Starting phenix.real_space_refine on Sat Dec 28 10:38:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n74_24219/12_2024/7n74_24219_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n74_24219/12_2024/7n74_24219.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7n74_24219/12_2024/7n74_24219.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n74_24219/12_2024/7n74_24219.map" model { file = "/net/cci-nas-00/data/ceres_data/7n74_24219/12_2024/7n74_24219_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n74_24219/12_2024/7n74_24219_trim.cif" } resolution = 2.8 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= 0.011 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 49 5.16 5 C 5085 2.51 5 N 1322 2.21 5 O 1399 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 7859 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1036, 7754 Classifications: {'peptide': 1036} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PCIS': 3, 'PTRANS': 69, 'TRANS': 963} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 264 Unresolved non-hydrogen angles: 335 Unresolved non-hydrogen dihedrals: 231 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 4, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 177 Chain: "A" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 105 Unusual residues: {' MG': 1, 'ATP': 1, 'Y01': 2} Classifications: {'undetermined': 4, 'water': 3} Link IDs: {None: 6} Time building chain proxies: 5.30, per 1000 atoms: 0.67 Number of scatterers: 7859 At special positions: 0 Unit cell: (84.723, 85.634, 131.184, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 49 16.00 P 3 15.00 Mg 1 11.99 O 1399 8.00 N 1322 7.00 C 5085 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: 2.30 Conformation dependent library (CDL) restraints added in 1.0 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: 44 helices and 9 sheets defined 53.8% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 43 through 57 removed outlier: 3.539A pdb=" N VAL A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 68 Processing helix chain 'A' and resid 68 through 77 removed outlier: 3.911A pdb=" N GLY A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 85 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 196 Processing helix chain 'A' and resid 200 through 212 removed outlier: 3.798A pdb=" N MET A 205 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N VAL A 206 " --> pdb=" O GLN A 202 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG A 207 " --> pdb=" O ASP A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 232 Processing helix chain 'A' and resid 233 through 249 Processing helix chain 'A' and resid 251 through 285 removed outlier: 3.576A pdb=" N MET A 283 " --> pdb=" O THR A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 298 removed outlier: 3.753A pdb=" N GLY A 297 " --> pdb=" O ARG A 294 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLU A 298 " --> pdb=" O PRO A 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 294 through 298' Processing helix chain 'A' and resid 305 through 307 No H-bonds generated for 'chain 'A' and resid 305 through 307' Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 364 through 366 No H-bonds generated for 'chain 'A' and resid 364 through 366' Processing helix 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: 3.685A pdb=" N LEU A 430 " --> pdb=" O ALA A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 463 removed outlier: 3.655A pdb=" N VAL A 463 " --> pdb=" O LEU A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 487 Processing helix chain 'A' and resid 494 through 500 removed outlier: 4.108A pdb=" N LEU A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY A 500 " --> pdb=" O ILE A 496 " (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: 3.806A 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 removed outlier: 3.626A pdb=" N TYR A 675 " --> pdb=" O MET A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 701 Processing helix chain 'A' and resid 703 through 709 Processing helix chain 'A' and resid 726 through 737 removed outlier: 3.678A 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 835 through 842 Processing helix chain 'A' and resid 850 through 864 removed outlier: 3.600A pdb=" N LEU A 864 " --> pdb=" O GLU A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 876 No H-bonds generated for 'chain 'A' and resid 874 through 876' Processing helix chain 'A' and resid 877 through 884 Processing helix chain 'A' and resid 909 through 949 removed outlier: 3.692A pdb=" N ILE A 949 " --> pdb=" O ILE A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 964 Processing helix chain 'A' and resid 965 through 974 removed outlier: 4.493A pdb=" N SER A 974 " --> pdb=" O ALA A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1019 Processing helix chain 'A' and resid 1039 through 1061 removed outlier: 4.033A pdb=" N LEU A1054 " --> pdb=" O SER A1050 " (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 1097 through 1102 removed outlier: 3.562A pdb=" N LEU A1101 " --> pdb=" O LEU A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1145 Proline residue: A1138 - end of helix Processing helix chain 'A' and resid 1152 through 1164 Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 41 removed outlier: 3.921A pdb=" N GLY A 39 " --> pdb=" O CYS A 80 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N CYS A 41 " --> pdb=" O ARG A 78 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ARG A 78 " --> pdb=" O CYS A 41 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 87 through 90 Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 109 removed outlier: 5.777A pdb=" N ARG A 159 " --> pdb=" O TRP A 170 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA A 176 " --> pdb=" O ILE A 171 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 289 through 291 Processing sheet with id=AA5, first strand: chain 'A' and resid 312 through 315 removed outlier: 4.397A pdb=" N VAL A 386 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU A 387 " --> pdb=" O VAL A 329 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ASP A 325 " --> pdb=" O THR A 391 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 347 through 350 removed outlier: 6.786A pdb=" N GLU A 332 " --> pdb=" O ALA A 378 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ALA A 378 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N MET A 334 " --> pdb=" O LEU A 376 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 488 through 490 removed outlier: 5.941A pdb=" N GLY A 887 " --> pdb=" O PHE A 901 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N SER A 903 " --> pdb=" O GLY A 887 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N SER A 889 " --> pdb=" O SER A 903 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ALA A 741 " --> pdb=" O THR A 844 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N PHE A 846 " --> pdb=" O ALA A 741 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N MET A 743 " --> pdb=" O PHE A 846 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR A 844 " --> pdb=" O ARG A 816 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LEU A 818 " --> pdb=" O THR A 844 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N PHE A 846 " --> pdb=" O LEU A 818 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU A 820 " --> pdb=" O PHE A 846 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N HIS A 767 " --> pdb=" O HIS A 817 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ALA A 819 " --> pdb=" O HIS A 767 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ILE A 769 " --> pdb=" O ALA A 819 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER A 783 " --> pdb=" O THR A 774 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 520 through 525 removed outlier: 6.694A pdb=" N LEU A 685 " --> pdb=" O LEU A 714 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LEU A 716 " --> pdb=" O VAL A 683 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL A 683 " --> pdb=" O LEU A 716 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VAL A 718 " --> pdb=" O ARG A 681 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARG A 681 " --> pdb=" O VAL A 718 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ARG A 631 " --> pdb=" O PHE A 625 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N PHE A 625 " --> pdb=" O ARG A 631 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA A 637 " --> pdb=" O VAL A 619 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N VAL A 619 " --> pdb=" O ALA A 637 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A 588 " --> pdb=" O VAL A 619 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 557 through 558 448 hydrogen bonds defined for protein. 1293 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: 3.28 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2000 1.33 - 1.45: 1310 1.45 - 1.57: 4636 1.57 - 1.69: 12 1.69 - 1.81: 73 Bond restraints: 8031 Sorted by residual: bond pdb=" C4 ATP A1201 " pdb=" C5 ATP A1201 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.78e+01 bond pdb=" C5 ATP A1201 " pdb=" C6 ATP A1201 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.39e+01 bond pdb=" C8 ATP A1201 " pdb=" N7 ATP A1201 " ideal model delta sigma weight residual 1.310 1.357 -0.047 1.00e-02 1.00e+04 2.18e+01 bond pdb=" C5 ATP A1201 " pdb=" N7 ATP A1201 " ideal model delta sigma weight residual 1.387 1.345 0.042 1.00e-02 1.00e+04 1.78e+01 bond pdb=" CAY Y01 A1203 " pdb=" OAW Y01 A1203 " ideal model delta sigma weight residual 1.332 1.413 -0.081 2.00e-02 2.50e+03 1.64e+01 ... (remaining 8026 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.51: 10859 3.51 - 7.02: 105 7.02 - 10.53: 16 10.53 - 14.04: 2 14.04 - 17.55: 4 Bond angle restraints: 10986 Sorted by residual: angle pdb=" PB ATP A1201 " pdb=" O3B ATP A1201 " pdb=" PG ATP A1201 " ideal model delta sigma weight residual 139.87 122.32 17.55 1.00e+00 1.00e+00 3.08e+02 angle pdb=" PA ATP A1201 " pdb=" O3A ATP A1201 " pdb=" PB ATP A1201 " ideal model delta sigma weight residual 136.83 121.71 15.12 1.00e+00 1.00e+00 2.29e+02 angle pdb=" C5 ATP A1201 " pdb=" C4 ATP A1201 " pdb=" N3 ATP A1201 " ideal model delta sigma weight residual 126.80 118.62 8.18 1.00e+00 1.00e+00 6.70e+01 angle pdb=" N3 ATP A1201 " pdb=" C4 ATP A1201 " pdb=" N9 ATP A1201 " ideal model delta sigma weight residual 127.04 134.83 -7.79 1.15e+00 7.59e-01 4.60e+01 angle pdb=" N LYS A 509 " pdb=" CA LYS A 509 " pdb=" C LYS A 509 " ideal model delta sigma weight residual 111.40 118.55 -7.15 1.22e+00 6.72e-01 3.44e+01 ... (remaining 10981 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.17: 4424 16.17 - 32.34: 413 32.34 - 48.51: 93 48.51 - 64.68: 11 64.68 - 80.85: 6 Dihedral angle restraints: 4947 sinusoidal: 1953 harmonic: 2994 Sorted by residual: dihedral pdb=" CA SER A 889 " pdb=" C SER A 889 " pdb=" N LEU A 890 " pdb=" CA LEU A 890 " ideal model delta harmonic sigma weight residual 180.00 -158.29 -21.71 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA ILE A 965 " pdb=" C ILE A 965 " pdb=" N THR A 966 " pdb=" CA THR A 966 " ideal model delta harmonic sigma weight residual -180.00 -162.22 -17.78 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA ARG A 207 " pdb=" C ARG A 207 " pdb=" N LYS A 208 " pdb=" CA LYS A 208 " ideal model delta harmonic sigma weight residual 180.00 162.29 17.71 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 4944 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.356: 1327 0.356 - 0.711: 3 0.711 - 1.067: 0 1.067 - 1.423: 1 1.423 - 1.778: 3 Chirality restraints: 1334 Sorted by residual: chirality pdb=" CG LEU A 702 " pdb=" CB LEU A 702 " pdb=" CD1 LEU A 702 " pdb=" CD2 LEU A 702 " both_signs ideal model delta sigma weight residual False -2.59 -0.81 -1.78 2.00e-01 2.50e+01 7.91e+01 chirality pdb=" CG LEU A 723 " pdb=" CB LEU A 723 " pdb=" CD1 LEU A 723 " pdb=" CD2 LEU A 723 " both_signs ideal model delta sigma weight residual False -2.59 -0.95 -1.64 2.00e-01 2.50e+01 6.70e+01 chirality pdb=" CG LEU A 787 " pdb=" CB LEU A 787 " pdb=" CD1 LEU A 787 " pdb=" CD2 LEU A 787 " both_signs ideal model delta sigma weight residual False -2.59 -1.09 -1.50 2.00e-01 2.50e+01 5.66e+01 ... (remaining 1331 not shown) Planarity restraints: 1373 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A1042 " -0.020 2.00e-02 2.50e+03 3.92e-02 1.54e+01 pdb=" CG ASN A1042 " 0.068 2.00e-02 2.50e+03 pdb=" OD1 ASN A1042 " -0.026 2.00e-02 2.50e+03 pdb=" ND2 ASN A1042 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 590 " 0.032 2.00e-02 2.50e+03 2.82e-02 1.39e+01 pdb=" CG PHE A 590 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 PHE A 590 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE A 590 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 590 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 590 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A 590 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1029 " -0.088 9.50e-02 1.11e+02 4.61e-02 7.94e+00 pdb=" NE ARG A1029 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG A1029 " -0.045 2.00e-02 2.50e+03 pdb=" NH1 ARG A1029 " 0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG A1029 " 0.012 2.00e-02 2.50e+03 ... (remaining 1370 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.46: 27 2.46 - 3.07: 5346 3.07 - 3.68: 11985 3.68 - 4.29: 18008 4.29 - 4.90: 30848 Nonbonded interactions: 66214 Sorted by model distance: nonbonded pdb=" OD1 ASN A 508 " pdb=" OG1 THR A 512 " model vdw 1.844 3.040 nonbonded pdb=" OG1 THR A 642 " pdb=" OE1 GLN A 643 " model vdw 1.982 3.040 nonbonded pdb=" OG SER A 633 " pdb=" OE2 GLU A 708 " model vdw 2.078 3.040 nonbonded pdb=" NH2 ARG A 740 " pdb=" O GLY A 843 " model vdw 2.100 3.120 nonbonded pdb=" OH TYR A 235 " pdb=" O PRO A 465 " model vdw 2.109 3.040 ... (remaining 66209 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: 1.370 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: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 23.120 Find NCS groups from input model: 0.080 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:12.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 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 0.081 8031 Z= 0.388 Angle : 0.887 17.547 10986 Z= 0.479 Chirality : 0.102 1.778 1334 Planarity : 0.006 0.060 1373 Dihedral : 13.215 80.848 3013 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % 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: 0.74 (0.26), residues: 1024 helix: 1.13 (0.23), residues: 499 sheet: -0.22 (0.39), residues: 167 loop : 0.13 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 301 HIS 0.023 0.002 HIS A 385 PHE 0.064 0.002 PHE A 590 TYR 0.010 0.002 TYR A 931 ARG 0.046 0.001 ARG A1029 *********************** 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 105 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.901 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 1.1519 time to fit residues: 129.4296 Evaluate side-chains 52 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 721 ASN A1042 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8031 Z= 0.219 Angle : 0.612 7.906 10986 Z= 0.298 Chirality : 0.042 0.145 1334 Planarity : 0.005 0.048 1373 Dihedral : 7.918 87.105 1284 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.18 % Allowed : 7.98 % Favored : 89.84 % 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: 1.29 (0.26), residues: 1024 helix: 1.67 (0.23), residues: 502 sheet: 0.00 (0.41), residues: 159 loop : 0.25 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 301 HIS 0.008 0.001 HIS A 554 PHE 0.028 0.002 PHE A 958 TYR 0.011 0.001 TYR A 478 ARG 0.007 0.001 ARG A 379 *********************** 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 77 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 HIS cc_start: 0.6924 (OUTLIER) cc_final: 0.6705 (p90) outliers start: 18 outliers final: 4 residues processed: 71 average time/residue: 1.0329 time to fit residues: 79.6056 Evaluate side-chains 54 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 463 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 25 optimal weight: 0.0570 chunk 93 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8031 Z= 0.189 Angle : 0.545 7.318 10986 Z= 0.264 Chirality : 0.041 0.140 1334 Planarity : 0.005 0.046 1373 Dihedral : 7.323 80.468 1284 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.66 % Allowed : 8.95 % Favored : 88.39 % 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: 1.63 (0.26), residues: 1024 helix: 1.98 (0.23), residues: 505 sheet: -0.02 (0.40), residues: 160 loop : 0.47 (0.34), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 301 HIS 0.005 0.001 HIS A 554 PHE 0.020 0.001 PHE A 958 TYR 0.011 0.001 TYR A 931 ARG 0.013 0.000 ARG A 289 *********************** 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 81 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 59 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 10 residues processed: 73 average time/residue: 1.0125 time to fit residues: 80.4231 Evaluate side-chains 61 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 1128 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 92 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 49 optimal weight: 0.2980 chunk 89 optimal weight: 0.0270 chunk 26 optimal weight: 0.9980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 775 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8031 Z= 0.165 Angle : 0.524 7.814 10986 Z= 0.252 Chirality : 0.040 0.139 1334 Planarity : 0.005 0.046 1373 Dihedral : 6.851 76.695 1284 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.54 % Allowed : 11.00 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.27), residues: 1024 helix: 2.20 (0.23), residues: 507 sheet: 0.11 (0.41), residues: 162 loop : 0.60 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 301 HIS 0.005 0.001 HIS A 554 PHE 0.017 0.001 PHE A1123 TYR 0.010 0.001 TYR A 931 ARG 0.008 0.000 ARG A 379 *********************** 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 81 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 60 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 8 residues processed: 73 average time/residue: 0.9322 time to fit residues: 74.5480 Evaluate side-chains 59 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 873 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 2.9990 chunk 56 optimal weight: 0.0970 chunk 1 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 chunk 41 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 50 optimal weight: 0.7980 chunk 89 optimal weight: 8.9990 chunk 25 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8031 Z= 0.172 Angle : 0.519 7.353 10986 Z= 0.252 Chirality : 0.040 0.155 1334 Planarity : 0.004 0.046 1373 Dihedral : 6.652 73.947 1284 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.66 % Allowed : 12.58 % Favored : 84.76 % 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: 2.28 (0.23), residues: 509 sheet: 0.06 (0.41), residues: 156 loop : 0.69 (0.34), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 301 HIS 0.004 0.001 HIS A 554 PHE 0.020 0.001 PHE A1123 TYR 0.009 0.001 TYR A 931 ARG 0.007 0.000 ARG A 379 *********************** 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 76 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 54 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 10 residues processed: 70 average time/residue: 0.9900 time to fit residues: 75.4909 Evaluate side-chains 64 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 1128 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 33 optimal weight: 1.9990 chunk 89 optimal weight: 0.0060 chunk 19 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 32 optimal weight: 8.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 775 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8031 Z= 0.206 Angle : 0.531 7.969 10986 Z= 0.256 Chirality : 0.040 0.139 1334 Planarity : 0.004 0.046 1373 Dihedral : 6.568 71.986 1284 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.42 % Allowed : 13.78 % Favored : 83.80 % 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: 2.06 (0.27), residues: 1024 helix: 2.31 (0.23), residues: 510 sheet: 0.01 (0.40), residues: 158 loop : 0.78 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 301 HIS 0.005 0.001 HIS A 554 PHE 0.022 0.001 PHE A1123 TYR 0.009 0.001 TYR A 931 ARG 0.005 0.000 ARG A 379 *********************** 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 76 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 56 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 69 average time/residue: 1.0432 time to fit residues: 78.2246 Evaluate side-chains 62 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 1128 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 55 optimal weight: 0.4980 chunk 99 optimal weight: 0.8980 chunk 62 optimal weight: 0.0370 chunk 60 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8031 Z= 0.165 Angle : 0.518 8.520 10986 Z= 0.249 Chirality : 0.040 0.138 1334 Planarity : 0.004 0.046 1373 Dihedral : 6.444 70.615 1284 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.66 % Allowed : 13.78 % Favored : 83.56 % 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: 2.12 (0.27), residues: 1024 helix: 2.36 (0.23), residues: 510 sheet: -0.01 (0.40), residues: 158 loop : 0.82 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 301 HIS 0.004 0.001 HIS A 554 PHE 0.023 0.001 PHE A1123 TYR 0.009 0.001 TYR A 931 ARG 0.008 0.000 ARG A 379 *********************** 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 75 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 53 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 385 HIS cc_start: 0.6970 (OUTLIER) cc_final: 0.6766 (p90) outliers start: 22 outliers final: 13 residues processed: 71 average time/residue: 0.9792 time to fit residues: 75.7439 Evaluate side-chains 66 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 1128 MET Chi-restraints excluded: chain A residue 1137 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 0.9990 chunk 59 optimal weight: 0.0470 chunk 29 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 9 optimal weight: 0.0770 chunk 78 optimal weight: 1.9990 chunk 90 optimal weight: 0.2980 chunk 95 optimal weight: 0.6980 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 775 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8031 Z= 0.138 Angle : 0.509 8.463 10986 Z= 0.243 Chirality : 0.039 0.136 1334 Planarity : 0.004 0.047 1373 Dihedral : 6.233 68.588 1284 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.93 % Allowed : 15.11 % Favored : 82.95 % 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: 2.30 (0.27), residues: 1024 helix: 2.56 (0.23), residues: 497 sheet: 0.06 (0.41), residues: 158 loop : 0.90 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 301 HIS 0.004 0.001 HIS A 554 PHE 0.024 0.001 PHE A1123 TYR 0.009 0.001 TYR A 931 ARG 0.009 0.000 ARG A 379 *********************** 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 75 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 72 average time/residue: 1.0437 time to fit residues: 81.3940 Evaluate side-chains 67 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 1128 MET Chi-restraints excluded: chain A residue 1137 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 55 optimal weight: 0.3980 chunk 40 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 97 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8031 Z= 0.166 Angle : 0.538 8.086 10986 Z= 0.256 Chirality : 0.040 0.136 1334 Planarity : 0.004 0.046 1373 Dihedral : 6.193 67.824 1284 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.93 % Allowed : 15.48 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.27), residues: 1024 helix: 2.56 (0.24), residues: 499 sheet: 0.01 (0.40), residues: 158 loop : 0.93 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 301 HIS 0.004 0.001 HIS A 554 PHE 0.024 0.001 PHE A1123 TYR 0.009 0.001 TYR A 931 ARG 0.008 0.000 ARG A 379 *********************** 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 73 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 MET cc_start: 0.8303 (ppp) cc_final: 0.8080 (ptm) outliers start: 16 outliers final: 10 residues processed: 70 average time/residue: 0.9932 time to fit residues: 75.5363 Evaluate side-chains 66 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 775 HIS Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 1137 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 0.3980 chunk 46 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 94 optimal weight: 0.0870 chunk 81 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8031 Z= 0.161 Angle : 0.549 11.296 10986 Z= 0.256 Chirality : 0.040 0.136 1334 Planarity : 0.004 0.046 1373 Dihedral : 6.148 67.297 1284 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.33 % Allowed : 16.20 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.35 (0.27), residues: 1024 helix: 2.58 (0.24), residues: 499 sheet: 0.04 (0.41), residues: 158 loop : 0.97 (0.35), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 301 HIS 0.005 0.001 HIS A 554 PHE 0.025 0.001 PHE A1123 TYR 0.009 0.001 TYR A 931 ARG 0.005 0.000 ARG A 379 ********************** 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 71 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 282 ASP cc_start: 0.7114 (p0) cc_final: 0.6867 (p0) outliers start: 11 outliers final: 9 residues processed: 69 average time/residue: 1.1013 time to fit residues: 82.2482 Evaluate side-chains 65 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 1137 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 0.0270 chunk 75 optimal weight: 0.3980 chunk 12 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 34 optimal weight: 8.9990 chunk 84 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.091984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.066632 restraints weight = 15907.682| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.80 r_work: 0.2847 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8031 Z= 0.163 Angle : 0.559 10.417 10986 Z= 0.262 Chirality : 0.040 0.138 1334 Planarity : 0.004 0.046 1373 Dihedral : 6.148 67.057 1284 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.33 % Allowed : 16.44 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.27), residues: 1024 helix: 2.59 (0.24), residues: 499 sheet: 0.06 (0.40), residues: 158 loop : 1.01 (0.35), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 301 HIS 0.004 0.001 HIS A 554 PHE 0.025 0.001 PHE A1123 TYR 0.009 0.001 TYR A 931 ARG 0.005 0.000 ARG A 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2420.31 seconds wall clock time: 44 minutes 28.13 seconds (2668.13 seconds total)