Starting phenix.real_space_refine on Fri Dec 8 07:05:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n77_24222/12_2023/7n77_24222_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n77_24222/12_2023/7n77_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_24222/12_2023/7n77_24222.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n77_24222/12_2023/7n77_24222.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n77_24222/12_2023/7n77_24222_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n77_24222/12_2023/7n77_24222_trim.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 7470 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 7470 Unusual residues: {' MG': 1, 'ALF': 1, 'Y01': 2} Classifications: {'peptide': 1036, 'undetermined': 4, 'water': 2} Incomplete info: {'truncation_to_alanine': 178} Link IDs: {'PCIS': 3, 'PTRANS': 69, 'TRANS': 963, None: 6} Not linked: pdbres="PRO A1168 " pdbres="ALF A1201 " Not linked: pdbres="ALF A1201 " pdbres=" MG A1202 " Not linked: pdbres=" MG A1202 " pdbres="Y01 A1203 " Not linked: pdbres="Y01 A1203 " pdbres="Y01 A1204 " Not linked: pdbres="Y01 A1204 " pdbres="HOH A1301 " Not linked: pdbres="HOH A1301 " pdbres="HOH A1302 " Chain breaks: 5 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 655 Unresolved non-hydrogen angles: 845 Unresolved non-hydrogen dihedrals: 552 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, 'Y01:plan-2': 1, 'Y01:plan-1': 1, 'PHE:plan': 6, 'GLU:plan': 14, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 347 Time building chain proxies: 4.85, per 1000 atoms: 0.65 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.96 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 43 through 58 removed outlier: 3.646A pdb=" N VAL A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA A 58 " --> pdb=" O VAL A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 68 Processing helix chain 'A' and resid 68 through 77 removed outlier: 3.697A pdb=" N GLY A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.617A pdb=" N ALA A 85 " --> pdb=" O LEU A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 200 through 212 removed outlier: 3.835A pdb=" N VAL A 206 " --> pdb=" O GLN A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 233 through 248 Processing helix chain 'A' and resid 251 through 284 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 393 through 396 removed outlier: 4.007A pdb=" N CYS A 396 " --> pdb=" O THR A 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 393 through 396' Processing helix chain 'A' and resid 397 through 408 Processing helix chain 'A' and resid 419 through 445 removed outlier: 4.472A pdb=" N LEU A 430 " --> pdb=" O ALA A 426 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 463 removed outlier: 3.804A pdb=" N ILE A 454 " --> pdb=" O ASN A 450 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 459 " --> pdb=" O ARG A 455 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL A 463 " --> pdb=" O LEU A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 487 removed outlier: 3.741A pdb=" N GLN A 486 " --> pdb=" O ARG A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 501 removed outlier: 4.381A pdb=" N LEU A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS A 501 " --> pdb=" O ASN A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 541 Processing helix chain 'A' and resid 544 through 553 Processing helix chain 'A' and resid 566 through 577 removed outlier: 3.751A pdb=" N THR A 576 " --> pdb=" O MET A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 659 Processing helix chain 'A' and resid 667 through 677 Processing helix chain 'A' and resid 695 through 700 Processing helix chain 'A' and resid 703 through 709 Processing helix chain 'A' and resid 726 through 736 removed outlier: 3.901A pdb=" N VAL A 730 " --> pdb=" O GLN A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 759 Processing helix chain 'A' and resid 821 through 832 Processing helix chain 'A' and resid 836 through 841 Processing helix chain 'A' and resid 850 through 863 removed outlier: 3.936A pdb=" N THR A 855 " --> pdb=" O PRO A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 878 No H-bonds generated for 'chain 'A' and resid 876 through 878' Processing helix chain 'A' and resid 879 through 884 removed outlier: 4.019A pdb=" N ALA A 883 " --> pdb=" O GLY A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 949 removed outlier: 3.592A pdb=" N MET A 913 " --> pdb=" O GLU A 909 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU A 917 " --> pdb=" O MET A 913 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE A 926 " --> pdb=" O LEU A 922 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE A 949 " --> pdb=" O ILE A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 964 removed outlier: 3.605A pdb=" N LEU A 959 " --> pdb=" O ASP A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 973 Processing helix chain 'A' and resid 974 through 976 No H-bonds generated for 'chain 'A' and resid 974 through 976' Processing helix chain 'A' and resid 993 through 1021 removed outlier: 4.077A pdb=" N ALA A1020 " --> pdb=" O PHE A1016 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN A1021 " --> pdb=" O LEU A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1061 removed outlier: 3.701A pdb=" N PHE A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU A1054 " --> pdb=" O SER A1050 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER A1061 " --> pdb=" O ALA A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1072 Processing helix chain 'A' and resid 1073 through 1093 Processing helix chain 'A' and resid 1109 through 1145 Proline residue: A1138 - end of helix removed outlier: 3.611A pdb=" N ARG A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) Processing helix chain 'A' and resid 1152 through 1164 Processing sheet with id=AA1, first strand: chain 'A' and resid 88 through 91 removed outlier: 3.563A pdb=" N VAL A 105 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 108 through 109 removed outlier: 5.542A pdb=" N ARG A 159 " --> pdb=" O TRP A 170 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A 176 " --> pdb=" O ILE A 171 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 300 through 303 removed outlier: 3.507A pdb=" N VAL A 302 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N CYS A 291 " --> pdb=" O VAL A 314 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N CYS A 312 " --> pdb=" O CYS A 293 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL A 386 " --> pdb=" O LEU A 315 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 320 through 321 removed outlier: 6.785A pdb=" N MET A 334 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ALA A 378 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLU A 332 " --> pdb=" O ALA A 378 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 783 through 788 removed outlier: 3.647A pdb=" N SER A 783 " --> pdb=" O THR A 774 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N HIS A 767 " --> pdb=" O HIS A 817 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ALA A 819 " --> pdb=" O HIS A 767 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE A 769 " --> pdb=" O ALA A 819 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR A 844 " --> pdb=" O ARG A 816 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU A 818 " --> pdb=" O THR A 844 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N PHE A 846 " --> pdb=" O LEU A 818 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU A 820 " --> pdb=" O PHE A 846 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ALA A 741 " --> pdb=" O THR A 844 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N PHE A 846 " --> pdb=" O ALA A 741 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N MET A 743 " --> pdb=" O PHE A 846 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL A 505 " --> pdb=" O VAL A 742 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL A 744 " --> pdb=" O VAL A 505 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N PHE A 507 " --> pdb=" O VAL A 744 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU A 504 " --> pdb=" O GLY A 869 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N CYS A 871 " --> pdb=" O LEU A 504 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N CYS A 506 " --> pdb=" O CYS A 871 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N ILE A 888 " --> pdb=" O VAL A 868 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N MET A 870 " --> pdb=" O ILE A 888 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 519 through 525 removed outlier: 6.726A pdb=" N VAL A 718 " --> pdb=" O MET A 521 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL A 523 " --> pdb=" O LEU A 716 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU A 716 " --> pdb=" O VAL A 523 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N LEU A 714 " --> pdb=" O PRO A 525 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N LEU A 713 " --> pdb=" O SER A 687 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N SER A 687 " --> pdb=" O LEU A 713 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ARG A 631 " --> pdb=" O PHE A 625 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N PHE A 625 " --> pdb=" O ARG A 631 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER A 633 " --> pdb=" O PHE A 623 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALA A 637 " --> pdb=" O VAL A 619 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N VAL A 619 " --> pdb=" O ALA A 637 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N SER A 588 " --> pdb=" O VAL A 619 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL A 579 " --> pdb=" O GLY A 591 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 557 through 558 414 hydrogen bonds defined for protein. 1191 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.96 Time building geometry restraints manager: 3.17 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: 89.44 - 107.41: 347 107.41 - 125.39: 9962 125.39 - 143.37: 103 143.37 - 161.34: 0 161.34 - 179.32: 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 2.440 nonbonded pdb=" OD2 ASP A 508 " pdb=" F2 ALF A1201 " model vdw 2.116 2.390 nonbonded pdb=" OG SER A 889 " pdb=" OG SER A 899 " model vdw 2.189 2.440 ... (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: 1.790 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: 5.800 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 25.580 Find NCS groups from input model: 0.220 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: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.350 ------------------------------------------------------------------------------- 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 : 0.846 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 51 average time/residue: 0.1606 time to fit residues: 12.4634 Evaluate side-chains 39 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 0.772 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1021 time to fit residues: 1.1845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 53 optimal weight: 30.0000 chunk 42 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 49 optimal weight: 9.9990 chunk 60 optimal weight: 8.9990 chunk 94 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 862 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: 0.7287 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7611 Z= 0.196 Angle : 0.854 30.246 10414 Z= 0.346 Chirality : 0.041 0.184 1281 Planarity : 0.004 0.034 1320 Dihedral : 5.514 44.256 1236 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.56 % Allowed : 8.60 % 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: 0.32 (0.27), residues: 1024 helix: 1.14 (0.24), residues: 484 sheet: -0.94 (0.40), residues: 159 loop : -0.33 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1166 HIS 0.002 0.000 HIS A 831 PHE 0.014 0.001 PHE A 958 TYR 0.010 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: 4 poor density : 41 time to evaluate : 0.909 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 42 average time/residue: 0.1423 time to fit residues: 10.0362 Evaluate side-chains 39 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 36 time to evaluate : 0.808 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0751 time to fit residues: 1.4885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 40.0000 chunk 29 optimal weight: 7.9990 chunk 78 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 93 optimal weight: 0.0970 chunk 32 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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: 0.7313 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7611 Z= 0.211 Angle : 0.846 30.704 10414 Z= 0.338 Chirality : 0.041 0.146 1281 Planarity : 0.004 0.036 1320 Dihedral : 4.973 51.615 1236 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.99 % Allowed : 11.71 % Favored : 87.31 % 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: 1.02 (0.27), residues: 1024 helix: 1.79 (0.24), residues: 490 sheet: -0.84 (0.39), residues: 164 loop : 0.03 (0.35), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 301 HIS 0.002 0.001 HIS A 385 PHE 0.010 0.001 PHE A 958 TYR 0.010 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 46 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 0.811 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 45 average time/residue: 0.1389 time to fit residues: 10.2702 Evaluate side-chains 42 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 0.912 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1016 time to fit residues: 1.6122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 63 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- 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 862 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: 0.7323 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7611 Z= 0.216 Angle : 0.843 30.547 10414 Z= 0.334 Chirality : 0.040 0.128 1281 Planarity : 0.004 0.033 1320 Dihedral : 4.715 57.525 1236 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.99 % Allowed : 13.40 % Favored : 85.61 % 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: 1.35 (0.28), residues: 1024 helix: 2.08 (0.24), residues: 498 sheet: -0.86 (0.39), residues: 169 loop : 0.23 (0.35), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1166 HIS 0.002 0.000 HIS A 385 PHE 0.022 0.001 PHE A 241 TYR 0.011 0.001 TYR A1053 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 47 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 40 time to evaluate : 0.954 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 46 average time/residue: 0.1351 time to fit residues: 10.4174 Evaluate side-chains 41 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.841 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0768 time to fit residues: 1.4506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 74 optimal weight: 0.9980 chunk 41 optimal weight: 0.3980 chunk 85 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 51 optimal weight: 40.0000 chunk 90 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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: 0.7333 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7611 Z= 0.221 Angle : 0.850 30.707 10414 Z= 0.335 Chirality : 0.040 0.127 1281 Planarity : 0.004 0.032 1320 Dihedral : 4.558 52.874 1236 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.56 % Allowed : 14.25 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.28), residues: 1024 helix: 2.28 (0.24), residues: 498 sheet: -0.96 (0.38), residues: 173 loop : 0.33 (0.35), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1166 HIS 0.002 0.000 HIS A 385 PHE 0.019 0.001 PHE A 241 TYR 0.013 0.001 TYR A1053 ARG 0.002 0.000 ARG A1068 *********************** 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 44 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 40 time to evaluate : 0.798 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 44 average time/residue: 0.1404 time to fit residues: 10.0855 Evaluate side-chains 41 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 0.785 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1103 time to fit residues: 1.2588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 59 optimal weight: 40.0000 chunk 24 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 46 optimal weight: 7.9990 chunk 8 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 50.0000 chunk 97 optimal weight: 0.8980 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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: 0.7335 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7611 Z= 0.213 Angle : 0.843 30.579 10414 Z= 0.332 Chirality : 0.040 0.127 1281 Planarity : 0.004 0.032 1320 Dihedral : 4.428 47.891 1236 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.13 % Allowed : 14.53 % Favored : 84.34 % 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: 1.67 (0.28), residues: 1024 helix: 2.39 (0.24), residues: 500 sheet: -0.97 (0.38), residues: 167 loop : 0.42 (0.35), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1166 HIS 0.002 0.000 HIS A 385 PHE 0.021 0.001 PHE A 241 TYR 0.009 0.001 TYR A1053 ARG 0.002 0.000 ARG A1068 *********************** 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 48 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 40 time to evaluate : 0.857 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 46 average time/residue: 0.1459 time to fit residues: 10.9557 Evaluate side-chains 43 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 40 time to evaluate : 0.849 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0820 time to fit residues: 1.5857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 84 optimal weight: 0.4980 chunk 100 optimal weight: 1.9990 chunk 62 optimal weight: 0.2980 chunk 61 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7611 Z= 0.238 Angle : 0.859 30.840 10414 Z= 0.338 Chirality : 0.041 0.127 1281 Planarity : 0.004 0.032 1320 Dihedral : 4.444 47.961 1236 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.42 % Allowed : 16.78 % 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 (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: 1.69 (0.28), residues: 1024 helix: 2.44 (0.24), residues: 501 sheet: -1.05 (0.37), residues: 172 loop : 0.46 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1166 HIS 0.002 0.001 HIS A 385 PHE 0.020 0.001 PHE A 241 TYR 0.015 0.001 TYR A1053 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 44 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 0.848 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 44 average time/residue: 0.1438 time to fit residues: 10.4839 Evaluate side-chains 40 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.915 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0702 time to fit residues: 1.2646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 49 optimal weight: 20.0000 chunk 9 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 93 optimal weight: 0.0020 overall best weight: 1.1590 ------------------------------------------------------------------------------- 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: 0.7338 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7611 Z= 0.211 Angle : 0.845 30.679 10414 Z= 0.331 Chirality : 0.040 0.125 1281 Planarity : 0.004 0.032 1320 Dihedral : 4.316 44.081 1236 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.71 % Allowed : 15.94 % Favored : 83.36 % 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: 1.77 (0.27), residues: 1024 helix: 2.52 (0.24), residues: 502 sheet: -1.12 (0.37), residues: 171 loop : 0.52 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1166 HIS 0.002 0.000 HIS A 385 PHE 0.022 0.001 PHE A 241 TYR 0.010 0.001 TYR A1053 ARG 0.002 0.000 ARG A 740 *********************** 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 46 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 41 time to evaluate : 0.970 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 45 average time/residue: 0.1362 time to fit residues: 10.4100 Evaluate side-chains 41 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 0.802 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0913 time to fit residues: 1.2887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 40 optimal weight: 0.2980 chunk 73 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 84 optimal weight: 0.0870 chunk 88 optimal weight: 0.9980 chunk 93 optimal weight: 0.0970 chunk 61 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 overall best weight: 0.3956 ------------------------------------------------------------------------------- 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 862 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: 0.7285 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7611 Z= 0.140 Angle : 0.848 30.088 10414 Z= 0.329 Chirality : 0.039 0.126 1281 Planarity : 0.004 0.033 1320 Dihedral : 4.022 32.583 1236 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.00 % Allowed : 16.93 % Favored : 83.07 % 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: 1.90 (0.27), residues: 1024 helix: 2.57 (0.23), residues: 509 sheet: -1.07 (0.37), residues: 166 loop : 0.62 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 170 HIS 0.001 0.000 HIS A 831 PHE 0.021 0.001 PHE A 241 TYR 0.010 0.001 TYR A1053 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 43 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.960 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.1451 time to fit residues: 10.4183 Evaluate side-chains 42 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.873 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 10.0000 chunk 68 optimal weight: 0.3980 chunk 103 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 50 optimal weight: 20.0000 chunk 65 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7305 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7611 Z= 0.163 Angle : 0.834 30.394 10414 Z= 0.325 Chirality : 0.040 0.125 1281 Planarity : 0.004 0.034 1320 Dihedral : 4.006 32.811 1236 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.28 % Allowed : 17.07 % 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 (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: 2.68 (0.23), residues: 509 sheet: -1.14 (0.36), residues: 172 loop : 0.75 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1166 HIS 0.001 0.000 HIS A 831 PHE 0.022 0.001 PHE A 241 TYR 0.010 0.001 TYR A1053 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 46 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 44 time to evaluate : 0.880 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 45 average time/residue: 0.1481 time to fit residues: 10.8905 Evaluate side-chains 44 residues out of total 887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.867 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0719 time to fit residues: 1.2930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 9.9990 chunk 12 optimal weight: 0.4980 chunk 22 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 84 optimal weight: 0.0010 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 4 optimal weight: 0.0970 chunk 59 optimal weight: 40.0000 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.083059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.061190 restraints weight = 26489.735| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 3.47 r_work: 0.3051 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7611 Z= 0.140 Angle : 0.850 30.088 10414 Z= 0.329 Chirality : 0.039 0.140 1281 Planarity : 0.004 0.034 1320 Dihedral : 3.853 31.520 1236 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.14 % Allowed : 16.93 % 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 (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: 2.14 (0.27), residues: 1024 helix: 2.76 (0.23), residues: 509 sheet: -0.97 (0.38), residues: 166 loop : 0.75 (0.35), residues: 349 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 0.022 0.001 PHE A 241 TYR 0.009 0.001 TYR A1053 ARG 0.002 0.000 ARG A1068 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1630.53 seconds wall clock time: 30 minutes 17.81 seconds (1817.81 seconds total)