Starting phenix.real_space_refine on Mon Jun 9 13:48:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7myo_24082/06_2025/7myo_24082.cif Found real_map, /net/cci-nas-00/data/ceres_data/7myo_24082/06_2025/7myo_24082.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7myo_24082/06_2025/7myo_24082.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7myo_24082/06_2025/7myo_24082.map" model { file = "/net/cci-nas-00/data/ceres_data/7myo_24082/06_2025/7myo_24082.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7myo_24082/06_2025/7myo_24082.cif" } resolution = 2.92 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= -0.000 sd= 1.000 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: 5 Type Number sf(0) Gaussians S 77 5.16 5 C 6763 2.51 5 N 1848 2.21 5 O 1943 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 10634 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 2412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2412 Classifications: {'peptide': 286} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 281} Chain: "A" Number of atoms: 8192 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 992, 8107 Classifications: {'peptide': 992} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 945} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 992, 8107 Classifications: {'peptide': 992} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 945} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 8193 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'1LT': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 9 residue: pdb=" N AARG A 617 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 617 " occ=0.50 residue: pdb=" N ALYS A 621 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 621 " occ=0.50 residue: pdb=" N AARG A 662 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 662 " occ=0.50 residue: pdb=" N AARG A 899 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 899 " occ=0.50 residue: pdb=" N AARG A 951 " occ=0.63 ... (20 atoms not shown) pdb=" NH2BARG A 951 " occ=0.37 residue: pdb=" N AVAL A 952 " occ=0.63 ... (12 atoms not shown) pdb=" CG2BVAL A 952 " occ=0.37 residue: pdb=" N APRO A 953 " occ=0.63 ... (12 atoms not shown) pdb=" CD BPRO A 953 " occ=0.37 residue: pdb=" N APHE A 954 " occ=0.63 ... (20 atoms not shown) pdb=" CZ BPHE A 954 " occ=0.37 residue: pdb=" N AVAL A 955 " occ=0.63 ... (12 atoms not shown) pdb=" CG2BVAL A 955 " occ=0.37 Time building chain proxies: 9.85, per 1000 atoms: 0.93 Number of scatterers: 10634 At special positions: 0 Unit cell: (89.87, 108.68, 135.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 77 16.00 F 3 9.00 O 1943 8.00 N 1848 7.00 C 6763 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=0, symmetry=0 Time building additional restraints: 2.28 Conformation dependent library (CDL) restraints added in 2.2 seconds 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2466 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 10 sheets defined 50.5% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'B' and resid 339 through 348 Processing helix chain 'B' and resid 385 through 389 removed outlier: 4.091A pdb=" N GLY B 388 " --> pdb=" O HIS B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 411 Processing helix chain 'B' and resid 432 through 436 Processing helix chain 'B' and resid 441 through 506 removed outlier: 3.595A pdb=" N VAL B 445 " --> pdb=" O ASN B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 515 removed outlier: 3.799A pdb=" N PHE B 512 " --> pdb=" O TYR B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 588 removed outlier: 3.927A pdb=" N LEU B 531 " --> pdb=" O ASN B 527 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS B 532 " --> pdb=" O TYR B 528 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP B 548 " --> pdb=" O ARG B 544 " (cutoff:3.500A) Proline residue: B 568 - end of helix Processing helix chain 'B' and resid 593 through 599 removed outlier: 3.915A pdb=" N TRP B 597 " --> pdb=" O LYS B 593 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU B 598 " --> pdb=" O LEU B 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 56 removed outlier: 3.605A pdb=" N HIS A 47 " --> pdb=" O ILE A 43 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLU A 48 " --> pdb=" O THR A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 122 removed outlier: 3.815A pdb=" N LYS A 111 " --> pdb=" O ASN A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 131 removed outlier: 3.990A pdb=" N PHE A 128 " --> pdb=" O PRO A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 155 removed outlier: 3.541A pdb=" N GLN A 137 " --> pdb=" O ASP A 133 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASN A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL A 146 " --> pdb=" O ASN A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 167 Processing helix chain 'A' and resid 178 through 183 removed outlier: 3.657A pdb=" N ASN A 183 " --> pdb=" O LYS A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 229 removed outlier: 3.785A pdb=" N VAL A 220 " --> pdb=" O VAL A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 248 Processing helix chain 'A' and resid 270 through 280 Processing helix chain 'A' and resid 290 through 297 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 326 through 330 removed outlier: 3.690A pdb=" N VAL A 329 " --> pdb=" O SER A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 488 through 502 removed outlier: 3.863A pdb=" N ILE A 492 " --> pdb=" O ASP A 488 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 500 " --> pdb=" O ALA A 496 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER A 501 " --> pdb=" O ASN A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 536 removed outlier: 3.824A pdb=" N LYS A 528 " --> pdb=" O ARG A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 554 Processing helix chain 'A' and resid 564 through 571 Processing helix chain 'A' and resid 577 through 589 removed outlier: 3.620A pdb=" N ALA A 581 " --> pdb=" O ARG A 577 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP A 589 " --> pdb=" O CYS A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 599 Processing helix chain 'A' and resid 600 through 603 removed outlier: 4.119A pdb=" N ASP A 603 " --> pdb=" O GLU A 600 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 600 through 603' Processing helix chain 'A' and resid 608 through 623 Processing helix chain 'A' and resid 624 through 631 Processing helix chain 'A' and resid 631 through 642 removed outlier: 3.902A pdb=" N LYS A 640 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N TYR A 641 " --> pdb=" O GLN A 637 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU A 642 " --> pdb=" O VAL A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 658 Processing helix chain 'A' and resid 660 through 673 Processing helix chain 'A' and resid 680 through 695 Processing helix chain 'A' and resid 697 through 721 removed outlier: 3.807A pdb=" N HIS A 701 " --> pdb=" O MET A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 740 Processing helix chain 'A' and resid 741 through 746 Processing helix chain 'A' and resid 747 through 749 No H-bonds generated for 'chain 'A' and resid 747 through 749' Processing helix chain 'A' and resid 787 through 793 removed outlier: 4.438A pdb=" N GLU A 791 " --> pdb=" O ILE A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 828 Processing helix chain 'A' and resid 857 through 867 Processing helix chain 'A' and resid 875 through 885 Processing helix chain 'A' and resid 886 through 888 No H-bonds generated for 'chain 'A' and resid 886 through 888' Processing helix chain 'A' and resid 889 through 911 removed outlier: 4.451A pdb=" N VAL A 906 " --> pdb=" O ALA A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 965 removed outlier: 3.521A pdb=" N LEU A 961 " --> pdb=" O THR A 957 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER A 965 " --> pdb=" O LEU A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 993 removed outlier: 4.092A pdb=" N GLU A 978 " --> pdb=" O THR A 974 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG A 979 " --> pdb=" O ARG A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1004 removed outlier: 3.696A pdb=" N PHE A 998 " --> pdb=" O HIS A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1026 Processing helix chain 'A' and resid 1031 through 1045 Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 355 Processing sheet with id=AA2, first strand: chain 'B' and resid 373 through 374 Processing sheet with id=AA3, first strand: chain 'A' and resid 31 through 36 removed outlier: 3.615A pdb=" N VAL A 32 " --> pdb=" O CYS A 24 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N LEU A 99 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLU A 23 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N VAL A 101 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU A 25 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N PHE A 98 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N VAL A 73 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N PHE A 70 " --> pdb=" O PHE A 82 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER A 72 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 207 through 212 removed outlier: 8.429A pdb=" N LEU A 285 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N VAL A 193 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N LEU A 287 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS A 253 " --> pdb=" O MET A 286 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU A 252 " --> pdb=" O PHE A 261 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 382 through 392 removed outlier: 6.393A pdb=" N TRP A 383 " --> pdb=" O CYS A 340 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N CYS A 340 " --> pdb=" O TRP A 383 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU A 334 " --> pdb=" O TYR A 389 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLU A 474 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ALA A 341 " --> pdb=" O CYS A 472 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N CYS A 472 " --> pdb=" O ALA A 341 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 365 through 366 removed outlier: 3.516A pdb=" N VAL A 409 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LYS A 353 " --> pdb=" O VAL A 409 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 365 through 366 removed outlier: 6.430A pdb=" N SER A 408 " --> pdb=" O PRO A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 752 through 753 removed outlier: 5.885A pdb=" N HIS A 759 " --> pdb=" O SER A 753 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 770 through 771 Processing sheet with id=AB1, first strand: chain 'A' and resid 854 through 856 499 hydrogen bonds defined for protein. 1437 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.41 Time building geometry restraints manager: 2.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1774 1.32 - 1.44: 2816 1.44 - 1.56: 6146 1.56 - 1.69: 2 1.69 - 1.81: 121 Bond restraints: 10859 Sorted by residual: bond pdb=" C3 1LT A1101 " pdb=" N1 1LT A1101 " ideal model delta sigma weight residual 1.391 1.485 -0.094 2.00e-02 2.50e+03 2.23e+01 bond pdb=" C2 1LT A1101 " pdb=" N1 1LT A1101 " ideal model delta sigma weight residual 1.368 1.458 -0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" C3 1LT A1101 " pdb=" N2 1LT A1101 " ideal model delta sigma weight residual 1.348 1.435 -0.087 2.00e-02 2.50e+03 1.87e+01 bond pdb=" N 1LT A1101 " pdb=" C1 1LT A1101 " ideal model delta sigma weight residual 1.368 1.445 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" C7 1LT A1101 " pdb=" N2 1LT A1101 " ideal model delta sigma weight residual 1.444 1.520 -0.076 2.00e-02 2.50e+03 1.43e+01 ... (remaining 10854 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 14279 2.57 - 5.14: 306 5.14 - 7.71: 57 7.71 - 10.28: 5 10.28 - 12.86: 4 Bond angle restraints: 14651 Sorted by residual: angle pdb=" N ASP A1017 " pdb=" CA ASP A1017 " pdb=" C ASP A1017 " ideal model delta sigma weight residual 114.31 108.20 6.11 1.29e+00 6.01e-01 2.25e+01 angle pdb=" C ASP A 939 " pdb=" N HIS A 940 " pdb=" CA HIS A 940 " ideal model delta sigma weight residual 121.54 129.94 -8.40 1.91e+00 2.74e-01 1.93e+01 angle pdb=" N GLU B 537 " pdb=" CA GLU B 537 " pdb=" CB GLU B 537 " ideal model delta sigma weight residual 110.30 117.00 -6.70 1.54e+00 4.22e-01 1.90e+01 angle pdb=" CB MET A1040 " pdb=" CG MET A1040 " pdb=" SD MET A1040 " ideal model delta sigma weight residual 112.70 125.56 -12.86 3.00e+00 1.11e-01 1.84e+01 angle pdb=" CG1 ILE A 211 " pdb=" CB ILE A 211 " pdb=" CG2 ILE A 211 " ideal model delta sigma weight residual 110.70 99.90 10.80 3.00e+00 1.11e-01 1.30e+01 ... (remaining 14646 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 5886 17.47 - 34.95: 618 34.95 - 52.42: 113 52.42 - 69.89: 32 69.89 - 87.36: 13 Dihedral angle restraints: 6662 sinusoidal: 2859 harmonic: 3803 Sorted by residual: dihedral pdb=" CA LEU A 209 " pdb=" C LEU A 209 " pdb=" N LYS A 210 " pdb=" CA LYS A 210 " ideal model delta harmonic sigma weight residual -180.00 -153.50 -26.50 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA PHE B 512 " pdb=" C PHE B 512 " pdb=" N LYS B 513 " pdb=" CA LYS B 513 " ideal model delta harmonic sigma weight residual 180.00 159.45 20.55 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA LEU A 262 " pdb=" C LEU A 262 " pdb=" N GLU A 263 " pdb=" CA GLU A 263 " ideal model delta harmonic sigma weight residual -180.00 -161.54 -18.46 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 6659 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1062 0.044 - 0.088: 374 0.088 - 0.132: 117 0.132 - 0.175: 19 0.175 - 0.219: 9 Chirality restraints: 1581 Sorted by residual: chirality pdb=" CB ILE A 921 " pdb=" CA ILE A 921 " pdb=" CG1 ILE A 921 " pdb=" CG2 ILE A 921 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA ASN A 202 " pdb=" N ASN A 202 " pdb=" C ASN A 202 " pdb=" CB ASN A 202 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.93e-01 chirality pdb=" CG LEU A 267 " pdb=" CB LEU A 267 " pdb=" CD1 LEU A 267 " pdb=" CD2 LEU A 267 " both_signs ideal model delta sigma weight residual False -2.59 -2.79 0.20 2.00e-01 2.50e+01 9.71e-01 ... (remaining 1578 not shown) Planarity restraints: 1883 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 426 " 0.082 5.00e-02 4.00e+02 1.24e-01 2.44e+01 pdb=" N PRO B 427 " -0.214 5.00e-02 4.00e+02 pdb=" CA PRO B 427 " 0.067 5.00e-02 4.00e+02 pdb=" CD PRO B 427 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 177 " -0.076 5.00e-02 4.00e+02 1.15e-01 2.11e+01 pdb=" N PRO A 178 " 0.198 5.00e-02 4.00e+02 pdb=" CA PRO A 178 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO A 178 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 457 " -0.069 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO A 458 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO A 458 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 458 " -0.056 5.00e-02 4.00e+02 ... (remaining 1880 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1491 2.76 - 3.29: 10714 3.29 - 3.83: 18393 3.83 - 4.36: 21335 4.36 - 4.90: 35211 Nonbonded interactions: 87144 Sorted by model distance: nonbonded pdb=" O TYR A1038 " pdb=" OE1 GLN A1042 " model vdw 2.225 3.040 nonbonded pdb=" OH TYR A 988 " pdb=" O LEU A1026 " model vdw 2.247 3.040 nonbonded pdb=" OG SER A 499 " pdb=" OE1 GLN A 582 " model vdw 2.253 3.040 nonbonded pdb=" O ASP A 895 " pdb=" OG1 THR A 898 " model vdw 2.257 3.040 nonbonded pdb=" OE2 GLU B 332 " pdb=" OH TYR B 431 " model vdw 2.268 3.040 ... (remaining 87139 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.37 max=1.00 mean=0.99 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: 0.400 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: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 30.800 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 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 : 0.005 0.094 10859 Z= 0.224 Angle : 0.894 12.856 14651 Z= 0.455 Chirality : 0.051 0.219 1581 Planarity : 0.008 0.124 1883 Dihedral : 15.195 87.363 4196 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.59 % Allowed : 0.85 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -1.97 (0.22), residues: 1281 helix: -0.71 (0.19), residues: 593 sheet: -1.80 (0.43), residues: 137 loop : -1.73 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP B 335 HIS 0.017 0.001 HIS A 940 PHE 0.035 0.003 PHE A 937 TYR 0.031 0.002 TYR A 165 ARG 0.016 0.001 ARG A 115 Details of bonding type rmsd hydrogen bonds : bond 0.15595 ( 495) hydrogen bonds : angle 6.51487 ( 1437) covalent geometry : bond 0.00480 (10859) covalent geometry : angle 0.89438 (14651) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 305 time to evaluate : 1.151 Fit side-chains revert: symmetry clash REVERT: A 526 ASN cc_start: 0.7934 (p0) cc_final: 0.7636 (p0) REVERT: A 988 TYR cc_start: 0.5782 (t80) cc_final: 0.5575 (t80) outliers start: 1 outliers final: 0 residues processed: 305 average time/residue: 1.1038 time to fit residues: 365.3748 Evaluate side-chains 211 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 chunk 53 optimal weight: 0.6980 chunk 32 optimal weight: 0.0030 chunk 64 optimal weight: 0.0170 chunk 51 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 overall best weight: 0.5228 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 407 HIS ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN A 160 HIS A 426 ASN A 661 GLN A 701 HIS ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 749 GLN A 785 ASN ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4801 r_free = 0.4801 target = 0.224832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.185368 restraints weight = 45400.631| |-----------------------------------------------------------------------------| r_work (start): 0.4413 rms_B_bonded: 6.21 r_work: 0.4186 rms_B_bonded: 5.79 restraints_weight: 2.0000 r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4206 r_free = 0.4206 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4204 r_free = 0.4204 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4204 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10859 Z= 0.147 Angle : 0.753 12.050 14651 Z= 0.376 Chirality : 0.045 0.171 1581 Planarity : 0.006 0.087 1883 Dihedral : 6.206 70.254 1437 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.29 % Allowed : 17.44 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.23), residues: 1281 helix: 0.10 (0.20), residues: 610 sheet: -1.75 (0.43), residues: 140 loop : -1.70 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 333 HIS 0.012 0.001 HIS A 940 PHE 0.040 0.002 PHE A 667 TYR 0.021 0.002 TYR A 432 ARG 0.010 0.001 ARG A 141 Details of bonding type rmsd hydrogen bonds : bond 0.04329 ( 495) hydrogen bonds : angle 4.91936 ( 1437) covalent geometry : bond 0.00340 (10859) covalent geometry : angle 0.75317 (14651) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 240 time to evaluate : 1.121 Fit side-chains revert: symmetry clash REVERT: B 479 MET cc_start: 0.7303 (pp-130) cc_final: 0.7072 (pp-130) REVERT: A 164 MET cc_start: 0.7694 (mpp) cc_final: 0.6714 (mpt) REVERT: A 330 ILE cc_start: 0.6168 (mt) cc_final: 0.5888 (mt) REVERT: A 391 ILE cc_start: 0.7929 (OUTLIER) cc_final: 0.7549 (tp) REVERT: A 427 ILE cc_start: 0.8489 (mp) cc_final: 0.8116 (mt) REVERT: A 812 LEU cc_start: 0.7500 (tp) cc_final: 0.7191 (tp) REVERT: A 979 ARG cc_start: 0.7777 (mtp180) cc_final: 0.7425 (tpt-90) REVERT: A 1000 ASN cc_start: 0.7131 (t0) cc_final: 0.6580 (m-40) REVERT: A 1039 PHE cc_start: 0.6218 (OUTLIER) cc_final: 0.5799 (m-80) outliers start: 21 outliers final: 6 residues processed: 250 average time/residue: 0.9601 time to fit residues: 263.8193 Evaluate side-chains 228 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 220 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 1039 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 11 optimal weight: 0.0980 chunk 22 optimal weight: 9.9990 chunk 105 optimal weight: 0.9990 chunk 108 optimal weight: 0.6980 chunk 42 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 66 optimal weight: 0.0980 chunk 93 optimal weight: 3.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 499 GLN ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 170 ASN A 202 ASN ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 HIS ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.220839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.180323 restraints weight = 47502.402| |-----------------------------------------------------------------------------| r_work (start): 0.4332 rms_B_bonded: 6.40 r_work: 0.4126 rms_B_bonded: 5.76 restraints_weight: 2.0000 r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4157 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4157 r_free = 0.4157 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4157 r_free = 0.4157 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10859 Z= 0.144 Angle : 0.721 10.559 14651 Z= 0.359 Chirality : 0.044 0.289 1581 Planarity : 0.005 0.074 1883 Dihedral : 5.892 67.515 1437 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.30 % Allowed : 20.07 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -1.00 (0.23), residues: 1281 helix: 0.44 (0.21), residues: 604 sheet: -1.78 (0.43), residues: 142 loop : -1.59 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 333 HIS 0.010 0.001 HIS A 59 PHE 0.044 0.002 PHE A 667 TYR 0.022 0.002 TYR A 985 ARG 0.012 0.001 ARG B 472 Details of bonding type rmsd hydrogen bonds : bond 0.03895 ( 495) hydrogen bonds : angle 4.67183 ( 1437) covalent geometry : bond 0.00334 (10859) covalent geometry : angle 0.72145 (14651) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 235 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 420 LEU cc_start: 0.6524 (OUTLIER) cc_final: 0.6297 (mm) REVERT: B 479 MET cc_start: 0.7411 (pp-130) cc_final: 0.7092 (pp-130) REVERT: B 499 GLN cc_start: 0.6957 (tm130) cc_final: 0.6586 (tm130) REVERT: B 537 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7599 (pm20) REVERT: A 58 LEU cc_start: 0.6813 (OUTLIER) cc_final: 0.6316 (mm) REVERT: A 330 ILE cc_start: 0.6380 (mt) cc_final: 0.6084 (mt) REVERT: A 427 ILE cc_start: 0.8492 (mp) cc_final: 0.8173 (mt) REVERT: A 563 GLU cc_start: 0.6698 (tp30) cc_final: 0.6172 (tp30) REVERT: A 760 GLN cc_start: 0.8076 (pt0) cc_final: 0.7615 (pt0) REVERT: A 812 LEU cc_start: 0.7632 (tp) cc_final: 0.7399 (tp) REVERT: A 833 MET cc_start: 0.6306 (ptm) cc_final: 0.5828 (ptt) REVERT: A 979 ARG cc_start: 0.7861 (mtp180) cc_final: 0.7452 (tpt-90) REVERT: A 1000 ASN cc_start: 0.7077 (t0) cc_final: 0.6521 (m-40) outliers start: 33 outliers final: 11 residues processed: 248 average time/residue: 0.9720 time to fit residues: 264.4241 Evaluate side-chains 223 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 209 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 430 LYS Chi-restraints excluded: chain B residue 537 GLU Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 957 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 114 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 123 optimal weight: 0.0570 chunk 44 optimal weight: 0.2980 chunk 72 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 ASN ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 HIS ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.220369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.181718 restraints weight = 43899.939| |-----------------------------------------------------------------------------| r_work (start): 0.4368 rms_B_bonded: 5.44 r_work (final): 0.4368 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4372 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4372 r_free = 0.4372 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4372 r_free = 0.4372 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4372 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10859 Z= 0.134 Angle : 0.702 10.817 14651 Z= 0.350 Chirality : 0.044 0.262 1581 Planarity : 0.005 0.068 1883 Dihedral : 5.746 63.833 1437 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.79 % Allowed : 22.35 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.85 (0.23), residues: 1281 helix: 0.56 (0.21), residues: 609 sheet: -1.76 (0.43), residues: 142 loop : -1.50 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 333 HIS 0.010 0.001 HIS A 59 PHE 0.043 0.002 PHE A 667 TYR 0.021 0.001 TYR A 985 ARG 0.013 0.001 ARG A 141 Details of bonding type rmsd hydrogen bonds : bond 0.03589 ( 495) hydrogen bonds : angle 4.56976 ( 1437) covalent geometry : bond 0.00311 (10859) covalent geometry : angle 0.70192 (14651) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 229 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 420 LEU cc_start: 0.6491 (OUTLIER) cc_final: 0.6288 (mm) REVERT: B 422 VAL cc_start: 0.6375 (OUTLIER) cc_final: 0.5992 (t) REVERT: B 479 MET cc_start: 0.7077 (pp-130) cc_final: 0.6774 (pp-130) REVERT: B 534 ARG cc_start: 0.7828 (tpt-90) cc_final: 0.7553 (tpt-90) REVERT: B 537 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7540 (pm20) REVERT: B 563 MET cc_start: 0.6199 (ppp) cc_final: 0.4367 (mtm) REVERT: A 58 LEU cc_start: 0.6696 (OUTLIER) cc_final: 0.6280 (mm) REVERT: A 164 MET cc_start: 0.7229 (mpp) cc_final: 0.6785 (mpt) REVERT: A 330 ILE cc_start: 0.6236 (mt) cc_final: 0.5981 (mt) REVERT: A 427 ILE cc_start: 0.8309 (mp) cc_final: 0.8029 (mt) REVERT: A 760 GLN cc_start: 0.7570 (pt0) cc_final: 0.7187 (pt0) REVERT: A 979 ARG cc_start: 0.7658 (mtp180) cc_final: 0.7329 (tpt-90) REVERT: A 1000 ASN cc_start: 0.6414 (t0) cc_final: 0.6133 (m-40) outliers start: 27 outliers final: 10 residues processed: 244 average time/residue: 0.9408 time to fit residues: 252.3605 Evaluate side-chains 224 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 210 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 430 LYS Chi-restraints excluded: chain B residue 537 GLU Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 891 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.2849 > 50: distance: 52 - 82: 5.805 distance: 59 - 90: 15.874 distance: 63 - 99: 5.974 distance: 75 - 82: 3.895 distance: 83 - 84: 13.032 distance: 83 - 86: 7.274 distance: 84 - 85: 19.738 distance: 84 - 90: 6.165 distance: 86 - 87: 10.255 distance: 87 - 88: 7.919 distance: 87 - 89: 14.044 distance: 90 - 91: 17.043 distance: 91 - 92: 12.647 distance: 91 - 94: 11.815 distance: 92 - 93: 4.139 distance: 92 - 99: 16.253 distance: 94 - 95: 9.811 distance: 95 - 96: 14.778 distance: 96 - 97: 7.874 distance: 96 - 98: 4.599 distance: 99 - 100: 12.881 distance: 100 - 101: 14.440 distance: 101 - 102: 15.631 distance: 101 - 103: 19.992 distance: 103 - 104: 18.811 distance: 104 - 105: 7.140 distance: 104 - 107: 15.766 distance: 105 - 106: 11.009 distance: 105 - 111: 6.106 distance: 107 - 108: 4.956 distance: 108 - 109: 3.569 distance: 108 - 110: 13.947 distance: 111 - 112: 10.841 distance: 112 - 113: 13.137 distance: 112 - 115: 7.513 distance: 113 - 114: 12.040 distance: 113 - 119: 11.022 distance: 115 - 116: 6.853 distance: 119 - 120: 4.617 distance: 120 - 121: 3.714 distance: 120 - 123: 3.029 distance: 121 - 127: 3.656 distance: 123 - 124: 3.197 distance: 124 - 125: 3.564 distance: 124 - 126: 4.155 distance: 128 - 129: 7.724 distance: 128 - 131: 6.726 distance: 129 - 130: 10.854 distance: 129 - 138: 15.043 distance: 131 - 132: 5.383 distance: 132 - 133: 4.532 distance: 133 - 134: 6.068 distance: 139 - 140: 4.281 distance: 139 - 142: 16.764 distance: 140 - 141: 13.351 distance: 140 - 146: 10.018 distance: 142 - 143: 12.549 distance: 143 - 144: 6.117 distance: 144 - 145: 17.037 distance: 146 - 147: 9.657 distance: 147 - 148: 16.420 distance: 147 - 150: 18.912 distance: 148 - 149: 21.157 distance: 148 - 154: 13.024 distance: 150 - 151: 19.974 distance: 151 - 152: 4.933 distance: 151 - 153: 17.146 distance: 154 - 155: 12.738 distance: 154 - 160: 12.901 distance: 155 - 158: 8.517 distance: 156 - 157: 18.843 distance: 156 - 161: 11.323 distance: 158 - 159: 7.744 distance: 159 - 160: 9.069