Starting phenix.real_space_refine on Wed Sep 17 09:49:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n77_24222/09_2025/7n77_24222_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n77_24222/09_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_24222/09_2025/7n77_24222.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n77_24222/09_2025/7n77_24222.map" model { file = "/net/cci-nas-00/data/ceres_data/7n77_24222/09_2025/7n77_24222_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n77_24222/09_2025/7n77_24222_trim.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ARG:plan': 20, 'TRP:plan': 6, 'TYR:plan': 2, 'HIS:plan': 4, 'PHE:plan': 6, 'ASN:plan1': 2, 'GLU:plan': 14, 'GLN:plan1': 9, 'ASP:plan': 6} 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-1': 1, 'Y01:plan-2': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 1.86, per 1000 atoms: 0.25 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: 0.69 Conformation dependent library (CDL) restraints added in 478.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.28 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: 1.59 Time building geometry restraints manager: 0.92 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: 2.600 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.020 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.900 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.020 0.001 ARG A 379 TYR 0.028 0.002 TYR A 935 PHE 0.024 0.002 PHE A 940 TRP 0.012 0.001 TRP A1166 HIS 0.005 0.001 HIS A 492 Details of bonding type rmsd covalent geometry : bond 0.00613 ( 7611) covalent geometry : angle 1.31205 (10414) hydrogen bonds : bond 0.15058 ( 414) hydrogen bonds : angle 7.33179 ( 1191) 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 : 0.385 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 51 average time/residue: 0.0671 time to fit residues: 5.2349 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 : 0.291 ------------------------------------------------------------------------------- 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 49 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 30.0000 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 50.0000 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.3808 r_free = 0.3808 target = 0.082012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.060220 restraints weight = 25916.481| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 3.48 r_work: 0.3127 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7612 Z= 0.202 Angle : 0.890 31.103 10414 Z= 0.368 Chirality : 0.043 0.190 1281 Planarity : 0.005 0.037 1320 Dihedral : 5.928 59.589 1238 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.85 % Allowed : 8.04 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.27), residues: 1024 helix: 0.96 (0.24), residues: 489 sheet: -1.06 (0.39), residues: 164 loop : -0.34 (0.34), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1068 TYR 0.013 0.001 TYR A 40 PHE 0.013 0.001 PHE A 958 TRP 0.011 0.001 TRP A1166 HIS 0.002 0.001 HIS A 385 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 7611) covalent geometry : angle 0.88990 (10414) hydrogen bonds : bond 0.03731 ( 414) hydrogen bonds : angle 4.97330 ( 1191) Misc. bond : bond 0.00032 ( 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: 6 poor density : 39 time to evaluate : 0.364 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 42 average time/residue: 0.0608 time to fit residues: 4.2826 Evaluate side-chains 40 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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 24 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 78 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 = 0.3820 r_free = 0.3820 target = 0.082269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.060476 restraints weight = 25628.024| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 3.53 r_work: 0.3150 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7612 Z= 0.187 Angle : 0.870 30.055 10414 Z= 0.353 Chirality : 0.041 0.139 1281 Planarity : 0.004 0.034 1320 Dihedral : 5.467 58.452 1238 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.55 % Allowed : 11.85 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.28), residues: 1024 helix: 1.54 (0.24), residues: 497 sheet: -1.18 (0.38), residues: 173 loop : 0.07 (0.36), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1068 TYR 0.010 0.001 TYR A 931 PHE 0.011 0.001 PHE A 958 TRP 0.010 0.001 TRP A 301 HIS 0.002 0.001 HIS A 385 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 7611) covalent geometry : angle 0.87032 (10414) hydrogen bonds : bond 0.03536 ( 414) hydrogen bonds : angle 4.58423 ( 1191) Misc. bond : bond 0.00071 ( 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 52 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.295 Fit side-chains REVERT: A 421 MET cc_start: 0.7884 (pmm) cc_final: 0.7347 (pmm) outliers start: 11 outliers final: 7 residues processed: 49 average time/residue: 0.0638 time to fit residues: 5.1045 Evaluate side-chains 47 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 460 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 69 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 55 optimal weight: 50.0000 chunk 72 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 94 optimal weight: 0.0770 chunk 10 optimal weight: 6.9990 chunk 100 optimal weight: 0.0770 overall best weight: 0.4696 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.083001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.061418 restraints weight = 25822.814| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 3.45 r_work: 0.3155 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7612 Z= 0.095 Angle : 0.834 29.676 10414 Z= 0.329 Chirality : 0.040 0.123 1281 Planarity : 0.004 0.033 1320 Dihedral : 4.987 58.974 1238 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.55 % Allowed : 12.98 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.27), residues: 1024 helix: 2.03 (0.24), residues: 491 sheet: -0.97 (0.38), residues: 170 loop : 0.22 (0.35), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1068 TYR 0.007 0.001 TYR A 931 PHE 0.009 0.001 PHE A 958 TRP 0.008 0.001 TRP A 170 HIS 0.001 0.000 HIS A 831 Details of bonding type rmsd covalent geometry : bond 0.00214 ( 7611) covalent geometry : angle 0.83398 (10414) hydrogen bonds : bond 0.03016 ( 414) hydrogen bonds : angle 4.19633 ( 1191) Misc. bond : bond 0.00030 ( 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 53 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.359 Fit side-chains REVERT: A 421 MET cc_start: 0.7950 (pmm) cc_final: 0.7491 (pmm) outliers start: 11 outliers final: 6 residues processed: 50 average time/residue: 0.0591 time to fit residues: 4.8930 Evaluate side-chains 46 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.217 ------------------------------------------------------------------------------- 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 870 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 85 optimal weight: 0.2980 chunk 89 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 60 optimal weight: 20.0000 chunk 8 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 = 0.3809 r_free = 0.3809 target = 0.082405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.060897 restraints weight = 25904.676| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 3.46 r_work: 0.3188 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7612 Z= 0.109 Angle : 0.835 29.805 10414 Z= 0.328 Chirality : 0.040 0.125 1281 Planarity : 0.004 0.032 1320 Dihedral : 4.844 58.815 1238 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.27), residues: 1024 helix: 2.18 (0.24), residues: 499 sheet: -0.94 (0.38), residues: 170 loop : 0.37 (0.35), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1068 TYR 0.009 0.001 TYR A 931 PHE 0.021 0.001 PHE A 241 TRP 0.007 0.001 TRP A1166 HIS 0.001 0.000 HIS A 385 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 7611) covalent geometry : angle 0.83539 (10414) hydrogen bonds : bond 0.02963 ( 414) hydrogen bonds : angle 4.10367 ( 1191) 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 55 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.299 Fit side-chains REVERT: A 421 MET cc_start: 0.7961 (pmm) cc_final: 0.7588 (pmm) outliers start: 14 outliers final: 9 residues processed: 51 average time/residue: 0.0585 time to fit residues: 4.9322 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 : 0.270 ------------------------------------------------------------------------------- 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 870 MET 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 100 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 85 optimal weight: 0.0670 chunk 5 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 overall best weight: 0.9924 ------------------------------------------------------------------------------- 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 = 0.3807 r_free = 0.3807 target = 0.082109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.060935 restraints weight = 25775.944| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 3.38 r_work: 0.3175 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7612 Z= 0.125 Angle : 0.841 29.834 10414 Z= 0.329 Chirality : 0.040 0.123 1281 Planarity : 0.004 0.033 1320 Dihedral : 4.749 55.400 1238 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.28), residues: 1024 helix: 2.29 (0.24), residues: 503 sheet: -1.00 (0.37), residues: 174 loop : 0.52 (0.36), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1068 TYR 0.009 0.001 TYR A 931 PHE 0.020 0.001 PHE A 241 TRP 0.008 0.001 TRP A1166 HIS 0.001 0.000 HIS A 385 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 7611) covalent geometry : angle 0.84060 (10414) hydrogen bonds : bond 0.02967 ( 414) hydrogen bonds : angle 4.07983 ( 1191) Misc. bond : bond 0.00051 ( 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 54 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.294 Fit side-chains REVERT: A 421 MET cc_start: 0.7914 (pmm) cc_final: 0.7601 (pmm) outliers start: 13 outliers final: 9 residues processed: 50 average time/residue: 0.0606 time to fit residues: 4.9868 Evaluate side-chains 50 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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 870 MET 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 102 optimal weight: 0.9980 chunk 56 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 89 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.3728 r_free = 0.3728 target = 0.080116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.057854 restraints weight = 26477.148| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 3.56 r_work: 0.2996 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2510 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= 0.131 Angle : 0.848 29.810 10414 Z= 0.333 Chirality : 0.040 0.125 1281 Planarity : 0.004 0.033 1320 Dihedral : 4.695 55.374 1238 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.97 % Allowed : 15.09 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.27), residues: 1024 helix: 2.35 (0.24), residues: 504 sheet: -1.04 (0.37), residues: 173 loop : 0.56 (0.36), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 281 TYR 0.009 0.001 TYR A 931 PHE 0.022 0.001 PHE A 241 TRP 0.009 0.001 TRP A1166 HIS 0.001 0.000 HIS A 385 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 7611) covalent geometry : angle 0.84846 (10414) hydrogen bonds : bond 0.02972 ( 414) hydrogen bonds : angle 4.04618 ( 1191) Misc. bond : bond 0.00050 ( 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 55 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.308 Fit side-chains REVERT: A 1000 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8345 (mt) REVERT: A 1004 MET cc_start: 0.8783 (mmm) cc_final: 0.8567 (mmm) outliers start: 14 outliers final: 11 residues processed: 52 average time/residue: 0.0604 time to fit residues: 5.2035 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 : 0.354 ------------------------------------------------------------------------------- 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 870 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 17 optimal weight: 1.9990 chunk 54 optimal weight: 30.0000 chunk 53 optimal weight: 50.0000 chunk 67 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3727 r_free = 0.3727 target = 0.081429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.059198 restraints weight = 26838.882| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 3.55 r_work: 0.2996 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2585 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= 0.132 Angle : 0.842 29.789 10414 Z= 0.330 Chirality : 0.040 0.121 1281 Planarity : 0.004 0.033 1320 Dihedral : 4.650 54.897 1238 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.26 % Allowed : 15.09 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.27), residues: 1024 helix: 2.45 (0.24), residues: 504 sheet: -1.10 (0.37), residues: 173 loop : 0.60 (0.36), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1068 TYR 0.009 0.001 TYR A 931 PHE 0.023 0.001 PHE A 241 TRP 0.009 0.001 TRP A1166 HIS 0.001 0.000 HIS A 385 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 7611) covalent geometry : angle 0.84161 (10414) hydrogen bonds : bond 0.02972 ( 414) hydrogen bonds : angle 4.03364 ( 1191) Misc. bond : bond 0.00041 ( 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 : 0.314 Fit side-chains REVERT: A 1000 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8413 (mt) outliers start: 16 outliers final: 13 residues processed: 52 average time/residue: 0.0566 time to fit residues: 4.8710 Evaluate side-chains 55 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.246 ------------------------------------------------------------------------------- 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 462 VAL Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 870 MET 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 Chi-restraints excluded: chain A residue 1070 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 0 optimal weight: 8.9990 chunk 81 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 31 optimal weight: 0.9980 chunk 56 optimal weight: 9.9990 chunk 53 optimal weight: 50.0000 chunk 6 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3737 r_free = 0.3737 target = 0.081927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.059786 restraints weight = 26540.326| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 3.51 r_work: 0.3013 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2718 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 : 0.847 29.666 10414 Z= 0.331 Chirality : 0.040 0.121 1281 Planarity : 0.004 0.033 1320 Dihedral : 4.519 54.946 1238 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.40 % Allowed : 14.81 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.85 (0.27), residues: 1024 helix: 2.55 (0.24), residues: 502 sheet: -1.15 (0.36), residues: 175 loop : 0.71 (0.36), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 281 TYR 0.008 0.001 TYR A 931 PHE 0.022 0.001 PHE A 241 TRP 0.008 0.001 TRP A1166 HIS 0.001 0.000 HIS A 385 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 7611) covalent geometry : angle 0.84704 (10414) hydrogen bonds : bond 0.02857 ( 414) hydrogen bonds : angle 3.94526 ( 1191) Misc. bond : bond 0.00044 ( 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 57 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 40 time to evaluate : 0.269 Fit side-chains REVERT: A 956 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8974 (mm) REVERT: A 1000 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8312 (mt) outliers start: 17 outliers final: 12 residues processed: 54 average time/residue: 0.0517 time to fit residues: 4.6653 Evaluate side-chains 54 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 40 time to evaluate : 0.284 ------------------------------------------------------------------------------- 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 462 VAL Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 870 MET Chi-restraints excluded: chain A residue 935 TYR Chi-restraints excluded: chain A residue 956 LEU 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 28 optimal weight: 0.0980 chunk 66 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 9 optimal weight: 0.2980 chunk 22 optimal weight: 0.5980 chunk 51 optimal weight: 30.0000 chunk 85 optimal weight: 0.0170 chunk 90 optimal weight: 0.2980 chunk 2 optimal weight: 1.9990 overall best weight: 0.2618 ------------------------------------------------------------------------------- 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 = 0.3773 r_free = 0.3773 target = 0.083606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.061744 restraints weight = 26514.234| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 3.57 r_work: 0.3068 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7612 Z= 0.083 Angle : 0.828 29.533 10414 Z= 0.321 Chirality : 0.039 0.118 1281 Planarity : 0.004 0.034 1320 Dihedral : 4.243 54.220 1238 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.41 % Allowed : 15.80 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.07 (0.27), residues: 1024 helix: 2.68 (0.23), residues: 503 sheet: -0.99 (0.37), residues: 174 loop : 0.85 (0.35), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1068 TYR 0.008 0.001 TYR A 931 PHE 0.023 0.001 PHE A 241 TRP 0.009 0.001 TRP A 170 HIS 0.001 0.000 HIS A 831 Details of bonding type rmsd covalent geometry : bond 0.00183 ( 7611) covalent geometry : angle 0.82810 (10414) hydrogen bonds : bond 0.02587 ( 414) hydrogen bonds : angle 3.78625 ( 1191) Misc. bond : bond 0.00050 ( 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 53 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.322 Fit side-chains REVERT: A 288 MET cc_start: 0.8685 (ptp) cc_final: 0.8124 (ptp) REVERT: A 1000 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8364 (mt) outliers start: 10 outliers final: 7 residues processed: 51 average time/residue: 0.0615 time to fit residues: 5.1605 Evaluate side-chains 49 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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 462 VAL Chi-restraints excluded: chain A residue 935 TYR Chi-restraints excluded: chain A residue 973 MET 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 63 optimal weight: 0.4980 chunk 68 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 84 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3750 r_free = 0.3750 target = 0.082466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.060413 restraints weight = 26329.981| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 3.51 r_work: 0.3032 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3004 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= 0.109 Angle : 0.844 29.825 10414 Z= 0.329 Chirality : 0.040 0.119 1281 Planarity : 0.004 0.034 1320 Dihedral : 4.287 54.135 1238 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.41 % Allowed : 16.78 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.15 (0.28), residues: 1024 helix: 2.75 (0.24), residues: 503 sheet: -0.95 (0.37), residues: 174 loop : 0.88 (0.36), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1068 TYR 0.008 0.001 TYR A 931 PHE 0.024 0.001 PHE A1123 TRP 0.007 0.001 TRP A1166 HIS 0.001 0.000 HIS A 385 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 7611) covalent geometry : angle 0.84443 (10414) hydrogen bonds : bond 0.02716 ( 414) hydrogen bonds : angle 3.82336 ( 1191) Misc. bond : bond 0.00057 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2141.29 seconds wall clock time: 37 minutes 22.11 seconds (2242.11 seconds total)