Starting phenix.real_space_refine on Tue Sep 24 10:41:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n77_24222/09_2024/7n77_24222_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n77_24222/09_2024/7n77_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n77_24222/09_2024/7n77_24222.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n77_24222/09_2024/7n77_24222.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n77_24222/09_2024/7n77_24222_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n77_24222/09_2024/7n77_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-5461/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: 5.22, per 1000 atoms: 0.70 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: 2.15 Conformation dependent library (CDL) restraints added in 961.5 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: 0.96 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: 3.01 Time building geometry restraints manager: 2.46 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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.170 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.910 ------------------------------------------------------------------------------- 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 : 0.006 0.098 7611 Z= 0.399 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 *********************** 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 fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.961 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 51 average time/residue: 0.1599 time to fit residues: 12.4268 Evaluate side-chains 39 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 0.849 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 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 7611 Z= 0.187 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 *********************** 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 fitting. rotamer outliers: 5 poor density : 40 time to evaluate : 0.848 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 42 average time/residue: 0.1418 time to fit residues: 9.7587 Evaluate side-chains 41 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 37 time to evaluate : 0.836 ------------------------------------------------------------------------------- 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 51 optimal weight: 50.0000 chunk 29 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 25 optimal weight: 0.0980 chunk 93 optimal weight: 0.0050 chunk 101 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 overall best weight: 0.4594 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7611 Z= 0.145 Angle : 0.835 29.817 10414 Z= 0.332 Chirality : 0.040 0.139 1281 Planarity : 0.004 0.035 1320 Dihedral : 5.179 58.369 1238 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.27 % Allowed : 10.72 % Favored : 88.01 % 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: 0.98 (0.27), residues: 1024 helix: 1.71 (0.24), residues: 496 sheet: -0.77 (0.39), residues: 164 loop : -0.01 (0.35), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 170 HIS 0.001 0.000 HIS A 831 PHE 0.011 0.001 PHE A 958 TYR 0.009 0.001 TYR A 931 ARG 0.005 0.000 ARG A1068 *********************** 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 50 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 41 time to evaluate : 0.764 Fit side-chains REVERT: A 459 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7689 (mt) outliers start: 9 outliers final: 4 residues processed: 48 average time/residue: 0.1393 time to fit residues: 11.4964 Evaluate side-chains 45 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 40 time to evaluate : 0.761 ------------------------------------------------------------------------------- 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 459 LEU Chi-restraints excluded: chain A residue 935 TYR 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 92 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 44 optimal weight: 0.0370 chunk 62 optimal weight: 1.9990 chunk 94 optimal weight: 0.0770 chunk 99 optimal weight: 0.9990 chunk 49 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 overall best weight: 0.6020 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7611 Z= 0.155 Angle : 0.827 29.787 10414 Z= 0.325 Chirality : 0.040 0.123 1281 Planarity : 0.004 0.032 1320 Dihedral : 4.850 58.275 1238 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.27 % Allowed : 12.27 % Favored : 86.46 % 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: 1.37 (0.27), residues: 1024 helix: 2.09 (0.24), residues: 496 sheet: -0.84 (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 A1166 HIS 0.001 0.000 HIS A 385 PHE 0.023 0.001 PHE A 241 TYR 0.010 0.001 TYR A 931 ARG 0.003 0.000 ARG A1068 *********************** 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 49 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 40 time to evaluate : 0.876 Fit side-chains REVERT: A 459 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7795 (mt) outliers start: 9 outliers final: 5 residues processed: 47 average time/residue: 0.1345 time to fit residues: 10.4338 Evaluate side-chains 45 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 0.764 ------------------------------------------------------------------------------- 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 459 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 74 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 68 optimal weight: 0.0030 chunk 0 optimal weight: 7.9990 chunk 50 optimal weight: 50.0000 chunk 89 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.7998 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 7611 Z= 0.303 Angle : 0.875 30.209 10414 Z= 0.352 Chirality : 0.042 0.129 1281 Planarity : 0.004 0.032 1320 Dihedral : 5.177 59.302 1238 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.55 % Allowed : 12.69 % Favored : 85.75 % 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: 1.47 (0.28), residues: 1024 helix: 2.19 (0.24), residues: 492 sheet: -0.95 (0.38), residues: 173 loop : 0.41 (0.36), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 301 HIS 0.002 0.001 HIS A 197 PHE 0.018 0.001 PHE A 241 TYR 0.011 0.001 TYR A 931 ARG 0.002 0.000 ARG A 281 *********************** 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 50 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 39 time to evaluate : 0.750 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 48 average time/residue: 0.1306 time to fit residues: 10.3167 Evaluate side-chains 46 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 38 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 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 33 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 58 optimal weight: 40.0000 chunk 24 optimal weight: 6.9990 chunk 99 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 52 optimal weight: 50.0000 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7611 Z= 0.266 Angle : 0.857 30.096 10414 Z= 0.341 Chirality : 0.041 0.124 1281 Planarity : 0.004 0.032 1320 Dihedral : 5.047 56.320 1238 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.55 % Allowed : 13.54 % Favored : 84.91 % 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: 1.49 (0.28), residues: 1024 helix: 2.17 (0.24), residues: 504 sheet: -0.99 (0.37), residues: 173 loop : 0.43 (0.36), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1166 HIS 0.002 0.001 HIS A 385 PHE 0.016 0.001 PHE A 241 TYR 0.010 0.001 TYR A 931 ARG 0.002 0.000 ARG A 455 *********************** 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 51 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 40 time to evaluate : 0.756 Fit side-chains outliers start: 11 outliers final: 10 residues processed: 49 average time/residue: 0.1415 time to fit residues: 11.1720 Evaluate side-chains 49 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 39 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 83 optimal weight: 0.3980 chunk 55 optimal weight: 30.0000 chunk 99 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 60 optimal weight: 30.0000 chunk 45 optimal weight: 20.0000 chunk 61 optimal weight: 0.0980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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** A 892 GLN ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7611 Z= 0.180 Angle : 0.850 29.643 10414 Z= 0.332 Chirality : 0.040 0.123 1281 Planarity : 0.004 0.032 1320 Dihedral : 4.777 55.712 1238 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.97 % Allowed : 13.96 % Favored : 84.06 % 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: 1.66 (0.27), residues: 1024 helix: 2.36 (0.24), residues: 503 sheet: -0.96 (0.38), residues: 166 loop : 0.44 (0.35), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1166 HIS 0.001 0.000 HIS A 385 PHE 0.014 0.001 PHE A 241 TYR 0.009 0.001 TYR A 931 ARG 0.002 0.000 ARG A 281 *********************** 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 55 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 41 time to evaluate : 0.844 Fit side-chains outliers start: 14 outliers final: 9 residues processed: 53 average time/residue: 0.1502 time to fit residues: 12.7459 Evaluate side-chains 48 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 39 time to evaluate : 0.871 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 0.6980 chunk 59 optimal weight: 40.0000 chunk 29 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 49 optimal weight: 20.0000 chunk 9 optimal weight: 0.0270 chunk 78 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7611 Z= 0.160 Angle : 0.834 29.643 10414 Z= 0.325 Chirality : 0.040 0.120 1281 Planarity : 0.004 0.033 1320 Dihedral : 4.582 55.813 1238 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.83 % Allowed : 14.39 % 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: 2.52 (0.23), residues: 502 sheet: -0.92 (0.38), residues: 166 loop : 0.47 (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 0.013 0.001 PHE A 241 TYR 0.009 0.001 TYR A 931 ARG 0.002 0.000 ARG A1068 *********************** 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 53 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 40 time to evaluate : 0.884 Fit side-chains REVERT: A 288 MET cc_start: 0.7296 (ptp) cc_final: 0.7080 (ptp) outliers start: 13 outliers final: 10 residues processed: 51 average time/residue: 0.1378 time to fit residues: 11.3756 Evaluate side-chains 49 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 39 time to evaluate : 0.794 ------------------------------------------------------------------------------- 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 997 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 86 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 55 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 28 optimal weight: 0.0980 chunk 83 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 60 optimal weight: 9.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7611 Z= 0.162 Angle : 0.846 29.685 10414 Z= 0.330 Chirality : 0.039 0.119 1281 Planarity : 0.004 0.033 1320 Dihedral : 4.478 54.956 1238 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.83 % Allowed : 14.67 % Favored : 83.50 % 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: 1.95 (0.27), residues: 1024 helix: 2.63 (0.23), residues: 502 sheet: -0.96 (0.38), residues: 168 loop : 0.62 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1166 HIS 0.001 0.000 HIS A 831 PHE 0.019 0.001 PHE A1123 TYR 0.009 0.001 TYR A 931 ARG 0.002 0.000 ARG A 281 *********************** 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 53 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 40 time to evaluate : 0.844 Fit side-chains REVERT: A 288 MET cc_start: 0.7324 (ptp) cc_final: 0.7121 (ptp) outliers start: 13 outliers final: 10 residues processed: 51 average time/residue: 0.1365 time to fit residues: 11.5781 Evaluate side-chains 50 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 40 time to evaluate : 0.843 ------------------------------------------------------------------------------- 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 997 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 59 optimal weight: 40.0000 chunk 46 optimal weight: 30.0000 chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 50 optimal weight: 50.0000 chunk 64 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7611 Z= 0.180 Angle : 0.844 29.775 10414 Z= 0.331 Chirality : 0.040 0.119 1281 Planarity : 0.004 0.033 1320 Dihedral : 4.473 55.314 1238 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.41 % Allowed : 14.95 % 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: 2.01 (0.27), residues: 1024 helix: 2.66 (0.23), residues: 502 sheet: -0.95 (0.38), residues: 166 loop : 0.67 (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 0.012 0.001 PHE A 241 TYR 0.009 0.001 TYR A 931 ARG 0.002 0.000 ARG A1068 ********************** 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 51 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 41 time to evaluate : 0.793 Fit side-chains outliers start: 10 outliers final: 10 residues processed: 49 average time/residue: 0.1403 time to fit residues: 11.2597 Evaluate side-chains 50 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 40 time to evaluate : 0.842 ------------------------------------------------------------------------------- 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 997 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 25 optimal weight: 0.6980 chunk 75 optimal weight: 0.4980 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 0.4980 chunk 81 optimal weight: 0.4980 chunk 34 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.082334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.060246 restraints weight = 26396.823| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 3.51 r_work: 0.3033 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7611 Z= 0.160 Angle : 0.845 29.671 10414 Z= 0.329 Chirality : 0.039 0.118 1281 Planarity : 0.004 0.033 1320 Dihedral : 4.370 54.363 1238 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.41 % Allowed : 15.37 % Favored : 83.22 % 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: 2.09 (0.27), residues: 1024 helix: 2.73 (0.23), residues: 502 sheet: -0.91 (0.38), residues: 166 loop : 0.72 (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 385 PHE 0.019 0.001 PHE A1123 TYR 0.009 0.001 TYR A 931 ARG 0.002 0.000 ARG A1068 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1648.21 seconds wall clock time: 30 minutes 0.24 seconds (1800.24 seconds total)