Starting phenix.real_space_refine on Mon Apr 28 17:21:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n77_24222/04_2025/7n77_24222_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n77_24222/04_2025/7n77_24222.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7n77_24222/04_2025/7n77_24222.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n77_24222/04_2025/7n77_24222.map" model { file = "/net/cci-nas-00/data/ceres_data/7n77_24222/04_2025/7n77_24222_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n77_24222/04_2025/7n77_24222_trim.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.023 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 Al 1 5.89 5 Mg 1 5.21 5 S 45 5.16 5 C 4805 2.51 5 N 1281 2.21 5 O 1333 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 7470 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1036, 7399 Classifications: {'peptide': 1036} Incomplete info: {'truncation_to_alanine': 178} Link IDs: {'PCIS': 3, 'PTRANS': 69, 'TRANS': 963} Chain breaks: 5 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 648 Unresolved non-hydrogen angles: 836 Unresolved non-hydrogen dihedrals: 546 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 6, 'HIS:plan': 4, 'PHE:plan': 6, 'GLU:plan': 14, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 340 Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {' MG': 1, 'ALF': 1, 'Y01': 2} Classifications: {'undetermined': 4, 'water': 2} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'Y01:plan-2': 1, 'Y01:plan-1': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 5.64, per 1000 atoms: 0.76 Number of scatterers: 7470 At special positions: 0 Unit cell: (91.43, 104.81, 130.455, 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 45 16.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1333 8.00 N 1281 7.00 C 4805 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 - 3.00 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: 2.69 Conformation dependent library (CDL) restraints added in 896.6 milliseconds 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1934 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 7 sheets defined 51.7% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 43 through 58 removed outlier: 3.646A pdb=" N VAL A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA A 58 " --> pdb=" O VAL A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 68 Processing helix chain 'A' and resid 68 through 77 removed outlier: 3.697A pdb=" N GLY A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.617A pdb=" N ALA A 85 " --> pdb=" O LEU A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 200 through 212 removed outlier: 3.835A pdb=" N VAL A 206 " --> pdb=" O GLN A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 233 through 248 Processing helix chain 'A' and resid 251 through 284 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 393 through 396 removed outlier: 4.007A pdb=" N CYS A 396 " --> pdb=" O THR A 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 393 through 396' Processing helix chain 'A' and resid 397 through 408 Processing helix chain 'A' and resid 419 through 445 removed outlier: 4.472A pdb=" N LEU A 430 " --> pdb=" O ALA A 426 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 463 removed outlier: 3.804A pdb=" N ILE A 454 " --> pdb=" O ASN A 450 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 459 " --> pdb=" O ARG A 455 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL A 463 " --> pdb=" O LEU A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 487 removed outlier: 3.741A pdb=" N GLN A 486 " --> pdb=" O ARG A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 501 removed outlier: 4.381A pdb=" N LEU A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS A 501 " --> pdb=" O ASN A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 541 Processing helix chain 'A' and resid 544 through 553 Processing helix chain 'A' and resid 566 through 577 removed outlier: 3.751A pdb=" N THR A 576 " --> pdb=" O MET A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 659 Processing helix chain 'A' and resid 667 through 677 Processing helix chain 'A' and resid 695 through 700 Processing helix chain 'A' and resid 703 through 709 Processing helix chain 'A' and resid 726 through 736 removed outlier: 3.901A pdb=" N VAL A 730 " --> pdb=" O GLN A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 759 Processing helix chain 'A' and resid 821 through 832 Processing helix chain 'A' and resid 836 through 841 Processing helix chain 'A' and resid 850 through 863 removed outlier: 3.936A pdb=" N THR A 855 " --> pdb=" O PRO A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 878 No H-bonds generated for 'chain 'A' and resid 876 through 878' Processing helix chain 'A' and resid 879 through 884 removed outlier: 4.019A pdb=" N ALA A 883 " --> pdb=" O GLY A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 949 removed outlier: 3.592A pdb=" N MET A 913 " --> pdb=" O GLU A 909 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU A 917 " --> pdb=" O MET A 913 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE A 926 " --> pdb=" O LEU A 922 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE A 949 " --> pdb=" O ILE A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 964 removed outlier: 3.605A pdb=" N LEU A 959 " --> pdb=" O ASP A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 973 Processing helix chain 'A' and resid 974 through 976 No H-bonds generated for 'chain 'A' and resid 974 through 976' Processing helix chain 'A' and resid 993 through 1021 removed outlier: 4.077A pdb=" N ALA A1020 " --> pdb=" O PHE A1016 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN A1021 " --> pdb=" O LEU A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1061 removed outlier: 3.701A pdb=" N PHE A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU A1054 " --> pdb=" O SER A1050 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER A1061 " --> pdb=" O ALA A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1072 Processing helix chain 'A' and resid 1073 through 1093 Processing helix chain 'A' and resid 1109 through 1145 Proline residue: A1138 - end of helix removed outlier: 3.611A pdb=" N ARG A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) Processing helix chain 'A' and resid 1152 through 1164 Processing sheet with id=AA1, first strand: chain 'A' and resid 88 through 91 removed outlier: 3.563A pdb=" N VAL A 105 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 108 through 109 removed outlier: 5.542A pdb=" N ARG A 159 " --> pdb=" O TRP A 170 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A 176 " --> pdb=" O ILE A 171 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 300 through 303 removed outlier: 3.507A pdb=" N VAL A 302 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N CYS A 291 " --> pdb=" O VAL A 314 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N CYS A 312 " --> pdb=" O CYS A 293 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL A 386 " --> pdb=" O LEU A 315 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 320 through 321 removed outlier: 6.785A pdb=" N MET A 334 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ALA A 378 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLU A 332 " --> pdb=" O ALA A 378 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 783 through 788 removed outlier: 3.647A pdb=" N SER A 783 " --> pdb=" O THR A 774 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N HIS A 767 " --> pdb=" O HIS A 817 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ALA A 819 " --> pdb=" O HIS A 767 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE A 769 " --> pdb=" O ALA A 819 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR A 844 " --> pdb=" O ARG A 816 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU A 818 " --> pdb=" O THR A 844 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N PHE A 846 " --> pdb=" O LEU A 818 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU A 820 " --> pdb=" O PHE A 846 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ALA A 741 " --> pdb=" O THR A 844 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N PHE A 846 " --> pdb=" O ALA A 741 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N MET A 743 " --> pdb=" O PHE A 846 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL A 505 " --> pdb=" O VAL A 742 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL A 744 " --> pdb=" O VAL A 505 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N PHE A 507 " --> pdb=" O VAL A 744 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU A 504 " --> pdb=" O GLY A 869 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N CYS A 871 " --> pdb=" O LEU A 504 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N CYS A 506 " --> pdb=" O CYS A 871 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N ILE A 888 " --> pdb=" O VAL A 868 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N MET A 870 " --> pdb=" O ILE A 888 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 519 through 525 removed outlier: 6.726A pdb=" N VAL A 718 " --> pdb=" O MET A 521 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL A 523 " --> pdb=" O LEU A 716 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU A 716 " --> pdb=" O VAL A 523 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N LEU A 714 " --> pdb=" O PRO A 525 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N LEU A 713 " --> pdb=" O SER A 687 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N SER A 687 " --> pdb=" O LEU A 713 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ARG A 631 " --> pdb=" O PHE A 625 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N PHE A 625 " --> pdb=" O ARG A 631 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER A 633 " --> pdb=" O PHE A 623 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALA A 637 " --> pdb=" O VAL A 619 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N VAL A 619 " --> pdb=" O ALA A 637 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N SER A 588 " --> pdb=" O VAL A 619 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL A 579 " --> pdb=" O GLY A 591 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 557 through 558 414 hydrogen bonds defined for protein. 1191 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: 2.84 Time building geometry restraints manager: 3.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1197 1.31 - 1.43: 1857 1.43 - 1.56: 4476 1.56 - 1.68: 10 1.68 - 1.81: 71 Bond restraints: 7611 Sorted by residual: bond pdb=" F2 ALF A1201 " pdb="AL ALF A1201 " ideal model delta sigma weight residual 1.685 1.783 -0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" F3 ALF A1201 " pdb="AL ALF A1201 " ideal model delta sigma weight residual 1.685 1.780 -0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" F1 ALF A1201 " pdb="AL ALF A1201 " ideal model delta sigma weight residual 1.684 1.778 -0.094 2.00e-02 2.50e+03 2.21e+01 bond pdb=" F4 ALF A1201 " pdb="AL ALF A1201 " ideal model delta sigma weight residual 1.686 1.779 -0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" C TYR A 935 " pdb=" O TYR A 935 " ideal model delta sigma weight residual 1.236 1.182 0.054 1.29e-02 6.01e+03 1.74e+01 ... (remaining 7606 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.13: 10407 14.13 - 28.26: 5 28.26 - 42.39: 0 42.39 - 56.51: 0 56.51 - 70.64: 2 Bond angle restraints: 10414 Sorted by residual: angle pdb=" F1 ALF A1201 " pdb="AL ALF A1201 " pdb=" F2 ALF A1201 " ideal model delta sigma weight residual 108.68 179.32 -70.64 3.00e+00 1.11e-01 5.54e+02 angle pdb=" F3 ALF A1201 " pdb="AL ALF A1201 " pdb=" F4 ALF A1201 " ideal model delta sigma weight residual 109.63 178.41 -68.78 3.00e+00 1.11e-01 5.26e+02 angle pdb=" F2 ALF A1201 " pdb="AL ALF A1201 " pdb=" F4 ALF A1201 " ideal model delta sigma weight residual 110.21 89.91 20.30 3.00e+00 1.11e-01 4.58e+01 angle pdb=" F1 ALF A1201 " pdb="AL ALF A1201 " pdb=" F3 ALF A1201 " ideal model delta sigma weight residual 109.69 89.44 20.25 3.00e+00 1.11e-01 4.56e+01 angle pdb=" F1 ALF A1201 " pdb="AL ALF A1201 " pdb=" F4 ALF A1201 " ideal model delta sigma weight residual 109.02 90.03 18.99 3.00e+00 1.11e-01 4.01e+01 ... (remaining 10409 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 4299 18.01 - 36.02: 288 36.02 - 54.03: 51 54.03 - 72.04: 7 72.04 - 90.05: 7 Dihedral angle restraints: 4652 sinusoidal: 1659 harmonic: 2993 Sorted by residual: dihedral pdb=" CA PHE A 507 " pdb=" C PHE A 507 " pdb=" N ASP A 508 " pdb=" CA ASP A 508 " ideal model delta harmonic sigma weight residual 180.00 160.81 19.19 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ALA A 85 " pdb=" C ALA A 85 " pdb=" N GLU A 86 " pdb=" CA GLU A 86 " ideal model delta harmonic sigma weight residual 180.00 161.99 18.01 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA HIS A 492 " pdb=" C HIS A 492 " pdb=" N PRO A 493 " pdb=" CA PRO A 493 " ideal model delta harmonic sigma weight residual 180.00 -163.27 -16.73 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 4649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1154 0.086 - 0.172: 115 0.172 - 0.258: 5 0.258 - 0.343: 2 0.343 - 0.429: 5 Chirality restraints: 1281 Sorted by residual: chirality pdb=" CA TYR A 935 " pdb=" N TYR A 935 " pdb=" C TYR A 935 " pdb=" CB TYR A 935 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.61e+00 chirality pdb=" CBH Y01 A1204 " pdb=" CAT Y01 A1204 " pdb=" CAZ Y01 A1204 " pdb=" CBF Y01 A1204 " both_signs ideal model delta sigma weight residual False -2.85 -2.45 -0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" CBG Y01 A1203 " pdb=" CAQ Y01 A1203 " pdb=" CBD Y01 A1203 " pdb=" CBI Y01 A1203 " both_signs ideal model delta sigma weight residual False -2.33 -2.72 0.39 2.00e-01 2.50e+01 3.80e+00 ... (remaining 1278 not shown) Planarity restraints: 1320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 856 " 0.013 2.00e-02 2.50e+03 2.72e-02 7.41e+00 pdb=" CD GLU A 856 " -0.047 2.00e-02 2.50e+03 pdb=" OE1 GLU A 856 " 0.017 2.00e-02 2.50e+03 pdb=" OE2 GLU A 856 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 317 " 0.011 2.00e-02 2.50e+03 2.26e-02 5.09e+00 pdb=" CD GLN A 317 " -0.039 2.00e-02 2.50e+03 pdb=" OE1 GLN A 317 " 0.015 2.00e-02 2.50e+03 pdb=" NE2 GLN A 317 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 894 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.00e+00 pdb=" CD GLU A 894 " 0.039 2.00e-02 2.50e+03 pdb=" OE1 GLU A 894 " -0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU A 894 " -0.014 2.00e-02 2.50e+03 ... (remaining 1317 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.33: 10 2.33 - 2.98: 3652 2.98 - 3.62: 11022 3.62 - 4.26: 16324 4.26 - 4.90: 28408 Nonbonded interactions: 59416 Sorted by model distance: nonbonded pdb=" OD2 ASP A 508 " pdb="MG MG A1202 " model vdw 1.692 2.170 nonbonded pdb=" F2 ALF A1201 " pdb="MG MG A1202 " model vdw 1.857 2.120 nonbonded pdb=" OE2 GLU A 110 " pdb=" OH TYR A 160 " model vdw 2.024 3.040 nonbonded pdb=" OD2 ASP A 508 " pdb=" F2 ALF A1201 " model vdw 2.116 2.990 nonbonded pdb=" OG SER A 889 " pdb=" OG SER A 899 " model vdw 2.189 3.040 ... (remaining 59411 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: 2.020 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 23.300 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 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 : 0.007 0.356 7612 Z= 0.504 Angle : 1.312 70.642 10414 Z= 0.526 Chirality : 0.056 0.429 1281 Planarity : 0.006 0.050 1320 Dihedral : 13.195 90.046 2718 Min Nonbonded Distance : 1.692 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.14 % Allowed : 1.41 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: -1.56 (0.24), residues: 1024 helix: -0.52 (0.22), residues: 482 sheet: -1.63 (0.37), residues: 178 loop : -1.15 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1166 HIS 0.005 0.001 HIS A 492 PHE 0.024 0.002 PHE A 940 TYR 0.028 0.002 TYR A 935 ARG 0.020 0.001 ARG A 379 Details of bonding type rmsd hydrogen bonds : bond 0.15058 ( 414) hydrogen bonds : angle 7.33179 ( 1191) covalent geometry : bond 0.00613 ( 7611) covalent geometry : angle 1.31205 (10414) Misc. bond : bond 0.35563 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.803 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 51 average time/residue: 0.1634 time to fit residues: 12.6644 Evaluate side-chains 39 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 935 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 52 optimal weight: 30.0000 chunk 41 optimal weight: 0.7980 chunk 80 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 93 optimal weight: 0.3980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 ASN ** 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 = 0.3913 r_free = 0.3913 target = 0.086564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.065194 restraints weight = 25397.423| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 3.66 r_work: 0.3189 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7612 Z= 0.122 Angle : 0.857 30.536 10414 Z= 0.348 Chirality : 0.041 0.179 1281 Planarity : 0.005 0.036 1320 Dihedral : 5.739 59.872 1238 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.71 % Allowed : 8.46 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 0.29 (0.27), residues: 1024 helix: 1.07 (0.24), residues: 484 sheet: -0.92 (0.40), residues: 158 loop : -0.29 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1166 HIS 0.002 0.000 HIS A 831 PHE 0.014 0.001 PHE A 958 TYR 0.012 0.001 TYR A 40 ARG 0.006 0.000 ARG A1068 Details of bonding type rmsd hydrogen bonds : bond 0.03521 ( 414) hydrogen bonds : angle 4.85263 ( 1191) covalent geometry : bond 0.00279 ( 7611) covalent geometry : angle 0.85741 (10414) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 1.129 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 42 average time/residue: 0.2184 time to fit residues: 15.3739 Evaluate side-chains 41 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 935 TYR Chi-restraints excluded: chain A residue 973 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 101 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 2 optimal weight: 10.0000 chunk 4 optimal weight: 0.0870 chunk 99 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 overall best weight: 1.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 ASN ** 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 = 0.3813 r_free = 0.3813 target = 0.082244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.060763 restraints weight = 25883.197| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 3.47 r_work: 0.3122 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7612 Z= 0.160 Angle : 0.858 30.065 10414 Z= 0.346 Chirality : 0.041 0.141 1281 Planarity : 0.004 0.035 1320 Dihedral : 5.363 58.376 1238 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.27 % Allowed : 11.14 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 1024 helix: 1.64 (0.24), residues: 497 sheet: -0.88 (0.39), residues: 164 loop : 0.00 (0.35), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 301 HIS 0.002 0.001 HIS A 385 PHE 0.010 0.001 PHE A 958 TYR 0.011 0.001 TYR A 931 ARG 0.004 0.000 ARG A1068 Details of bonding type rmsd hydrogen bonds : bond 0.03414 ( 414) hydrogen bonds : angle 4.48047 ( 1191) covalent geometry : bond 0.00371 ( 7611) covalent geometry : angle 0.85775 (10414) Misc. bond : bond 0.00063 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.770 Fit side-chains REVERT: A 421 MET cc_start: 0.7946 (pmm) cc_final: 0.7371 (pmm) outliers start: 9 outliers final: 5 residues processed: 47 average time/residue: 0.1288 time to fit residues: 10.0233 Evaluate side-chains 44 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 935 TYR Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 973 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 75 optimal weight: 2.9990 chunk 30 optimal weight: 0.2980 chunk 41 optimal weight: 0.2980 chunk 45 optimal weight: 20.0000 chunk 72 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 96 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 55 optimal weight: 40.0000 chunk 23 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 ASN ** 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 = 0.3821 r_free = 0.3821 target = 0.083000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.061306 restraints weight = 25608.334| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 3.42 r_work: 0.3223 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7612 Z= 0.103 Angle : 0.835 29.668 10414 Z= 0.329 Chirality : 0.040 0.124 1281 Planarity : 0.004 0.032 1320 Dihedral : 4.975 58.062 1238 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.69 % Allowed : 12.41 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 1.31 (0.28), residues: 1024 helix: 2.02 (0.24), residues: 496 sheet: -0.89 (0.39), residues: 170 loop : 0.26 (0.35), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 170 HIS 0.002 0.000 HIS A 385 PHE 0.021 0.001 PHE A 241 TYR 0.009 0.001 TYR A 931 ARG 0.003 0.000 ARG A1068 Details of bonding type rmsd hydrogen bonds : bond 0.03012 ( 414) hydrogen bonds : angle 4.18313 ( 1191) covalent geometry : bond 0.00237 ( 7611) covalent geometry : angle 0.83503 (10414) Misc. bond : bond 0.00044 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.821 Fit side-chains REVERT: A 421 MET cc_start: 0.8014 (pmm) cc_final: 0.7514 (pmm) outliers start: 12 outliers final: 7 residues processed: 50 average time/residue: 0.1330 time to fit residues: 10.8901 Evaluate side-chains 48 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 932 MET Chi-restraints excluded: chain A residue 935 TYR Chi-restraints excluded: chain A residue 973 MET Chi-restraints excluded: chain A residue 1025 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 30.0000 chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 51 optimal weight: 20.0000 chunk 19 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 ASN ** 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 = 0.3794 r_free = 0.3794 target = 0.081388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.060052 restraints weight = 25873.758| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 3.43 r_work: 0.3172 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7612 Z= 0.172 Angle : 0.859 30.076 10414 Z= 0.342 Chirality : 0.041 0.127 1281 Planarity : 0.004 0.031 1320 Dihedral : 5.095 59.517 1238 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.55 % Allowed : 13.26 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.28), residues: 1024 helix: 2.16 (0.24), residues: 499 sheet: -0.99 (0.38), residues: 174 loop : 0.39 (0.36), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1166 HIS 0.002 0.001 HIS A 197 PHE 0.019 0.001 PHE A 241 TYR 0.011 0.001 TYR A 931 ARG 0.003 0.000 ARG A 281 Details of bonding type rmsd hydrogen bonds : bond 0.03236 ( 414) hydrogen bonds : angle 4.23281 ( 1191) covalent geometry : bond 0.00401 ( 7611) covalent geometry : angle 0.85927 (10414) Misc. bond : bond 0.00049 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.861 Fit side-chains REVERT: A 421 MET cc_start: 0.7979 (pmm) cc_final: 0.7566 (pmm) outliers start: 11 outliers final: 9 residues processed: 50 average time/residue: 0.1385 time to fit residues: 11.3195 Evaluate side-chains 49 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 935 TYR Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 973 MET Chi-restraints excluded: chain A residue 1025 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 89 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 100 optimal weight: 0.4980 chunk 27 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 0.0970 chunk 14 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 ASN ** 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 = 0.3824 r_free = 0.3824 target = 0.083021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.061862 restraints weight = 25628.602| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 3.42 r_work: 0.3177 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7612 Z= 0.098 Angle : 0.832 29.576 10414 Z= 0.325 Chirality : 0.039 0.124 1281 Planarity : 0.004 0.033 1320 Dihedral : 4.709 56.825 1238 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.69 % Allowed : 13.68 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 1.65 (0.28), residues: 1024 helix: 2.36 (0.24), residues: 501 sheet: -0.97 (0.38), residues: 173 loop : 0.46 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1166 HIS 0.001 0.000 HIS A 385 PHE 0.021 0.001 PHE A 241 TYR 0.009 0.001 TYR A 931 ARG 0.002 0.000 ARG A1068 Details of bonding type rmsd hydrogen bonds : bond 0.02883 ( 414) hydrogen bonds : angle 4.01777 ( 1191) covalent geometry : bond 0.00223 ( 7611) covalent geometry : angle 0.83196 (10414) Misc. bond : bond 0.00048 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.843 Fit side-chains REVERT: A 421 MET cc_start: 0.7898 (pmm) cc_final: 0.7568 (pmm) outliers start: 12 outliers final: 9 residues processed: 49 average time/residue: 0.1374 time to fit residues: 10.9753 Evaluate side-chains 49 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 935 TYR Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 973 MET Chi-restraints excluded: chain A residue 1025 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 21 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 92 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 ASN ** 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 = 0.3820 r_free = 0.3820 target = 0.082661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.061559 restraints weight = 25387.242| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 3.41 r_work: 0.3133 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7612 Z= 0.116 Angle : 0.843 29.829 10414 Z= 0.328 Chirality : 0.040 0.122 1281 Planarity : 0.004 0.033 1320 Dihedral : 4.648 55.598 1238 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.83 % Allowed : 14.25 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 1.78 (0.28), residues: 1024 helix: 2.48 (0.24), residues: 501 sheet: -0.88 (0.38), residues: 166 loop : 0.45 (0.35), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1166 HIS 0.001 0.000 HIS A 385 PHE 0.022 0.001 PHE A 241 TYR 0.009 0.001 TYR A 931 ARG 0.002 0.000 ARG A 281 Details of bonding type rmsd hydrogen bonds : bond 0.02908 ( 414) hydrogen bonds : angle 3.99092 ( 1191) covalent geometry : bond 0.00269 ( 7611) covalent geometry : angle 0.84280 (10414) Misc. bond : bond 0.00055 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.759 Fit side-chains REVERT: A 1004 MET cc_start: 0.8719 (mmm) cc_final: 0.8496 (mmm) outliers start: 13 outliers final: 9 residues processed: 52 average time/residue: 0.1384 time to fit residues: 11.6456 Evaluate side-chains 49 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 935 TYR Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 973 MET Chi-restraints excluded: chain A residue 1025 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 13 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 37 optimal weight: 0.0470 chunk 57 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 59 optimal weight: 40.0000 chunk 100 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 overall best weight: 1.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** 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 = 0.3721 r_free = 0.3721 target = 0.081250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.058930 restraints weight = 26785.459| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 3.51 r_work: 0.2987 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7612 Z= 0.157 Angle : 0.854 29.956 10414 Z= 0.338 Chirality : 0.041 0.123 1281 Planarity : 0.004 0.032 1320 Dihedral : 4.765 55.250 1238 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.26 % Allowed : 13.82 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 1.74 (0.28), residues: 1024 helix: 2.44 (0.24), residues: 504 sheet: -1.02 (0.37), residues: 174 loop : 0.56 (0.36), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1166 HIS 0.002 0.000 HIS A 385 PHE 0.023 0.001 PHE A 241 TYR 0.010 0.001 TYR A 931 ARG 0.002 0.000 ARG A1068 Details of bonding type rmsd hydrogen bonds : bond 0.03090 ( 414) hydrogen bonds : angle 4.07433 ( 1191) covalent geometry : bond 0.00366 ( 7611) covalent geometry : angle 0.85361 (10414) Misc. bond : bond 0.00042 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 40 time to evaluate : 0.820 Fit side-chains REVERT: A 108 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8543 (pm20) REVERT: A 414 PHE cc_start: 0.7588 (m-80) cc_final: 0.7349 (m-80) REVERT: A 1000 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8361 (mt) outliers start: 16 outliers final: 10 residues processed: 54 average time/residue: 0.1327 time to fit residues: 11.6954 Evaluate side-chains 52 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 935 TYR Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 973 MET Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1025 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 59 optimal weight: 40.0000 chunk 23 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 2 optimal weight: 0.0270 chunk 93 optimal weight: 1.9990 overall best weight: 1.2042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** 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 = 0.3726 r_free = 0.3726 target = 0.079918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.057570 restraints weight = 26405.097| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 3.54 r_work: 0.2990 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7612 Z= 0.141 Angle : 0.856 29.726 10414 Z= 0.337 Chirality : 0.040 0.121 1281 Planarity : 0.004 0.032 1320 Dihedral : 4.705 55.468 1238 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.12 % Allowed : 14.10 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 1.81 (0.27), residues: 1024 helix: 2.50 (0.24), residues: 504 sheet: -0.99 (0.38), residues: 166 loop : 0.53 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1166 HIS 0.002 0.000 HIS A 385 PHE 0.023 0.001 PHE A 241 TYR 0.009 0.001 TYR A 931 ARG 0.002 0.000 ARG A 281 Details of bonding type rmsd hydrogen bonds : bond 0.03012 ( 414) hydrogen bonds : angle 4.01821 ( 1191) covalent geometry : bond 0.00329 ( 7611) covalent geometry : angle 0.85587 (10414) Misc. bond : bond 0.00041 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 40 time to evaluate : 0.857 Fit side-chains REVERT: A 414 PHE cc_start: 0.7609 (m-80) cc_final: 0.7385 (m-80) REVERT: A 1000 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8273 (mt) outliers start: 15 outliers final: 11 residues processed: 53 average time/residue: 0.1503 time to fit residues: 13.3757 Evaluate side-chains 51 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 935 TYR Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 973 MET Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1025 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 75 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 53 optimal weight: 50.0000 chunk 16 optimal weight: 0.9990 chunk 83 optimal weight: 0.0670 chunk 98 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** 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 = 0.3738 r_free = 0.3738 target = 0.081890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.059713 restraints weight = 26831.680| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 3.54 r_work: 0.3013 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7612 Z= 0.110 Angle : 0.838 29.631 10414 Z= 0.328 Chirality : 0.040 0.120 1281 Planarity : 0.004 0.033 1320 Dihedral : 4.536 55.370 1238 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.69 % Allowed : 14.39 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 1.92 (0.27), residues: 1024 helix: 2.62 (0.23), residues: 502 sheet: -0.96 (0.38), residues: 166 loop : 0.56 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1166 HIS 0.001 0.000 HIS A 385 PHE 0.023 0.001 PHE A 241 TYR 0.009 0.001 TYR A 931 ARG 0.002 0.000 ARG A1068 Details of bonding type rmsd hydrogen bonds : bond 0.02864 ( 414) hydrogen bonds : angle 3.93091 ( 1191) covalent geometry : bond 0.00254 ( 7611) covalent geometry : angle 0.83797 (10414) Misc. bond : bond 0.00044 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.825 Fit side-chains REVERT: A 288 MET cc_start: 0.8806 (ptp) cc_final: 0.8280 (ptp) REVERT: A 414 PHE cc_start: 0.7598 (m-80) cc_final: 0.7394 (m-80) REVERT: A 1000 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8276 (mt) outliers start: 12 outliers final: 11 residues processed: 50 average time/residue: 0.1465 time to fit residues: 11.9702 Evaluate side-chains 52 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 935 TYR Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 973 MET Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1025 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 33 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 21 optimal weight: 0.3980 chunk 71 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 85 optimal weight: 0.0470 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** 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 = 0.3749 r_free = 0.3749 target = 0.082508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.060404 restraints weight = 26673.490| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 3.51 r_work: 0.3034 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7612 Z= 0.096 Angle : 0.845 29.626 10414 Z= 0.329 Chirality : 0.039 0.117 1281 Planarity : 0.004 0.033 1320 Dihedral : 4.393 55.078 1238 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.69 % Allowed : 14.67 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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 (0.27), residues: 1024 helix: 2.71 (0.24), residues: 502 sheet: -0.95 (0.38), residues: 166 loop : 0.71 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1166 HIS 0.001 0.000 HIS A 831 PHE 0.023 0.001 PHE A 241 TYR 0.008 0.001 TYR A 931 ARG 0.002 0.000 ARG A1068 Details of bonding type rmsd hydrogen bonds : bond 0.02755 ( 414) hydrogen bonds : angle 3.83992 ( 1191) covalent geometry : bond 0.00221 ( 7611) covalent geometry : angle 0.84469 (10414) Misc. bond : bond 0.00051 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4536.05 seconds wall clock time: 79 minutes 56.20 seconds (4796.20 seconds total)