERT: B 65 GLU cc_start: 0.9373 (tt0) cc_final: 0.9157 (tm-30) REVERT: C 62 MET cc_start: 0.7186 (pmm) cc_final: 0.6977 (pmm) REVERT: C 96 GLU cc_start: 0.8982 (mp0) cc_final: 0.8493 (mp0) REVERT: D 86 GLN cc_start: 0.9146 (OUTLIER) cc_final: 0.8487 (mt0) REVERT: D 175 GLN cc_start: 0.8890 (mp10) cc_final: 0.8653 (pm20) outliers start: 29 outliers final: 14 residues processed: 81 average time/residue: 0.2179 time to fit residues: 26.1886 Evaluate side-chains 60 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 44 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 133 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 12 optimal weight: 0.3980 chunk 54 optimal weight: 6.9990 chunk 76 optimal weight: 8.9990 chunk 115 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 chunk 60 optimal weight: 0.4980 chunk 109 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10348 Z= 0.134 Angle : 0.490 11.061 14022 Z= 0.242 Chirality : 0.037 0.139 1660 Planarity : 0.003 0.038 1769 Dihedral : 5.528 113.090 1372 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.79 % Allowed : 29.07 % Favored : 68.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.24), residues: 1263 helix: 1.97 (0.17), residues: 888 sheet: 1.59 (0.92), residues: 37 loop : -0.09 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 66 HIS 0.002 0.000 HIS A 207 PHE 0.022 0.001 PHE A 887 TYR 0.011 0.001 TYR B 51 ARG 0.007 0.000 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 51 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 MET cc_start: 0.9261 (mmm) cc_final: 0.8920 (mmt) REVERT: A 578 PHE cc_start: 0.8977 (OUTLIER) cc_final: 0.8566 (t80) REVERT: B 57 GLU cc_start: 0.9063 (pt0) cc_final: 0.8555 (pt0) REVERT: C 57 ILE cc_start: 0.3853 (OUTLIER) cc_final: 0.2723 (tp) REVERT: C 62 MET cc_start: 0.7308 (pmm) cc_final: 0.6261 (ppp) REVERT: C 96 GLU cc_start: 0.8832 (mp0) cc_final: 0.8482 (mp0) REVERT: D 175 GLN cc_start: 0.8897 (mp10) cc_final: 0.8646 (pm20) outliers start: 32 outliers final: 18 residues processed: 82 average time/residue: 0.1872 time to fit residues: 24.1995 Evaluate side-chains 63 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 43 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain C residue 52 HIS Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 133 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 1 optimal weight: 0.0970 chunk 90 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 103 optimal weight: 10.0000 chunk 84 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10348 Z= 0.199 Angle : 0.516 11.183 14022 Z= 0.256 Chirality : 0.038 0.158 1660 Planarity : 0.003 0.039 1769 Dihedral : 5.494 115.133 1372 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.96 % Allowed : 29.24 % Favored : 67.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.24), residues: 1263 helix: 1.94 (0.17), residues: 896 sheet: 1.30 (0.90), residues: 37 loop : -0.11 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 28 HIS 0.003 0.001 HIS A 207 PHE 0.016 0.001 PHE A 887 TYR 0.012 0.001 TYR D 82 ARG 0.004 0.000 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 49 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 MET cc_start: 0.9272 (mmm) cc_final: 0.8967 (mmt) REVERT: A 578 PHE cc_start: 0.8983 (OUTLIER) cc_final: 0.8599 (t80) REVERT: A 781 CYS cc_start: 0.9461 (OUTLIER) cc_final: 0.9126 (p) REVERT: C 57 ILE cc_start: 0.3877 (OUTLIER) cc_final: 0.3297 (tp) REVERT: C 96 GLU cc_start: 0.8849 (mp0) cc_final: 0.8493 (mp0) REVERT: D 86 GLN cc_start: 0.9097 (OUTLIER) cc_final: 0.8496 (mt0) REVERT: D 175 GLN cc_start: 0.8949 (mp10) cc_final: 0.8684 (pm20) outliers start: 34 outliers final: 20 residues processed: 81 average time/residue: 0.1910 time to fit residues: 23.9166 Evaluate side-chains 67 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 43 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 781 CYS Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain C residue 52 HIS Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 179 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 0.0470 chunk 109 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 101 optimal weight: 20.0000 chunk 56 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 64 optimal weight: 0.0670 chunk 117 optimal weight: 1.9990 overall best weight: 1.2020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10348 Z= 0.178 Angle : 0.502 11.361 14022 Z= 0.249 Chirality : 0.038 0.155 1660 Planarity : 0.003 0.039 1769 Dihedral : 5.437 114.895 1372 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.05 % Allowed : 28.81 % Favored : 68.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.24), residues: 1263 helix: 1.97 (0.17), residues: 894 sheet: 1.24 (0.81), residues: 47 loop : -0.12 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 813 HIS 0.003 0.000 HIS A 207 PHE 0.019 0.001 PHE A 887 TYR 0.014 0.001 TYR B 51 ARG 0.008 0.000 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 48 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 MET cc_start: 0.9267 (mmm) cc_final: 0.8958 (mmt) REVERT: A 578 PHE cc_start: 0.8980 (OUTLIER) cc_final: 0.8576 (t80) REVERT: C 57 ILE cc_start: 0.3997 (OUTLIER) cc_final: 0.3390 (tp) REVERT: C 96 GLU cc_start: 0.8841 (mp0) cc_final: 0.8478 (mp0) REVERT: D 86 GLN cc_start: 0.9067 (OUTLIER) cc_final: 0.8466 (mt0) REVERT: D 175 GLN cc_start: 0.8937 (mp10) cc_final: 0.8727 (pm20) outliers start: 35 outliers final: 21 residues processed: 82 average time/residue: 0.1943 time to fit residues: 25.2323 Evaluate side-chains 68 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 44 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASN Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 179 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 121 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10348 Z= 0.210 Angle : 0.512 11.371 14022 Z= 0.256 Chirality : 0.039 0.215 1660 Planarity : 0.003 0.039 1769 Dihedral : 5.509 117.308 1372 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.44 % Allowed : 29.24 % Favored : 68.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.24), residues: 1263 helix: 1.95 (0.17), residues: 892 sheet: 1.18 (0.81), residues: 47 loop : -0.18 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 28 HIS 0.003 0.001 HIS A 207 PHE 0.016 0.001 PHE A 887 TYR 0.012 0.001 TYR D 82 ARG 0.006 0.000 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 45 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 MET cc_start: 0.9278 (mmm) cc_final: 0.8989 (mmt) REVERT: A 781 CYS cc_start: 0.9522 (OUTLIER) cc_final: 0.9208 (p) REVERT: C 96 GLU cc_start: 0.8846 (mp0) cc_final: 0.8449 (mp0) REVERT: C 102 ARG cc_start: 0.8216 (mmm160) cc_final: 0.8015 (mmm160) REVERT: D 86 GLN cc_start: 0.9087 (OUTLIER) cc_final: 0.8497 (mt0) REVERT: D 175 GLN cc_start: 0.8964 (mp10) cc_final: 0.8729 (pm20) outliers start: 28 outliers final: 21 residues processed: 73 average time/residue: 0.1991 time to fit residues: 22.5843 Evaluate side-chains 69 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 46 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASN Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 781 CYS Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 179 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 95 optimal weight: 20.0000 chunk 110 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 chunk 106 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10348 Z= 0.163 Angle : 0.497 11.850 14022 Z= 0.247 Chirality : 0.038 0.139 1660 Planarity : 0.003 0.039 1769 Dihedral : 5.429 116.310 1372 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.09 % Allowed : 28.89 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.24), residues: 1263 helix: 1.94 (0.17), residues: 892 sheet: 1.20 (0.81), residues: 47 loop : -0.16 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 28 HIS 0.002 0.000 HIS A 207 PHE 0.015 0.001 PHE A 887 TYR 0.012 0.001 TYR B 51 ARG 0.005 0.000 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 47 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 MET cc_start: 0.9272 (mmm) cc_final: 0.8981 (mmt) REVERT: A 781 CYS cc_start: 0.9512 (OUTLIER) cc_final: 0.9194 (p) REVERT: C 96 GLU cc_start: 0.8864 (mp0) cc_final: 0.8452 (mp0) REVERT: D 86 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8400 (mt0) REVERT: D 175 GLN cc_start: 0.8969 (mp10) cc_final: 0.8727 (pm20) outliers start: 24 outliers final: 18 residues processed: 71 average time/residue: 0.1983 time to fit residues: 21.3278 Evaluate side-chains 64 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 44 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 781 CYS Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 133 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 102 optimal weight: 30.0000 chunk 107 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10348 Z= 0.197 Angle : 0.526 11.969 14022 Z= 0.258 Chirality : 0.038 0.153 1660 Planarity : 0.003 0.039 1769 Dihedral : 5.471 117.876 1372 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.26 % Allowed : 29.16 % Favored : 68.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.24), residues: 1263 helix: 1.97 (0.17), residues: 892 sheet: 1.16 (0.81), residues: 47 loop : -0.11 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 28 HIS 0.002 0.000 HIS A 207 PHE 0.014 0.001 PHE A 249 TYR 0.012 0.001 TYR D 82 ARG 0.010 0.000 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 45 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 MET cc_start: 0.9269 (mmm) cc_final: 0.8963 (mmt) REVERT: A 781 CYS cc_start: 0.9532 (OUTLIER) cc_final: 0.9215 (p) REVERT: C 62 MET cc_start: 0.7265 (pmm) cc_final: 0.6707 (ppp) REVERT: C 96 GLU cc_start: 0.8846 (mp0) cc_final: 0.8424 (mp0) REVERT: D 86 GLN cc_start: 0.9016 (OUTLIER) cc_final: 0.8425 (mt0) REVERT: D 175 GLN cc_start: 0.9005 (mp10) cc_final: 0.8757 (pm20) outliers start: 26 outliers final: 21 residues processed: 71 average time/residue: 0.1792 time to fit residues: 20.2628 Evaluate side-chains 68 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 45 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASN Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 781 CYS Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 179 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 83 optimal weight: 8.9990 chunk 125 optimal weight: 1.9990 chunk 115 optimal weight: 0.0000 chunk 99 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 106 optimal weight: 8.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 627 ASN ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10348 Z= 0.144 Angle : 0.518 12.721 14022 Z= 0.252 Chirality : 0.038 0.143 1660 Planarity : 0.003 0.043 1769 Dihedral : 5.353 115.355 1372 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.91 % Allowed : 29.33 % Favored : 68.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.24), residues: 1263 helix: 1.99 (0.17), residues: 893 sheet: 1.19 (0.81), residues: 47 loop : -0.17 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 165 HIS 0.002 0.000 HIS B 83 PHE 0.015 0.001 PHE A 887 TYR 0.012 0.001 TYR B 51 ARG 0.011 0.000 ARG C 102 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 46 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 MET cc_start: 0.9266 (mmm) cc_final: 0.8986 (mmt) REVERT: A 781 CYS cc_start: 0.9521 (OUTLIER) cc_final: 0.9185 (p) REVERT: C 62 MET cc_start: 0.7229 (pmm) cc_final: 0.6695 (ppp) REVERT: C 96 GLU cc_start: 0.8835 (mp0) cc_final: 0.8399 (mp0) REVERT: D 86 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.8319 (mt0) REVERT: D 175 GLN cc_start: 0.8995 (mp10) cc_final: 0.8752 (pm20) outliers start: 22 outliers final: 20 residues processed: 68 average time/residue: 0.1877 time to fit residues: 20.3300 Evaluate side-chains 68 residues out of total 1149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 46 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASN Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 781 CYS Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 179 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 102 optimal weight: 30.0000 chunk 12 optimal weight: 0.0570 chunk 18 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.071366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.047397 restraints weight = 39127.417| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 3.50 r_work: 0.2757 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10348 Z= 0.201 Angle : 0.531 12.237 14022 Z= 0.260 Chirality : 0.039 0.155 1660 Planarity : 0.003 0.039 1769 Dihedral : 5.418 117.868 1372 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.18 % Allowed : 29.07 % Favored : 68.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.24), residues: 1263 helix: 2.00 (0.17), residues: 892 sheet: 1.15 (0.80), residues: 47 loop : -0.09 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 28 HIS 0.002 0.000 HIS A 207 PHE 0.015 0.001 PHE A 249 TYR 0.013 0.001 TYR D 82 ARG 0.011 0.000 ARG C 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2020.53 seconds wall clock time: 37 minutes 58.74 seconds (2278.74 seconds total)